diff --git a/.Rbuildignore b/.Rbuildignore
index 5954eef4..6aaa3e6d 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -14,8 +14,8 @@
 
 ^\.Rproj\.user$
 ^\.covrignore$
-^LICENSE$
 ^\.zenodo\.json$
 
 ^\.vscode$
-^source_odeint\.R
+^dummy\.R
+^LICENSE\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
index 1586e294..fdbe3656 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
-Version: 4.3.4
-Date: 2023-03-16
+Version: 4.4.0
+Date: 2023-03-29
 Depends: R (>= 4.2.0)
 biocViews:
 Imports: 
@@ -105,11 +105,11 @@ Authors@R: c(
            email = "r.scherrer@rug.nl",
            role = c("ctb"),
            comment = c(ORCID = "0000-0002-1447-7630")))
-License: GPL-3
+License: GPL (>= 3) | file LICENSE
+Copyright: See the file COPYRIGHTS for various DAISIE copyright details
 Description: Simulates and computes the (maximum) likelihood of a dynamical 
     model of island biota assembly through speciation, immigration and
-    extinction. See e.g. Valente et al. 2015. Ecology Letters 18: 844-852,
-    <DOI:10.1111/ele.12461>.
+    extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
 NeedsCompilation: yes
 SystemRequirements: C++17
 Encoding: UTF-8
diff --git a/LICENSE.note b/LICENSE.note
new file mode 100644
index 00000000..1482fef8
--- /dev/null
+++ b/LICENSE.note
@@ -0,0 +1,9 @@
+The DAISIE package as a whole is distributed under >= GPL-3, the license of which can be found in the distributed file LICENSE. The DAISIE package includes code written by two of the package authors that is distributed under BSL-1.0:
+
+* src/DAISIE_CS.cpp
+* src/DAISIE_IW.cpp
+* src/DAISIE_odeint.h
+* src/DAISIE_types.h
+* src/DAISIE_loglik_rhs_FORTRAN.f95
+
+Full copies of the BSL-1.0 license used by these files is included in `inst/LICENSE_1_0.txt`, as is a license and copyright notice on said files, while details are also in `inst/COPYRIGHTS`.
diff --git a/NAMESPACE b/NAMESPACE
index 9f793cfe..4835adfd 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -34,7 +34,6 @@ export(DAISIE_sim_relaxed_rate)
 export(DAISIE_sim_time_dep)
 export(DAISIE_sim_trait_dep)
 export(DAISIE_sim_trait_dep_2K)
-export(are_area_pars)
 export(create_CS_version)
 export(create_area_pars)
 export(create_hyper_pars)
@@ -42,6 +41,7 @@ export(create_pars)
 export(create_trait_pars)
 export(create_trait_pars_2K)
 export(daisie_odeint_cs)
+export(daisie_odeint_iw)
 import(Rcpp)
 importFrom(doParallel,registerDoParallel)
 importFrom(foreach,"%dopar%")
diff --git a/NEWS.md b/NEWS.md
index 7819a59e..bc057db3 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,27 @@
+# DAISIE 4.4.0
+
+* No longer include patched version of `boost/numeric/odeint/stepper/bulirsch_stoer.hpp`,
+address the issue by passing previously uninitialised variable as `boost::units::quantity<boost::units::si::dimensionless, double>`.
+* Document return type of exported Rcpp functions.
+* Move all internal non-error printing to console `message()` and `warning()`. 
+Add internal functions to address this. `verbose` variable is now numeric, 
+varying from 0 to 3. Increasing values increase amount of messages to be 
+printed. Change default of printing some output to golden rule of silence 
+`verbose == 0`. To print again, set `verbose >= 1`.
+* Remove calls to `options(warn = -1)` that suppress warnings in non standard 
+way. Use `suppressWarnings()` where appropriate.
+* Safely restore graphics settings after plot.
+* Fix references in `DESCRIPTION`.
+* Remove internal (unnecessary) calls to internal functions via `:::`.
+* No longer use roxygen2 tag `internal` to document without index but use
+`noRd` instead. `are_area_pars()` is now internal.
+* Replace `\dontrun` examples in documentation with `\donttest`. Speed up 
+examples.
+* License package C++ source files as BSL-1.0 (c) Hanno Hildenbrandt, FORTRAN 
+files as BSL-1.0 (c) Rampal S. Etienne.
+* Add `LICENSE.note`, `inst/COPYRIGHTS` to clarify license and copyrights. Pipe
+such files in `DESCRIPTION`.
+
 # DAISIE 4.3.4
 
 * Require C++17 via `CXX_STD` flag on Makevars[.win].
diff --git a/R/DAISIE_ML1.R b/R/DAISIE_ML1.R
index 2f0df0d7..d3b3ca20 100644
--- a/R/DAISIE_ML1.R
+++ b/R/DAISIE_ML1.R
@@ -61,8 +61,7 @@ DAISIE_loglik_all_choosepar <- function(trparsopt,
       )
     }
     if (is.nan(loglik) || is.na(loglik)) {
-      cat("There are parameter values used
-             which cause numerical problems.\n")
+      message("There are parameter values used which cause numerical problems.")
       loglik <- -Inf
     }
   }
@@ -221,66 +220,56 @@ DAISIE_ML1 <- function(
                                        position = 'lambda_a',
                                        column_to_insert = nc)
   }
-  if (length(namepars[idparsopt]) == 0) {
-    optstr <- "nothing"
-  } else {
-    optstr <- namepars[idparsopt]
-  }
 
-  cat("You are optimizing", optstr, "\n")
-  if (length(namepars[idparsfix]) == 0) {
-    fixstr <- "nothing"
-  } else {
-    fixstr <- namepars[idparsfix]
-  }
-  cat("You are fixing", fixstr, "\n")
+  print_ml_par_settings(
+    namepars = namepars,
+    idparsopt = idparsopt,
+    idparsfix = idparsfix,
+    idparsnoshift = idparsnoshift,
+    all_no_shift = all_no_shift,
+    verbose = verbose
+  )
 
-  if (sum(idparsnoshift %in% (all_no_shift)) != 5) {
-    noshiftstring <- namepars[idparsnoshift]
-    cat("You are not shifting", noshiftstring, "\n")
-  }
   idpars <- sort(c(idparsopt, idparsfix, idparsnoshift, idparseq))
 
   missnumspec <- unlist(lapply(datalist, function(list) {list$missing_species})) # nolint
   if (max(missnumspec) > (res - 1)) {
-    cat(
+    warning(
       "The number of missing species is too large relative to the
-        resolution of the ODE.\n")
+       resolution of the ODE.")
     return(out2err)
   }
 
   if (max(missnumspec) > res/10) {
     warning(
       "The number of missing species is quite low relative to the
-        resolution of the ODE.\n")
+        resolution of the ODE.")
   }
 
   if ((length(idpars) != max(idpars))) {
-    cat("The parameters to be optimized and/or fixed are incoherent.\n")
+    warning("The parameters to be optimized and/or fixed are incoherent.")
     return(out2err)
   }
 
   if ((!all(idpars == 1:max(idpars))) || # nolint
       (length(initparsopt) != length(idparsopt)) ||
       (length(parsfix) != length(idparsfix))) {
-    cat("The parameters to be optimized and/or fixed are incoherent.\n")
+    warning("The parameters to be optimized and/or fixed are incoherent.")
     return(out2err)
   }
   if (length(idparseq) == 0) {
   } else {
     if (ddmodel == 3) {
-      cat("Equilibrium optimization is not implemented for ddmodel = 3\n")
+      warning("Equilibrium optimization is not implemented for ddmodel = 3")
     } else {
-      cat(
+      message(
         "You are assuming equilibrium. Extinction and/or immigration will
           be considered a function of the other parameters, the species
           pool size, the number of endemics,
-          and/or the number of non-endemics\n"
+          and/or the number of non-endemics"
       )
     }
   }
-  cat("Calculating the likelihood for the initial parameters.", "\n")
-  utils::flush.console()
   trparsopt <- initparsopt / (1 + initparsopt)
   trparsopt[which(initparsopt == Inf)] <- 1
   trparsfix <- parsfix / (1 + parsfix)
@@ -313,20 +302,17 @@ DAISIE_ML1 <- function(
     abstolint = tolint[1],
     reltolint = tolint[2]
   )
-  cat(
-    "The loglikelihood for the initial parameter values is",
-    initloglik,
-    "\n"
-  )
+
+  print_init_ll(initloglik = initloglik, verbose = verbose)
+
   if (initloglik == -Inf) {
-    cat(
+    warning(
       "The initial parameter values have a likelihood that is equal to 0 or
-       below machine precision. Try again with different initial values.\n"
+       below machine precision. Try again with different initial values."
     )
     return(out2err)
   }
-  cat("Optimizing the likelihood - this may take a while.", "\n")
-  utils::flush.console()
+
   out <- DDD::optimizer(
     optimmethod = optimmethod,
     optimpars = optimpars,
@@ -347,9 +333,9 @@ DAISIE_ML1 <- function(
     num_cycles = num_cycles
   )
   if (out$conv != 0) {
-    cat(
+    warning(
       "Optimization has not converged.
-        Try again with different initial values.\n")
+       Try again with different initial values.")
     out2 <- out2err
     out2$conv <- out$conv
     return(out2)
@@ -414,7 +400,7 @@ DAISIE_ML1 <- function(
       conv = unlist(out$conv)
     )
     pars_to_print <- MLpars1[1:6]
-    parnames <- c('lambda^c','mu','K','gamma','lambda^a','prob_init_pres')
+    parnames <- c("lambda^c", "mu", "K", "gamma", "lambda^a", "prob_init_pres")
   } else {
     out2 <- data.frame(
       lambda_c = MLpars1[1],
@@ -431,17 +417,16 @@ DAISIE_ML1 <- function(
   }
   print_parameters_and_loglik(pars = pars_to_print,
                               loglik = ML,
-                              verbose = TRUE,
+                              verbose = verbose,
                               parnames = parnames,
                               type = 'island_ML')
   if (eqmodel > 0) {
     M <- calcMN(datalist, MLpars1)
     ExpEIN <- DAISIE_ExpEIN(datalist[[1]]$island_age, MLpars1, M) # nolint start
-    cat("The expected number of endemics, non-endemics, and the total at
-        these parameters is: ",
-        ExpEIN[[1]],
-        ExpEIN[[2]],
-        ExpEIN[[3]]
+    message(
+      paste0("The expected number of endemics, non-endemics, and the total at ",
+        "these parameters is: "),
+      paste(ExpEIN[[1]], ExpEIN[[2]], ExpEIN[[3]])
     ) # nolint end
   }
   return(invisible(out2))
diff --git a/R/DAISIE_ML2.R b/R/DAISIE_ML2.R
index 3bd3702c..c716139c 100644
--- a/R/DAISIE_ML2.R
+++ b/R/DAISIE_ML2.R
@@ -30,7 +30,7 @@ DAISIE_loglik_all_choosepar2 <- function(
       }
    }
    if (is.nan(loglik) || is.na(loglik)) {
-      cat("There are parameter values used which cause numerical problems.\n")
+      warning("There are parameter values used which cause numerical problems.")
       loglik <- -Inf
    }
    return(loglik)
@@ -120,8 +120,6 @@ DAISIE_ML2 <- function(
 # - cond = conditioning; currently only cond = 0 is possible
 #  . cond == 0 : no conditioning
 #  . cond == 1 : conditioning on presence on the island
-
-  options(warn = -1)
   out2err <- data.frame(lambda_c = NA, mu = NA, K = NA, gamma = NA, lambda_a = NA, loglik = NA, df = NA, conv = NA)
   out2err <- invisible(out2err)
   numisl <- length(datalist)
@@ -131,17 +129,16 @@ DAISIE_ML2 <- function(
   }
 
   if (missnumspec > (res - 1)) {
-    cat("The number of missing species is too large relative to the resolution of the ODE.\n")
+    warning("The number of missing species is too large relative to the resolution of the ODE.")
     return(out2err)
   }
   if (all((sort(unique(as.vector(idparsmat))) != sort(c(idparsopt, idparsfix)))) ||
       (length(initparsopt) != length(idparsopt)) ||
       (length(parsfix) != length(idparsfix))) {
-    cat("The parameters to be optimized and/or fixed are incoherent.\n")
+    warning("The parameters to be optimized and/or fixed are incoherent.")
     return(out2err)
   }
-  cat("Calculating the likelihood for the initial parameters.", "\n")
-  utils::flush.console()
+
   trparsopt <- initparsopt / (1 + initparsopt)
   trparsopt[which(initparsopt == Inf)] <- 1
   trparsfix <- parsfix / (1 + parsfix)
@@ -149,13 +146,13 @@ DAISIE_ML2 <- function(
   pars2 <- c(res, ddmodel, cond, 0, island_ontogeny)
   optimpars <- c(tol, maxiter)
   initloglik <- DAISIE_loglik_all_choosepar2(trparsopt = trparsopt, trparsfix = trparsfix, idparsopt = idparsopt, idparsfix = idparsfix, idparsmat = idparsmat, pars2 = pars2, datalist = datalist, methode, abstolint = tolint[1], reltolint = tolint[2])
-  cat("The loglikelihood for the initial parameter values is", initloglik, "\n")
+
+  print_init_ll(initloglik = initloglik, verbose = verbose)
+
   if (initloglik == -Inf) {
-    cat("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.\n")
+    warning("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.")
     return(out2err)
   }
-  cat("Optimizing the likelihood - this may take a while.", "\n")
-  utils::flush.console()
   out <- DDD::optimizer(
     optimmethod = optimmethod,
     optimpars = optimpars,
@@ -174,7 +171,7 @@ DAISIE_ML2 <- function(
     num_cycles = num_cycles
   )
   if (out$conv != 0) {
-    cat("Optimization has not converged. Try again with different initial values.\n")
+    warning("Optimization has not converged. Try again with different initial values.")
     out2 <- out2err
     out2$conv <- out$conv
     return(out2err)
@@ -206,7 +203,7 @@ DAISIE_ML2 <- function(
                      conv = unlist(out$conv))
   print_parameters_and_loglik(pars = MLpars1,
                               loglik = ML,
-                              verbose = TRUE,
+                              verbose = verbose,
                               type = 'multiple_island_ML')
   return(invisible(out2))
 }
diff --git a/R/DAISIE_ML4.R b/R/DAISIE_ML4.R
index cc76e033..f739071d 100644
--- a/R/DAISIE_ML4.R
+++ b/R/DAISIE_ML4.R
@@ -39,8 +39,7 @@ DAISIE_loglik_all_choosepar4 <- function(trparsopt,
       )
     }
     if (is.nan(loglik) || is.na(loglik)) {
-      cat("There are parameter values used
-          which cause numerical problems.\n")
+      message("There are parameter values used which cause numerical problems.")
       loglik <- -Inf
     }
   }
@@ -122,33 +121,31 @@ DAISIE_ML4 <- function(
   } else {
     optstr <- namepars[idparsopt]
   }
-  cat("You are optimizing", optstr, "\n")
-  if (length(namepars[idparsfix]) == 0) {
-    fixstr <- "nothing"
-  } else {
-    fixstr <- namepars[idparsfix]
-  }
-  cat("You are fixing", fixstr, "\n")
+  print_ml_par_settings(
+    namepars = namepars,
+    idparsopt = idparsopt,
+    idparsfix = idparsfix,
+    idparsnoshift = NA,
+    all_no_shift = NA,
+    verbose = verbose
+  )
   idpars <- sort(c(idparsopt, idparsfix))
   missnumspec <- unlist(lapply(datalist, function(list) {list$missing_species})) # nolint
   if (sum(missnumspec) > (res - 1)) {
-    cat(
-      "The number of missing species is too large relative to the
-      resolution of the ODE.\n")
+    warning(
+      "The number of missing species is too large relative to the resolution of the ODE.")
     return(out2err)
   }
   if (length(idpars) != 6) {
-    cat("You have too few or too many parameters to be optimized or fixed.\n")
+    warning("You have too few or too many parameters to be optimized or fixed.")
     return(out2err)
   }
   if ((prod(idpars == (1:6)) != 1) || # nolint
       (length(initparsopt) != length(idparsopt)) ||
       (length(parsfix) != length(idparsfix))) {
-    cat("The parameters to be optimized and/or fixed are incoherent.\n")
+    warning("The parameters to be optimized and/or fixed are incoherent.")
     return(out2err)
   }
-  cat("Calculating the likelihood for the initial parameters.", "\n")
-  utils::flush.console()
   trparsopt <- initparsopt / (1 + initparsopt)
   trparsopt[which(initparsopt == Inf)] <- 1
   trparsfix <- parsfix / (1 + parsfix)
@@ -174,20 +171,16 @@ DAISIE_ML4 <- function(
     abstolint = tolint[1],
     reltolint = tolint[2]
   )
-  cat(
-    "The loglikelihood for the initial parameter values is",
-    initloglik,
-    "\n"
-  )
+
+  print_init_ll(initloglik = initloglik, verbose = verbose)
+
   if (initloglik == -Inf) {
-    cat(
+    warning(
       "The initial parameter values have a likelihood that is equal to 0 or
-      below machine precision. Try again with different initial values.\n"
+      below machine precision. Try again with different initial values."
     )
     return(out2err)
   }
-  cat("Optimizing the likelihood - this may take a while.", "\n")
-  utils::flush.console()
   out <- DDD::optimizer(
     optimmethod = optimmethod,
     optimpars = optimpars,
@@ -206,9 +199,9 @@ DAISIE_ML4 <- function(
     num_cycles = num_cycles
   )
   if (out$conv != 0) {
-    cat(
-      "Optimization has not converged.
-      Try again with different initial values.\n")
+    warning(
+      "Optimization has not converged`
+      Try again with different initial values.")
     out2 <- out2err
     out2$conv <- out$conv
     return(out2)
@@ -238,7 +231,7 @@ DAISIE_ML4 <- function(
   )
   print_parameters_and_loglik(pars = MLpars1[1:6],
                               loglik = ML,
-                              verbose = TRUE,
+                              verbose = verbose,
                               parnames = c('lambda^c','mu','K','gamma','lambda^a','sd'),
                               type = 'island_ML')
   return(invisible(out2))
diff --git a/R/DAISIE_ML_IW.R b/R/DAISIE_ML_IW.R
index 8fd289c4..b2c19933 100644
--- a/R/DAISIE_ML_IW.R
+++ b/R/DAISIE_ML_IW.R
@@ -32,7 +32,7 @@ DAISIE_loglik_IW_choosepar <- function(
       )
     }
     if (is.nan(loglik) || is.na(loglik)) {
-      cat("There are parameter values used which cause numerical problems.\n")
+      warning("There are parameter values used which cause numerical problems.")
       loglik <- -Inf
     }
   }
@@ -92,7 +92,7 @@ DAISIE_ML_IW <- function(
   tolint = c(1E-16, 1E-14),
   jitter = 0,
   num_cycles = 1) {
-  options(warn = -1)
+
   out2err <- data.frame(lambda_c = NA, mu = NA, K = NA, gamma = NA, lambda_a = NA, loglik = NA, df = NA, conv = NA)
   out2err <- invisible(out2err)
   if (is.null(datalist[[1]]$brts_table)) {
@@ -105,27 +105,31 @@ DAISIE_ML_IW <- function(
   np = datalist[[1]]$not_present
   if (is.null(np)) {
     np = datalist[[1]]$not_present_type1 + datalist[[1]]$not_present_type2
-    cat('Number of species not present is misspecified.\n')
+    warning('Number of species not present is misspecified.\n')
     return(invisible(out2err))
   }
   M <- length(datalist) - 1 + np
 
   idpars <- sort(c(idparsopt, idparsfix))
   if ((prod(idpars == (1:5)) != 1) || (length(initparsopt) != length(idparsopt)) || (length(parsfix) != length(idparsfix))) {
-    cat("The parameters to be optimized and/or fixed are incoherent.\n")
+    warning("The parameters to be optimized and/or fixed are incoherent.\n")
     return(out2err)
   }
   if (length(idparsopt) > 11) {
-    cat("The number of parameters to be optimized is too high.\n")
+    warning("The number of parameters to be optimized is too high.\n")
     return(out2err)
   }
   namepars <- c("lambda_c", "mu", "K'", "gamma", "lambda_a")
-  if (length(namepars[idparsopt]) == 0) { optstr = "nothing" } else { optstr = namepars[idparsopt] }
-  cat("You are optimizing", optstr, "\n")
-  if(length(namepars[idparsfix]) == 0) { fixstr = "nothing" } else { fixstr = namepars[idparsfix] }
-  cat("You are fixing", fixstr, "\n")
-  cat("Calculating the likelihood for the initial parameters.", "\n")
-  utils::flush.console()
+
+  print_ml_par_settings(
+    namepars = namepars,
+    idparsopt = idparsopt,
+    idparsfix = idparsfix,
+    idparsnoshift = NA,
+    all_no_shift = NA,
+    verbose = verbose
+  )
+
   trparsopt <- initparsopt / (1 + initparsopt)
   trparsopt[which(initparsopt == Inf)] <- 1
   trparsfix <- parsfix / (1 + parsfix)
@@ -133,13 +137,12 @@ DAISIE_ML_IW <- function(
   pars2 <- c(res, ddmodel, cond, verbose)
   optimpars <- c(tol, maxiter)
   initloglik <- DAISIE_loglik_IW_choosepar(trparsopt = trparsopt, trparsfix = trparsfix, idparsopt = idparsopt, idparsfix = idparsfix, M = M, pars2 = pars2, datalist = datalist, methode = methode, abstolint = tolint[1], reltolint = tolint[2])
-  cat("The loglikelihood for the initial parameter values is", initloglik, "\n")
+  message("The loglikelihood for the initial parameter values is ", initloglik)
   if (initloglik == -Inf) {
-    cat("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.\n")
+    warning("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.\n")
     return(out2err)
   }
-  cat("Optimizing the likelihood - this may take a while.", "\n")
-  utils::flush.console()
+  message("Optimizing the likelihood - this may take a while.")
   out <- DDD::optimizer(
     optimmethod = optimmethod,
     optimpars = optimpars,
@@ -158,7 +161,7 @@ DAISIE_ML_IW <- function(
     num_cycles = num_cycles
   )
   if (out$conv != 0) {
-    cat("Optimization has not converged. Try again with different initial values.\n")
+    warning("Optimization has not converged. Try again with different initial values.")
     out2 <- out2err
     out2$conv <- out$conv
     return(out2)
@@ -173,7 +176,7 @@ DAISIE_ML_IW <- function(
   out2 <- data.frame(lambda_c = MLpars1[1], mu = MLpars1[2], K = MLpars1[3], gamma = MLpars1[4], lambda_a = MLpars1[5], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
   print_parameters_and_loglik(pars = MLpars1[1:5],
                               loglik = ML,
-                              verbose = TRUE,
+                              verbose = verbose,
                               type = 'island_ML')
   return(invisible(out2))
 }
diff --git a/R/DAISIE_MW_ML.R b/R/DAISIE_MW_ML.R
index cf36cf04..a49f8529 100644
--- a/R/DAISIE_MW_ML.R
+++ b/R/DAISIE_MW_ML.R
@@ -156,23 +156,27 @@ DAISIE_MW_loglik_choosepar = function(
             {
               if(.Platform$OS.type != "unix")
               {
-                cat('cluster does not work on a non-unix environment, choose local instead.\n')
+                warning('cluster does not work on a non-unix environment, choose local instead.')
                 return(-Inf)
               }
               doMC::registerDoMC(cpus - 1)
             }
           X = NULL; rm(X)
-          loglik = foreach::foreach(X = datalist,
-                                    .combine = sum,
-                                    .export = c("pars2"),
-                                    .packages = c('DAISIE','foreach','deSolve','doParallel')) %dopar%
-            DAISIE_loglik_all(pars1 = X[[1]]$pars1new,
-                              pars2 = pars2,
-                              datalist = X,
-                              methode = methode,
-                              CS_version = CS_version,
-                              abstolint = abstolint,
-                              reltolint = reltolint)
+
+          suppressWarnings({
+            loglik = foreach::foreach(
+              X = datalist,
+              .combine = sum,
+              .export = c("pars2"),
+              .packages = c('DAISIE','foreach','deSolve','doParallel')) %dopar%
+              DAISIE_loglik_all(pars1 = X[[1]]$pars1new,
+                                pars2 = pars2,
+                                datalist = X,
+                                methode = methode,
+                                CS_version = CS_version,
+                                abstolint = abstolint,
+                                reltolint = reltolint)
+          })
         } else {
           loglik = 0
           if(pars2[4] == 0.5) pb <- utils::txtProgressBar(min = 0, max = length(datalist), style = 3)
@@ -191,7 +195,7 @@ DAISIE_MW_loglik_choosepar = function(
       }
       if(is.nan(loglik) || is.na(loglik))
       {
-        cat("There are parameter values used which cause numerical problems.\n")
+        warning("There are parameter values used which cause numerical problems.")
         loglik = -Inf
       }
     }
@@ -390,7 +394,6 @@ DAISIE_MW_ML = function(
   num_cycles = 1
 )
 {
-  options(warn=-1)
   distance_dep_options1 <- distance_dep_options1_fun()
   numpars <- 10 + is.element(distance_dep,distance_dep_options1) + 2 * (distance_dep == 'sigmoidal_col_ana')
   if(numpars == 11)
@@ -408,12 +411,12 @@ DAISIE_MW_ML = function(
   idpars = sort(c(idparsopt,idparsfix))
   if((prod(idpars == (1:numpars)) != 1) || (length(initparsopt) != length(idparsopt)) || (length(parsfix) != length(idparsfix)))
   {
-    cat("The parameters to be optimized and/or fixed are incoherent.\n")
+    warning("The parameters to be optimized and/or fixed are incoherent.\n")
     return(out2err)
   }
   if(length(idparsopt) > numpars)
   {
-    cat("The number of parameters to be optimized is too high.\n")
+    warning("The number of parameters to be optimized is too high.\n")
     return(out2err)
   }
   namepars = c("lambda_c0","y","mu_0","x","K_0","z","gamma_0","alpha","lambda_a0","beta")
@@ -424,12 +427,16 @@ DAISIE_MW_ML = function(
   {
     namepars = c(namepars,"d0_col","d0_ana")
   }
-  if(length(namepars[idparsopt]) == 0) { optstr = "nothing" } else { optstr = namepars[idparsopt] }
-  cat("You are optimizing",optstr,"\n")
-  if(length(namepars[idparsfix]) == 0) { fixstr = "nothing" } else { fixstr = namepars[idparsfix] }
-  cat("You are fixing",fixstr,"\n")
-  cat("Calculating the likelihood for the initial parameters.","\n")
-  utils::flush.console()
+
+  print_ml_par_settings(
+    namepars = namepars,
+    idparsopt = idparsopt,
+    idparsfix = idparsfix,
+    idparsnoshift = NA,
+    all_no_shift = NA,
+    verbose = verbose
+  )
+
   trparsopt = initparsopt/(1 + initparsopt)
   trparsopt[which(initparsopt == Inf)] = 1
   trparsfix = parsfix/(1 + parsfix)
@@ -437,14 +444,13 @@ DAISIE_MW_ML = function(
   pars2 = c(res,ddmodel,cond,verbose,island_ontogeny)
   optimpars = c(tol,maxiter)
   initloglik = DAISIE_MW_loglik_choosepar(trparsopt = trparsopt,trparsfix = trparsfix,idparsopt = idparsopt,idparsfix = idparsfix,pars2 = pars2,datalist = datalist,methode = methode,CS_version = CS_version,abstolint = tolint[1],reltolint = tolint[2],distance_type = distance_type,parallel = parallel,cpus = cpus,distance_dep = distance_dep)
-  cat("The loglikelihood for the initial parameter values is",initloglik,"\n")
+  message("The loglikelihood for the initial parameter values is ", initloglik)
   if(initloglik == -Inf)
   {
-    cat("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.\n")
+    warning("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.\n")
     return(out2err)
   }
-  cat("Optimizing the likelihood - this may take a while.","\n")
-  utils::flush.console()
+  message("Optimizing the likelihood - this may take a while.")
   out = DDD::optimizer(optimmethod = optimmethod,
                        optimpars = optimpars,
                        fun = DAISIE_MW_loglik_choosepar,
@@ -465,7 +471,7 @@ DAISIE_MW_ML = function(
                        num_cycles = num_cycles)
   if(out$conv != 0)
   {
-    cat("Optimization has not converged. Try again with different initial values.\n")
+    warning("Optimization has not converged. Try again with different initial values.\n")
     out2 = out2err
     out2$conv = out$conv
     return(out2)
@@ -491,7 +497,7 @@ DAISIE_MW_ML = function(
   }
   print_parameters_and_loglik(pars = MLpars1,
                               loglik = ML,
-                              verbose = TRUE,
+                              verbose = verbose,
                               type = 'global_ML',
                               distance_dep = distance_dep)
   return(invisible(out2))
diff --git a/R/DAISIE_PEI.R b/R/DAISIE_PEI.R
index 34e0c01b..3aba936d 100644
--- a/R/DAISIE_PEI.R
+++ b/R/DAISIE_PEI.R
@@ -1,6 +1,6 @@
 DAISIE_probdist_rhs <- function(t, x, m) {
    x <- pmax(x, 0)
-   #print(t)
+   #message(t)
    #utils::flush.console()
    nx <- sqrt(length(x))
    dim(x) <- c(nx, nx)
@@ -222,14 +222,14 @@ DAISIE_numcol_dist = function(pars1,
    dim(ee) <- c(lx, lx)
    expEtpapprox <- sum(ee * probstp)
    expEINtp <- DAISIE_ExpEIN(tvec[1], pars1, 1)
-   cat("The total sum of the probabilities at the first time is", sum(probstp), "\n")
-   cat("The approximation for the expected number of endemics is", expEtpapprox, "\n")
-   cat("The true value for the expected number of endemics is", expEINtp[[1]], "\n")
+   message("The total sum of the probabilities at the first time is ", sum(probstp))
+   message("The approximation for the expected number of endemics is ", expEtpapprox)
+   message("The true value for the expected number of endemics is ", expEINtp[[1]])
    expEteqapprox <- sum(ee * probseq)
    expEINteq <- DAISIE_ExpEIN(Inf, pars1, 1)
-   cat("The total sum of the probabilities at the second time is", sum(probstp), "\n")
-   cat("The approximation for the expected number of endemics is", expEteqapprox, "\n")
-   cat("The true value for the expected number of endemics is", expEINteq[[1]], "\n")
+   message("The total sum of the probabilities at the second time is ", sum(probstp))
+   message("The approximation for the expected number of endemics is ", expEteqapprox)
+   message("The true value for the expected number of endemics is ", expEINteq[[1]])
    utils::flush.console()
    M <- pars2[2]
    if (!is.na(pars1[11])) {
@@ -239,10 +239,8 @@ DAISIE_numcol_dist = function(pars1,
    }
    pC <- stats::dbinom(0:Mnonfinches, Mnonfinches, 1 - probs00)
    expC <- Mnonfinches * (1 - probs00)
-   cat(
-      'The approximation for the expected number of colonizations is',
-      expC,
-      "\n"
+   message(
+      "The approximation for the expected number of colonizations is ", expC
    )
    out <- list(pC, expC, expEINtp, expEtpapprox, expEINteq, expEteqapprox)
    names(out) <- list(
@@ -350,13 +348,13 @@ DAISIE_KLdist <- function(pars1, pars2, tvec) {
    ee <- rep(0:(lx - 1), lx)
    dim(ee) <- c(lx, lx)
    expEapprox <- sum(ee * probstp)
-   print(sum(probstp))
-   print(expEapprox)
-   print(DAISIE_ExpEIN(teq, pars1, M)[[1]])
+   message(sum(probstp))
+   message(expEapprox)
+   message(DAISIE_ExpEIN(teq, pars1, M)[[1]])
    expEapprox <- sum(ee * probseq)
-   print(sum(probseq))
-   print(expEapprox)
-   print(DAISIE_ExpEIN(Inf, pars1, M)[[1]])
+   message(sum(probseq))
+   message(expEapprox)
+   message(DAISIE_ExpEIN(Inf, pars1, M)[[1]])
    KLdist <- sum(probseq * log(probseq / probstp))
    return(KLdist)
 }
diff --git a/R/DAISIE_SR_ML_CS.R b/R/DAISIE_SR_ML_CS.R
index 76b0b3fd..6164e53a 100644
--- a/R/DAISIE_SR_ML_CS.R
+++ b/R/DAISIE_SR_ML_CS.R
@@ -33,12 +33,11 @@ DAISIE_SR_loglik_all_choosepar <- function(
            methode = methode,
            CS_version = CS_version,
            abstolint = abstolint,
-           reltolint = reltolint,
-           verbose = FALSE
+           reltolint = reltolint
            )
       }
       if (is.nan(loglik) || is.na(loglik)) {
-         cat("There are parameter values used which cause numerical problems.\n")
+         warning("There are parameter values used which cause numerical problems.\n")
          loglik <- -Inf
       }
    }
@@ -162,10 +161,13 @@ DAISIE_SR_loglik_all_choosepar <- function(
 #' @keywords models
 #' @examples
 #'
-#' \dontrun{
-#' ### When all species have the same rates, and we want to optimize all 5 parameters,
-#' # we use:
-#'
+#' \donttest{
+#' ## In all following DAISIE_ML calls very high tolerances and low system size
+#' ## are used  for fast computation for this example. Use default or better
+#' ## tol, tolint an res values in actual analyses.
+#' ##################
+#' ### When all species have the same rates, and we want to optimize all 5
+#' ### parameters, we use:
 #' utils::data(Galapagos_datalist)
 #' DAISIE_ML(
 #'    datalist = Galapagos_datalist,
@@ -173,7 +175,10 @@ DAISIE_SR_loglik_all_choosepar <- function(
 #'    ddmodel = 11,
 #'    idparsopt = 1:5,
 #'    parsfix = NULL,
-#'    idparsfix = NULL
+#'    idparsfix = NULL,
+#'    tol = c(0.1, 0.02, 0.01),
+#'    tolint = c(1e-4, 1e-2),
+#'    res = 50
 #' )
 #'
 #' ### When all species have the same rates, and we want to optimize all parameters
@@ -185,7 +190,10 @@ DAISIE_SR_loglik_all_choosepar <- function(
 #'    initparsopt = c(2.5,2.7,0.009,1.01),
 #'    idparsopt = c(1,2,4,5),
 #'    parsfix = Inf,
-#'    idparsfix = 3
+#'    idparsfix = 3,
+#'    tol = c(0.1, 0.02, 0.01),
+#'    tolint = c(1e-4, 1e-2),
+#'    res = 50
 #'    )
 #'
 #' ### When all species have the same rates except that the finches have a different
@@ -199,7 +207,10 @@ DAISIE_SR_loglik_all_choosepar <- function(
 #'    idparsopt = c(1,2,4,5,6),
 #'    parsfix = c(Inf,Inf,0.163),
 #'    idparsfix = c(3,8,11),
-#'    idparsnoshift = c(7,9,10)
+#'    idparsnoshift = c(7,9,10),
+#'    tol = c(0.1, 0.02, 0.01),
+#'    tolint = c(1e-4, 1e-2),
+#'    res = 50
 #'    )
 #'
 #' ### When all species have the same rates except that the finches have a different
@@ -214,7 +225,10 @@ DAISIE_SR_loglik_all_choosepar <- function(
 #'    idparsopt = c(1,2,4,5,6,7,8),
 #'    parsfix = c(Inf,0.163),
 #'    idparsfix = c(3,11),
-#'    idparsnoshift = c(9,10)
+#'    idparsnoshift = c(9,10),
+#'    tol = c(0.1, 0.02, 0.01),
+#'    tolint = c(1e-4, 1e-2),
+#'    res = 50
 #'    )
 #'
 #'
@@ -230,7 +244,10 @@ DAISIE_SR_loglik_all_choosepar <- function(
 #'    idparsopt = c(1,2,4,5,7,11),
 #'    parsfix = c(Inf,Inf),
 #'    idparsfix = c(3,8),
-#'    idparsnoshift = c(6,9,10)
+#'    idparsnoshift = c(6,9,10),
+#'    tol = c(0.1, 0.02, 0.01),
+#'    tolint = c(1e-4, 1e-2),
+#'    res = 50
 #'    )
 #'
 #' ### When we have two islands with the same rates except for immigration and anagenesis rate,
@@ -244,7 +261,10 @@ DAISIE_SR_loglik_all_choosepar <- function(
 #'    idparsmat = rbind(1:5,c(1:3,6,7)),
 #'    idparsopt = 1:7,
 #'    parsfix = NULL,
-#'    idparsfix = NULL
+#'    idparsfix = NULL,
+#'    tol = c(0.1, 0.02, 0.01),
+#'    tolint = c(1e-4, 1e-2),
+#'    res = 50
 #' )
 #'
 #' ### When we consider the four Macaronesia archipelagoes and set all parameters the same
@@ -261,7 +281,10 @@ DAISIE_SR_loglik_all_choosepar <- function(
 #'    idparsmat = rbind(1:5,c(6,2,3,7,5),1:5,1:5),
 #'    idparsopt = c(2,4,5,6,7),
 #'    parsfix = c(0,Inf),
-#'    idparsfix = c(1,3)
+#'    idparsfix = c(1,3),
+#'    tol = c(0.1, 0.02, 0.01),
+#'    tolint = c(1e-4, 1e-2),
+#'    res = 50
 #' )
 #'
 #' }
@@ -328,7 +351,6 @@ DAISIE_SR_ML_CS <- DAISIE_SR_ML <- function(
 #  . cond == 0 : no conditioning
 #  . cond == 1 : conditioning on presence on the island
 
-  options(warn = -1)
   out2err <- data.frame(lambda_c = NA, mu = NA, K = NA, gamma = NA, lambda_a2 = NA, lambda_c2 = NA, mu2 = NA, K2 = NA, gamma2 = NA, lambda_a2 = NA, tshift = NA, loglik = NA, df = NA, conv = NA)
   out2err <- invisible(out2err)
   idpars <- sort(c(idparsopt, idparsfix, idparsnoshift))
@@ -336,40 +358,45 @@ DAISIE_SR_ML_CS <- DAISIE_SR_ML <- function(
     list$missing_species
     }))
   if (CS_version != 1) {
-    cat("This version of CS is not yet implemented\n")
+    warning("This version of CS is not yet implemented")
     return(out2err)
   }
   if (sum(missnumspec) > (res - 1)) {
-    cat("The number of missing species is too large relative to the resolution of the ODE.\n")
+    warning("The number of missing species is too large relative to the resolution of the ODE.")
     return(out2err)
   }
   if ((prod(idpars == (1:11)) != 1) || (length(initparsopt) != length(idparsopt)) || (length(parsfix) != length(idparsfix))) {
-    cat("The parameters to be optimized and/or fixed are incoherent.\n")
+    warning("The parameters to be optimized and/or fixed are incoherent.")
     return(out2err)
   }
   if (length(idparsopt) > 11) {
-    cat("The number of parameters to be optimized is too high.\n")
+    warning("The number of parameters to be optimized is too high.")
     return(out2err)
   }
-  namepars <- c("lambda_c", "mu", "K", "gamma", "lambda_a", "lambda_c2", "mu2", "K2", "gamma2", "lambda_a2", "tshift")
-  if (length(namepars[idparsopt]) == 0) {
-    optstr <- "nothing"
-  } else {
-    optstr <- namepars[idparsopt]
-  }
-  cat("You are optimizing", optstr, "\n")
-  if (length(namepars[idparsfix]) == 0) {
-    fixstr <- "nothing"
-  } else {
-    fixstr <- namepars[idparsfix]
-  }
-  cat("You are fixing", fixstr, "\n")
-  if (sum(idparsnoshift == (6:10)) != 5) {
-    noshiftstring <- namepars[idparsnoshift]
-    cat("You are not shifting", noshiftstring, "\n")
-  }
-  cat("Calculating the likelihood for the initial parameters.", "\n")
-  utils::flush.console()
+  namepars <- c(
+    "lambda_c",
+    "mu",
+    "K",
+    "gamma",
+    "lambda_a",
+    "lambda_c2",
+    "mu2",
+    "K2",
+    "gamma2",
+    "lambda_a2",
+    "tshift"
+  )
+
+  print_ml_par_settings(
+    namepars = namepars,
+    idparsopt = idparsopt,
+    idparsfix = idparsfix,
+    idparsnoshift = idparsnoshift,
+    # Basic case, only needs to be specified case by case on ML1
+    all_no_shift = 6:10,
+    verbose = verbose
+  )
+
   trparsopt <- initparsopt / (1 + initparsopt)
   trparsopt[which(initparsopt == Inf)] <- 1
   trparsfix <- parsfix / (1 + parsfix)
@@ -377,34 +404,32 @@ DAISIE_SR_ML_CS <- DAISIE_SR_ML <- function(
   pars2 <- c(res, ddmodel, cond, verbose, island_ontogeny, tol, maxiter)
   optimpars <- c(tol, maxiter)
   initloglik <- DAISIE_SR_loglik_all_choosepar(trparsopt = trparsopt, trparsfix = trparsfix, idparsopt = idparsopt, idparsfix = idparsfix, idparsnoshift = idparsnoshift, pars2 = pars2, datalist = datalist, methode = methode, CS_version = CS_version, abstolint = tolint[1], reltolint = tolint[2])
-  cat("The loglikelihood for the initial parameter values is", initloglik, "\n")
+  message("The loglikelihood for the initial parameter values is ", initloglik)
   if (initloglik == -Inf) {
-    cat("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.\n")
+    message("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.")
     return(out2err)
   }
-  cat("Optimizing the likelihood - this may take a while.", "\n")
-  utils::flush.console()
-  out <-
-    DDD::optimizer(
-      optimmethod = optimmethod,
-      optimpars = optimpars,
-      fun = DAISIE_SR_loglik_all_choosepar,
-      trparsopt = trparsopt,
-      idparsopt = idparsopt,
-      trparsfix = trparsfix,
-      idparsfix = idparsfix,
-      idparsnoshift = idparsnoshift,
-      pars2 = pars2,
-      datalist = datalist,
-      methode = methode,
-      CS_version = CS_version,
-      abstolint = tolint[1],
-      reltolint = tolint[2],
-      jitter = jitter,
-      num_cycles = num_cycles
-    )
+  message("Optimizing the likelihood - this may take a while.", "\n")
+  out <- DDD::optimizer(
+    optimmethod = optimmethod,
+    optimpars = optimpars,
+    fun = DAISIE_SR_loglik_all_choosepar,
+    trparsopt = trparsopt,
+    idparsopt = idparsopt,
+    trparsfix = trparsfix,
+    idparsfix = idparsfix,
+    idparsnoshift = idparsnoshift,
+    pars2 = pars2,
+    datalist = datalist,
+    methode = methode,
+    CS_version = CS_version,
+    abstolint = tolint[1],
+    reltolint = tolint[2],
+    jitter = jitter,
+    num_cycles = num_cycles
+  )
   if (out$conv != 0) {
-    cat("Optimization has not converged. Try again with different initial values.\n")
+    warning("Optimization has not converged. Try again with different initial values.")
     out2 <- out2err
     out2$conv <- out$conv
     return(out2)
@@ -429,6 +454,6 @@ DAISIE_SR_ML_CS <- DAISIE_SR_ML <- function(
   out2 <- data.frame(lambda_c = MLpars1[1], mu = MLpars1[2], K = MLpars1[3], gamma = MLpars1[4], lambda_a = MLpars1[5], lambda_c2 = MLpars1[6], mu2 = MLpars1[7], K2 = MLpars1[8], gamma2 = MLpars1[9], lambda_a2 = MLpars1[10], tshift = MLpars1[11], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
   s1 <- sprintf("Maximum likelihood parameter estimates: lambda_c: %f, mu: %f, K: %f, gamma: %f, lambda_a: %f, lambda_c2: %f, mu2: %f, K2: %f, gamma2: %f, lambda_a2: %f, time of shift: %f", MLpars1[1], MLpars1[2], MLpars1[3], MLpars1[4], MLpars1[5], MLpars1[6], MLpars1[7], MLpars1[8], MLpars1[9], MLpars1[10], MLpars1[11])
   s2 <- sprintf("Maximum loglikelihood: %f", ML)
-  cat("\n", s1, "\n", s2, "\n")
+  message("\n", s1, "\n", s2, "\n")
   return(invisible(out2))
 }
diff --git a/R/DAISIE_SR_loglik_CS.R b/R/DAISIE_SR_loglik_CS.R
index e8a35ea7..2fc4671a 100644
--- a/R/DAISIE_SR_loglik_CS.R
+++ b/R/DAISIE_SR_loglik_CS.R
@@ -73,10 +73,10 @@ DAISIE_SR_loglik_CS_M1 <- DAISIE_SR_loglik <- function(
   missnumspec,
   methode = "lsodes",
   abstolint = abstolint,
-  reltolint = reltolint,
-  verbose = FALSE
+  reltolint = reltolint
 ) {
-  if (is.na(pars2[4])) {
+  verbose <- pars2[4]
+  if (is.na(verbose)) {
     pars2[4] <- 0
   }
   ddep <- pars2[2]
@@ -233,7 +233,7 @@ DAISIE_SR_loglik_CS_M1 <- DAISIE_SR_loglik <- function(
   }
   print_parameters_and_loglik(pars = c(stac,pars1[1:5]),
                               loglik = loglik,
-                              verbose = pars2[4],
+                              verbose = verbose,
                               type = 'clade_loglik')
   return(as.numeric(loglik))
 }
@@ -321,7 +321,6 @@ DAISIE_SR_loglik_CS_M1 <- DAISIE_SR_loglik <- function(
 #' @param methode Method of the ODE-solver. See package deSolve for details.
 #' Default is "lsodes"
 #' @param abstolint Absolute tolerance of the integration
-#' @param verbose Logical controling if progress is printed to console.
 #' @param reltolint Relative tolerance of the integration
 #'
 #' @return The loglikelihood
@@ -348,9 +347,9 @@ DAISIE_SR_loglik_CS <- DAISIE_SR_loglik_all <- function(
   methode = "lsodes",
   CS_version = 1,
   abstolint = 1E-16,
-  reltolint = 1E-10,
-  verbose = FALSE
+  reltolint = 1E-10
 ) {
+  verbose <- pars2[4]
   pars1 = as.numeric(pars1)
   check_shift_loglik = shift_before_certain_brts(datalist, pars1)
   if(check_shift_loglik != 0){
@@ -365,8 +364,7 @@ DAISIE_SR_loglik_CS <- DAISIE_SR_loglik_all <- function(
     missnumspec = 0,
     methode = methode,
     abstolint = abstolint,
-    reltolint = reltolint,
-    verbose = FALSE
+    reltolint = reltolint
   )
   if (is.null(datalist[[1]]$not_present)) {
     not_present <- (datalist[[1]]$not_present_type1 + datalist[[1]]$not_present_type2)
@@ -387,8 +385,7 @@ DAISIE_SR_loglik_CS <- DAISIE_SR_loglik_all <- function(
         missnumspec = datalist[[i]]$missing_species,
         methode = methode,
         abstolint = abstolint,
-        reltolint = reltolint,
-        verbose = FALSE
+        reltolint = reltolint
       )
     }
   }
diff --git a/R/DAISIE_SR_sim.R b/R/DAISIE_SR_sim.R
index 7b824f54..8133fe9a 100644
--- a/R/DAISIE_SR_sim.R
+++ b/R/DAISIE_SR_sim.R
@@ -75,20 +75,7 @@
 #' @references Hauffe, T., D. Delicado, R.S. Etienne and L. Valente (2020).
 #' Lake expansion increases equilibrium diversity via the target effect of
 #' island biogeography
-#' @keywords internal
-#' @examples
-#' # Simulate 15 islands for 4 million years with a shift in immigration rate
-#' # at 0.195 Ma, and plot the species-through-time plot. Pool size 296.
-#'
-#' pars_before_shift = c(0.079, 0.973, Inf, 0.136, 0.413)
-#' pars_after_shift = c(0.079, 0.973, Inf, 0.652, 0.413)
-#' tshift = 0.195
-#' island_shift_replicates = DAISIE:::DAISIE_SR_sim(
-#'    time = 4,
-#'    M = 296,
-#'    pars = c(pars_before_shift, pars_after_shift, tshift),
-#'    replicates = 15
-#'  )
+#' @noRd
 DAISIE_SR_sim <- function(time,
                           M,
                           pars,
@@ -118,7 +105,7 @@ DAISIE_SR_sim <- function(time,
     }
     island_replicates[[rep]] = full_list
     if (verbose)
-      print(paste("Island replicate ", rep, sep = ""))
+      message("Island replicate ", rep)
   }
   island_replicates = DAISIE_format_CS(
     island_replicates = island_replicates,
diff --git a/R/DAISIE_check_format.R b/R/DAISIE_check_format.R
index 094fd812..da07a498 100644
--- a/R/DAISIE_check_format.R
+++ b/R/DAISIE_check_format.R
@@ -37,9 +37,9 @@ are_rates <- function(rates) {
 #'
 #' @inheritParams default_params_doc
 #'
-#' @keywords internal
 #' @return \code{TRUE} if object max_rates is a list of rates,
 #' \code{FALSE} otherwise.
+#' @noRd
 are_max_rates <- function(max_rates) {
   if (!all(sapply(max_rates, is.numeric))) return(FALSE)
   if (!"ana_max_rate" %in% names(max_rates)) return(FALSE)
@@ -62,27 +62,7 @@ are_max_rates <- function(max_rates) {
 #' @author Joshua Lambert, Pedro Neves
 #' @seealso \code{\link{are_rates}}, \code{\link{are_max_rates}}
 #'
-#' @keywords internal
-#'
-#' @examples
-#' rates <- list(
-#'   ext_rate = 0.1,
-#'   immig_rate = 0.1,
-#'   ana_rate = 0.1,
-#'   clado_rate = 0.1
-#' )
-#' max_rates <- list(
-#'   ext_max_rate = 1,
-#'   immig_max_rate = 1,
-#'   ana_max_rate = 1,
-#'   clado_max_rate = 1
-#' )
-#' testthat::expect_true(
-#'   DAISIE:::are_max_rates_gt_rates(
-#'     rates = rates,
-#'     max_rates = max_rates
-#'   )
-#' )
+#' @noRd
 are_max_rates_gt_rates <- function(rates, max_rates) {
   if (!all(sapply(rates, is.numeric))) return(FALSE)
   if (!all(sapply(max_rates, is.numeric))) return(FALSE)
@@ -99,7 +79,7 @@ are_max_rates_gt_rates <- function(rates, max_rates) {
 #'
 #' @seealso is_island_ontogeny_runtime
 #' @return Boolean stating if island_ontogeny is correct.
-#' @keywords internal
+#' @noRd
 is_island_ontogeny_input <- function(island_ontogeny) {
   if (class(island_ontogeny) != class(character())) return(FALSE)
   if (island_ontogeny != "const" && island_ontogeny != "beta") return(FALSE)
@@ -112,7 +92,7 @@ is_island_ontogeny_input <- function(island_ontogeny) {
 #'
 #' @seealso is_sea_level_runtime
 #' @return Boolean stating if sea_level is correct.
-#' @keywords internal
+#' @noRd
 is_sea_level_input <- function(sea_level) {
   if (class(sea_level) != class(character())) return(FALSE)
   if (sea_level != "const" && sea_level != "sine") return(FALSE)
@@ -128,18 +108,7 @@ is_sea_level_input <- function(sea_level) {
 #' @return TRUE if the input is a valid collection of simulation
 #' outputs.
 #' @author Richel J.C Bilderbeek, Pedro Neves
-#' @examples
-#' testthat::expect_false(DAISIE:::is_simulation_outputs("nonsense"))
-#'
-#' simulation_outputs <- DAISIE_sim_cr(
-#'   time = 2,
-#'   M = 1000,
-#'   pars = c(2, 1, 20, 0.0001, 1),
-#'   replicates = 1,
-#'   plot_sims = FALSE
-#'  )
-#' testthat::expect_true(DAISIE:::is_simulation_outputs(simulation_outputs))
-#' @keywords internal
+#' @noRd
 is_simulation_outputs <- function(simulation_outputs) {
   for (n_replicate in seq_along(simulation_outputs)) {
     if (!"island_age" %in% names(simulation_outputs[[n_replicate]][[1]]))
@@ -164,22 +133,10 @@ is_simulation_outputs <- function(simulation_outputs) {
 #'
 #' @inheritParams default_params_doc
 #'
-#' @export
 #' @return Boolean that indicates if list conforms to expected area parameters
 #' as created by \link{create_area_pars}
 #' @author Richel J.C Bilderbeek, Joshua Lambert, Pedro Neves
-#' @keywords internal
-#'
-#' @examples
-#' testit::assert(DAISIE:::are_area_pars(
-#'   create_area_pars(
-#'     max_area = 10,
-#'     current_area = 4,
-#'     proportional_peak_t = 0.5,
-#'     total_island_age = 5,
-#'     sea_level_amplitude = 5,
-#'     sea_level_frequency = 10,
-#'     island_gradient_angle = 0)))
+#' @noRd
 are_area_pars <- function(area_pars) {
   if (is.null(area_pars) == TRUE) return(TRUE)
   if (class(area_pars) != class(list())) return(FALSE)
@@ -208,12 +165,7 @@ are_area_pars <- function(area_pars) {
 #' @return \code{TRUE} if list contains hyperparameters, \code{FALSE} otherwise.
 #' @author Pedro Neves, Joshua Lambert
 #'
-#' @keywords internal
-#'
-#' @examples
-#' testit::assert(
-#'   DAISIE:::are_hyper_pars(create_hyper_pars(d = 0.027, x = 0.15))
-#' )
+#' @noRd
 are_hyper_pars <- function(hyper_pars) {
   if (!is.list(hyper_pars)) return(FALSE)
   if (!is.numeric(unlist(hyper_pars))) return(FALSE)
@@ -231,18 +183,7 @@ are_hyper_pars <- function(hyper_pars) {
 #' @return Boolean that indicates if list conforms to expected area parameters
 #' as created by \link{create_trait_pars}
 #'
-#' @keywords internal
-#'
-#' @examples
-#' testit::assert(DAISIE:::are_trait_pars(
-#'   create_trait_pars(
-#'     trans_rate = 0.5,
-#'     immig_rate2 = 0.1,
-#'     ext_rate2 = 0.2,
-#'     ana_rate2 = 0.3,
-#'     clado_rate2 = 0.4,
-#'     trans_rate2 = 0.5,
-#'     M2 = 1000)) == TRUE)
+#' @noRd
 are_trait_pars <- function(trait_pars) {
   if (is.null(trait_pars) == TRUE) return(TRUE)
   if (class(trait_pars) != class(list())) return(FALSE)
diff --git a/R/DAISIE_dataprep.R b/R/DAISIE_dataprep.R
index 95a36060..d38340e8 100644
--- a/R/DAISIE_dataprep.R
+++ b/R/DAISIE_dataprep.R
@@ -196,11 +196,11 @@ DAISIE_dataprep = function(datatable,
 
     if(max(the_brts)>island_age){
       if (verbose == TRUE) {
-        print(paste("Colonisation time of ",
+        message("Colonisation time of ",
                     max(the_brts),
                     " for ",
                     as.character(datatable[i, "Clade_name"]),
-                    " is older than island age", sep = ""))
+                    " is older than island age")
       }
       if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
         datatable[i,"Status"] <-"Endemic_MaxAge"}
diff --git a/R/DAISIE_format_CS_full_stt.R b/R/DAISIE_format_CS_full_stt.R
index d46f23fd..4d92c5a8 100644
--- a/R/DAISIE_format_CS_full_stt.R
+++ b/R/DAISIE_format_CS_full_stt.R
@@ -147,10 +147,9 @@ DAISIE_format_CS_full_stt <- function(island_replicates,
     }
     several_islands[[rep]] <- island_list
     if (verbose == TRUE) {
-      message(paste0("Island being formatted: ",
-                  rep,
-                  "/",
-                  length(island_replicates)))
+      message(
+        "Island being formatted: ", rep, "/", length(island_replicates)
+      )
     }
   }
   return(several_islands)
diff --git a/R/DAISIE_format_GW.R b/R/DAISIE_format_GW.R
index 8a100753..61cf16c0 100644
--- a/R/DAISIE_format_GW.R
+++ b/R/DAISIE_format_GW.R
@@ -94,11 +94,9 @@ DAISIE_format_GW <- function(island_replicates,
 
       several_islands[[rep]] <- island_list
       if (verbose == TRUE) {
-        print(paste("Island being formatted: ",
-                    rep,
-                    "/",
-                    length(island_replicates),
-                    sep = ""))
+        message(
+          "Island being formatted: ", rep, "/", length(island_replicates)
+        )
       }
     }
   return(several_islands)
diff --git a/R/DAISIE_format_IW.R b/R/DAISIE_format_IW.R
index f9509aa4..9584c632 100644
--- a/R/DAISIE_format_IW.R
+++ b/R/DAISIE_format_IW.R
@@ -5,39 +5,7 @@
 #'
 #' @return List with CS DAISIE simulation output
 #'
-#' @keywords internal
-#'
-#' @examples
-#' island_replicates <- list()
-#' island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_cr(
-#'   time = 5,
-#'   mainland_n = 1000,
-#'   pars = c(2, 2, 40, 0.1, 1),
-#'   area_pars = DAISIE::create_area_pars(
-#'     max_area = 1,
-#'     current_area = 1,
-#'     proportional_peak_t = 0,
-#'     total_island_age = 0,
-#'     sea_level_amplitude = 0,
-#'     sea_level_frequency = 0,
-#'     island_gradient_angle = 0),
-#'   hyper_pars = create_hyper_pars(d = 0.2, x = 0.1),
-#'   nonoceanic_pars = c(0, 0)
-#')
-#' formatted_island_sampled <- DAISIE:::DAISIE_format_IW(
-#'   island_replicates = island_replicates,
-#'   time = 5,
-#'   M = 1000,
-#'   sample_freq = 25,
-#'   verbose = FALSE
-#')
-#' formatted_island_full <- DAISIE:::DAISIE_format_IW(
-#'   island_replicates = island_replicates,
-#'   time = 5,
-#'   M = 1000,
-#'   sample_freq = Inf,
-#'   verbose = FALSE
-#')
+#' @noRd
 DAISIE_format_IW <- function(island_replicates,
                              time,
                              M,
diff --git a/R/DAISIE_loglik_CS.R b/R/DAISIE_loglik_CS.R
index f290b764..d3677680 100644
--- a/R/DAISIE_loglik_CS.R
+++ b/R/DAISIE_loglik_CS.R
@@ -1048,7 +1048,7 @@ print_parameters_and_loglik <- function(pars,
                                         type = 'island_loglik',
                                         distance_dep = NULL)
 {
-  if (verbose >= 1) {
+  if (isTRUE(verbose >= 2)) {
     if(type == 'clade_loglik') {
       s1a <- sprintf("Status of colonist: %d", pars[1])
       s1b <- sprintf("Parameters:")
@@ -1056,12 +1056,12 @@ print_parameters_and_loglik <- function(pars,
       s2 <- paste(sprintf("%f", pars[-1]), collapse = ', ')
       s12 <- paste(s1, s2, collapse = ' ')
       s3 <- paste(sprintf("Loglikelihood: %f", loglik), collapse = '')
-      cat(s12, s3, sep = ', ')
+      message(paste(s12, s3, sep = ', '))
     } else {
       if(type == 'global_ML') {
         s1 <- s1output(pars, distance_dep)
         s3 <- sprintf("Maximum Loglikelihood: %f", loglik)
-        cat(s1,s3,sep = '\n')
+        message(paste(s1, s3, sep = '\n'))
       } else {
         if(is.null(ncol(pars))) {
           lpars <- length(pars)
@@ -1079,7 +1079,7 @@ print_parameters_and_loglik <- function(pars,
           s1 <- sprintf("Maximum likelihood parameters: ")
           s2 <- paste(sprintf("%f", pars), collapse = ', ')
           s3 <- sprintf("Maximum Loglikelihood: %f", loglik)
-          cat(s1, parnames, s2, s3, sep = '\n')
+          message(paste(s1, parnames, s2, s3, sep = '\n'))
         } else {
           if(type == 'multiple_island_ML') {
             s1 <- sprintf("Maximum likelihood parameters: ")
@@ -1088,13 +1088,13 @@ print_parameters_and_loglik <- function(pars,
                s2 <- paste(s2,paste(sprintf("%f", pars[i,]), collapse = ', '), sep = '\n')
             }
             s3 <- sprintf("Maximum Loglikelihood: %f", loglik)
-            cat(s1, s2, s3, sep = '\n')
+            message(paste(s1, s2, s3, sep = '\n'))
           } else {
             if(type == 'island_loglik') {
               s1 <- sprintf("Parameters: ")
               s2 <- paste(sprintf("%f", pars), collapse = ', ')
               s3 <- sprintf("Loglikelihood: %f", loglik)
-              cat(s1, parnames, s2, s3, sep = '\n')
+              message(paste(s1, parnames, s2, s3, sep = '\n'))
             } else {
               stop('Type of printing output unknown')
             }
@@ -1102,8 +1102,6 @@ print_parameters_and_loglik <- function(pars,
         }
       }
     }
-    cat('\n')
-    utils::flush.console()
   }
 }
 
@@ -1221,7 +1219,7 @@ DAISIE_integrate_const <- function(initprobs,tvec,rhs_func,pars,rtol,atol,method
   # During code coverage, 'function_as_text' may become:
   #
   # if (TRUE) {
-  #   covr:::count("DAISIE_loglik_CS.R:58:3:58:25:3:25:4657:4657")
+  #   covr::count("DAISIE_loglik_CS.R:58:3:58:25:3:25:4657:4657")
   #   lx <- (length(x) - 1)/2
   # }
   #
diff --git a/R/DAISIE_loglik_IW.R b/R/DAISIE_loglik_IW.R
index 72c7aa50..6a059c48 100644
--- a/R/DAISIE_loglik_IW.R
+++ b/R/DAISIE_loglik_IW.R
@@ -305,7 +305,7 @@ DAISIE_loglik_IW <- function(
      }
      if(is.null(np))
      {
-        cat('Number of species not present is misspecified.\n')
+        warning('Number of species not present is misspecified.')
         loglik <- NA
         return(loglik)
      }
@@ -315,7 +315,7 @@ DAISIE_loglik_IW <- function(
   if(length(pars1) == 6) {
     M <- pars1[6]
   } else {
-    cat("pars1 should contain 5 or 6 values.\n")
+    warning("pars1 should contain 5 or 6 values.")
     loglik <- NA
     return(loglik)
   }
@@ -381,10 +381,9 @@ DAISIE_loglik_IW <- function(
   expandvec <- NULL
   for (k in 0:(length(brts) - 2))
   {
-    if (pars2[4] == 2)
+    if (isTRUE(identical(pars2[4], 3)))
     {
-      cat(paste('k = ',k,', sysdim = ',sysdim,'\n',sep = ''))
-      utils::flush.console()
+      message(paste('k = ',k ,', sysdim = ', sysdim, sep = ''))
     }
     dime <- list(lxm = lxm, lxe = lxe, sysdim = sysdim)
     if (sysdimchange == 1) {
@@ -503,7 +502,7 @@ DAISIE_loglik_IW <- function(
       probs <- .Call("daisie_odeint_iw", probs, c(min(brts),0), iw_parms, methode, abstolint, reltolint)
     } else {
       y <- deSolve::ode(y = probs,
-                        times = c(min(brts),0),
+                        times = c(min(brts), 0),
                         func = DAISIE_loglik_rhs_IW,
                         parms = iw_parms,
                         rtol = reltolint,
diff --git a/R/DAISIE_make_archipelago.R b/R/DAISIE_make_archipelago.R
index 07189041..f06ccd07 100644
--- a/R/DAISIE_make_archipelago.R
+++ b/R/DAISIE_make_archipelago.R
@@ -53,7 +53,7 @@ DAISIE_make_global <- function(archipelago_list, M, phylo_data, archipelago_data
   global_object <- list()
   for (i in 1:length(archipelago_list)) {
     the_archipelago <- as.character(archipelago_list[i])
-    print(the_archipelago)
+    message(the_archipelago)
     global_object[[i]] <- DAISIE_make_archipelago(the_archipelago, M, phylo_data, archipelago_data)
   }
   return(global_object)
diff --git a/R/DAISIE_max_rates.R b/R/DAISIE_max_rates.R
index 45e6857e..77fa596e 100644
--- a/R/DAISIE_max_rates.R
+++ b/R/DAISIE_max_rates.R
@@ -60,8 +60,6 @@ update_max_rates <- function(gam,
     ana_max_rate = ana_max_rate,
     clado_max_rate = clado_max_rate
   )
-  # print("max rates")
-  # print(max_rates)
   return(max_rates)
 }
 
@@ -72,33 +70,7 @@ update_max_rates <- function(gam,
 #'
 #' @return Numeric maximum area during the simulation.
 #'
-#' @keywords internal
-#'
-#' @examples
-#' timeval <- 1
-#' total_time <- 10
-#' area_pars <- DAISIE::create_area_pars(
-#'   max_area = 5000,
-#'   current_area = 4000,
-#'   proportional_peak_t = 0.5,
-#'   total_island_age = 15,
-#'   sea_level_amplitude = 0,
-#'   sea_level_frequency = 0,
-#'   island_gradient_angle = 0
-#' )
-#' island_ontogeny <- 1
-#' sea_level <- 0
-#' peak <- DAISIE:::calc_peak(total_time = total_time, area_pars = area_pars)
-#' testthat::expect_silent(
-#'   global_max_area_time <- DAISIE:::get_global_max_area(
-#'     total_time = total_time,
-#'     peak = peak,
-#'     area_pars = area_pars,
-#'     island_ontogeny = island_ontogeny,
-#'     sea_level = sea_level
-#'   )
-#' )
-#'
+#' @noRd
 #' @author Pedro Neves, Joshua Lambert, Shu Xie
 get_global_max_area <- function(total_time,
                                 area_pars,
@@ -139,34 +111,7 @@ get_global_max_area <- function(total_time,
 #' @inheritParams default_params_doc
 #'
 #' @return Numeric with time at which area is minimum during the simulation
-#'
-#' @examples
-#' timeval <- 1
-#' total_time <- 10
-#' area_pars <- DAISIE::create_area_pars(
-#'   max_area = 5000,
-#'   current_area = 4000,
-#'   proportional_peak_t = 0.5,
-#'   total_island_age = 15,
-#'   sea_level_amplitude = 0,
-#'   sea_level_frequency = 0,
-#'   island_gradient_angle = 0
-#' )
-#' island_ontogeny <- 1
-#' sea_level <- 0
-#' peak <- DAISIE:::calc_peak(total_time = total_time, area_pars = area_pars)
-#'
-#' testthat::expect_silent(
-#'   DAISIE:::get_global_min_area(
-#'     total_time = total_time,
-#'     area_pars = area_pars,
-#'     peak = peak,
-#'     island_ontogeny = island_ontogeny,
-#'     sea_level = sea_level
-#'   )
-#' )
-#'
-#' @keywords internal
+#' @noRd
 #'
 #' @author Pedro Neves, Joshua Lambert, Shu Xie
 get_global_min_area <- function(total_time,
diff --git a/R/DAISIE_plot_comparison_stts.R b/R/DAISIE_plot_comparison_stts.R
index 1de3c0ee..409a4c17 100644
--- a/R/DAISIE_plot_comparison_stts.R
+++ b/R/DAISIE_plot_comparison_stts.R
@@ -2,14 +2,12 @@
 #'
 #' @inheritParams default_params_doc
 #'
-#' @seealso \code{\link{DAISIE_plot_sims}}, \code{\link{DAISIE_plot_stt}},
-#'   \code{\link{DAISIE_convert_to_classic_plot}}
+#' @seealso \code{\link{DAISIE_plot_sims}}, \code{\link{DAISIE_plot_stt}}
 #' @family plotting
 #' @return Standard \code{\link{DAISIE_plot_stt}} with overlaid additional
 #'   STT curves for comparison.
-#' @keywords internal
-#'
 #' @author Pedro Neves
+#' @noRd
 DAISIE_plot_comparison_stts <- function(
   time,
   plot_lists_simulations,
diff --git a/R/DAISIE_plot_sims.R b/R/DAISIE_plot_sims.R
index 37c00aa1..0af46f65 100644
--- a/R/DAISIE_plot_sims.R
+++ b/R/DAISIE_plot_sims.R
@@ -52,7 +52,7 @@ DAISIE_plot_sims <- function(
     plot_lists <- DAISIE_convert_to_classic_plot(island_replicates,
                                                  trait_pars = trait_pars)
   } else {
-    stop("Plotting STT with sample_freq = Inf not yet available. \n")
+    stop("Plotting STT with sample_freq = Inf not yet available.")
   }
   if (type == "all") {
     types <- names(plot_lists)
@@ -60,7 +60,8 @@ DAISIE_plot_sims <- function(
     types <- type
   }
   num_plots <- sum(!sapply(plot_lists[types], FUN = is.null))
-  graphics::par(mfrow = c(1, num_plots))
+  oldpar <- graphics::par(mfrow = c(1, num_plots))
+  on.exit(graphics::par(oldpar))
   for (type_here in types) {
     DAISIE_plot_stt(
       plot_plus_one = plot_plus_one,
diff --git a/R/DAISIE_plot_stt.R b/R/DAISIE_plot_stt.R
index c82b6d1a..2f0a0fc9 100644
--- a/R/DAISIE_plot_stt.R
+++ b/R/DAISIE_plot_stt.R
@@ -3,16 +3,9 @@
 #' @inheritParams default_params_doc
 #'
 #' @seealso \code{\link{DAISIE_plot_stt}}, \code{\link{DAISIE_plot_sims}}
-#' @examples
-#' utils::data("islands_1type_1000reps", package = "DAISIE")
-#' simulation_outuputs <- DAISIE:::DAISIE_convert_to_classic_plot(
-#' islands_1type_1000reps
-#' )
-#'
-#'
 #' @return a list with wrangled data to be used for plotting STT plots with
 #' DAISIE_plot_stt
-#' @keywords internal
+#' @noRd
 DAISIE_convert_to_classic_plot <- function(simulation_outputs,
                                            trait_pars = NULL) {
   if (!is_simulation_outputs(simulation_outputs)) {
diff --git a/R/DAISIE_rates.R b/R/DAISIE_rates.R
index 77586314..ee8a574c 100644
--- a/R/DAISIE_rates.R
+++ b/R/DAISIE_rates.R
@@ -283,14 +283,7 @@ island_area <- function(timeval,
 #' @inheritParams default_params_doc
 #'
 #' @return Numeric with per capita extinction rate, given A(t), x, and mu0.
-#' @keywords internal
-#'
-#' @examples
-#' ext_rate_per_capita <- DAISIE:::get_ext_rate_per_capita(
-#'   mu = 0.5,
-#'   x = 1,
-#'   A = 1000
-#' )
+#' @noRd
 get_ext_rate_per_capita <- function(mu,
                                     x,
                                     extcutoff = 1000,
@@ -404,15 +397,7 @@ get_ana_rate <- function(laa,
 #'
 #' @return Numeric with the per-capita cladogenesis rate given a base
 #' cladogenesis rate, K, A and the d hyperparameter.
-#' @keywords internal
-#'
-#' @examples
-#' lac <- 0.4
-#' d <- 0
-#' num_spec <- 2
-#' K <- 10
-#' A <- 1
-#' clado_rate_pc <- DAISIE:::get_clado_rate_per_capita(lac, d, num_spec, K, A)
+#' @noRd
 get_clado_rate_per_capita <- function(lac,
                                       d,
                                       num_spec,
@@ -494,15 +479,7 @@ get_clado_rate <- function(lac,
 #' @inheritParams default_params_doc
 #'
 #' @return A numeric with the per-capita immigration rate given A(t) and K.
-#' @keywords internal
-#'
-#' @examples
-#' immig_rate_per_capita <- DAISIE:::get_immig_rate_per_capita(
-#'   gam = 0.001,
-#'   num_spec = 5,
-#'   K = 20,
-#'   A = 1000
-#' )
+#' @noRd
 get_immig_rate_per_capita <- function(gam,
                                       num_spec,
                                       K,
diff --git a/R/DAISIE_sim_MW.R b/R/DAISIE_sim_MW.R
index b5795011..6f8d4365 100644
--- a/R/DAISIE_sim_MW.R
+++ b/R/DAISIE_sim_MW.R
@@ -245,9 +245,9 @@ DAISIE_sim_MW <- DAISIE_sim_global <- function(
 
   Archipelago <- as.character(Archipelago)
   archipelago_specific <- cbind(Archipelago,Area,Distance,Age,lambda_c,mu,K,gamma,lamda_a)
-  print('Input data and local parameters for each island:')
-  print(archipelago_specific)
-  print('Start of the simulations:')
+  message('Input data and local parameters for each island:')
+  message(archipelago_specific)
+  message('Start of the simulations:')
 
   global_sim <- list()
   for (i in 1:nrow(archipelago_specific)) {
@@ -270,7 +270,13 @@ DAISIE_sim_MW <- DAISIE_sim_global <- function(
       global_sim[[i]][[a]][[1]]$name <- the_archipelago
     }
 
-    print(paste('Simulation of',as.character(archipelago_specific[i,'Archipelago']),'for',island_age,'Myrs each completed',sep=' '))
+    message(
+      "Simulation of ",
+      as.character(archipelago_specific[i,'Archipelago']),
+      " for ",
+      island_age,
+      "Myrs each completed"
+    )
   }
   return(global_sim)
 }
diff --git a/R/DAISIE_sim_core_time_dep.R b/R/DAISIE_sim_core_time_dep.R
index a3c988db..f1388641 100644
--- a/R/DAISIE_sim_core_time_dep.R
+++ b/R/DAISIE_sim_core_time_dep.R
@@ -109,11 +109,6 @@ DAISIE_sim_core_time_dep <- function(
         num_immigrants = num_immigrants,
         mainland_n = mainland_n
       )
-      # print("rates")
-      # print(rates)
-      # print(island_spec)
-      # print(timeval)
-      # testit::assert(are_rates(rates))
       possible_event <- DAISIE_sample_event_time_dep(
         max_rates = max_rates
       )
diff --git a/R/DAISIE_sim_cr_cs.R b/R/DAISIE_sim_cr_cs.R
index 7e6e4839..d43bf2ce 100644
--- a/R/DAISIE_sim_cr_cs.R
+++ b/R/DAISIE_sim_cr_cs.R
@@ -44,7 +44,7 @@ DAISIE_sim_cr_cs <- function(total_time,
       }
       island_replicates[[rep]] <- full_list
       if (verbose == TRUE) {
-        print(paste("Island replicate ", rep, sep = ""))
+        message("Island replicate ", rep)
       }
     }
   } else if (length(pars) == 10) {
@@ -113,7 +113,7 @@ DAISIE_sim_cr_cs <- function(total_time,
         }
         island_replicates[[rep]] <- full_list
         if (verbose == TRUE) {
-          print(paste("Island replicate ", rep, sep = ""))
+          message("Island replicate ", rep)
         }
       }
     }
diff --git a/R/DAISIE_sim_cr_gw.R b/R/DAISIE_sim_cr_gw.R
index 072224f5..5c0aeab0 100644
--- a/R/DAISIE_sim_cr_gw.R
+++ b/R/DAISIE_sim_cr_gw.R
@@ -37,7 +37,7 @@ DAISIE_sim_cr_gw <- function(total_time,
     }
     island_replicates[[rep]] <- full_list
     if (verbose == TRUE) {
-      print(paste("Island replicate ", rep, sep = ""))
+      message("Island replicate ", rep)
     }
   }
   island_replicates <- DAISIE_format_GW(
diff --git a/R/DAISIE_sim_cr_iw.R b/R/DAISIE_sim_cr_iw.R
index d2db9bad..0769782e 100644
--- a/R/DAISIE_sim_cr_iw.R
+++ b/R/DAISIE_sim_cr_iw.R
@@ -36,7 +36,7 @@ DAISIE_sim_cr_iw <- function(total_time,
       number_present <- length(present)
     }
     if (verbose == TRUE) {
-      print(paste("Island replicate ", rep, sep = ""))
+      message("Island replicate ", rep)
     }
   }
   island_replicates <- DAISIE_format_IW(
diff --git a/R/DAISIE_sim_cr_shift.R b/R/DAISIE_sim_cr_shift.R
index 3b1741c5..3bbea482 100644
--- a/R/DAISIE_sim_cr_shift.R
+++ b/R/DAISIE_sim_cr_shift.R
@@ -105,7 +105,7 @@ DAISIE_sim_cr_shift <- function(
         shift_times = shift_times
       )
       if (verbose == TRUE) {
-        print(paste("Island replicate ", rep, sep = ""))
+        message("Island replicate ", rep)
       }
     }
     island_replicates <- DAISIE_format_IW(island_replicates = island_replicates,
@@ -141,7 +141,7 @@ DAISIE_sim_cr_shift <- function(
       }
       island_replicates[[rep]] <- full_list
       if (verbose == TRUE) {
-        print(paste("Island replicate ", rep, sep = ""))
+        message("Island replicate ", rep)
       }
     }
     island_replicates <- DAISIE_format_CS(
@@ -176,7 +176,7 @@ DAISIE_sim_cr_shift <- function(
       }
       island_replicates[[rep]] <- full_list
       if (verbose == TRUE) {
-        print(paste("Island replicate ", rep, sep = ""))
+        message("Island replicate ", rep)
       }
     }
     island_replicates <- DAISIE_format_GW(island_replicates = island_replicates,
diff --git a/R/DAISIE_sim_min_type2.R b/R/DAISIE_sim_min_type2.R
index 31a13f48..016ae579 100644
--- a/R/DAISIE_sim_min_type2.R
+++ b/R/DAISIE_sim_min_type2.R
@@ -68,14 +68,15 @@ DAISIE_sim_min_type2 <- function(time,
       island_replicates[[length(island_replicates) + 1]] <- list()
       island_replicates[[length(island_replicates)]] <- full_list
       if (verbose == TRUE) {
-        print(paste("Number of island replicates with type 2 species: ",
-                    length(island_replicates),
-                    sep = ""))
+        message(
+          "Number of island replicates with type 2 species: ",
+          length(island_replicates)
+        )
       }
     }
     counter <- counter + 1
     if (verbose == TRUE) {
-      print(paste("Island ", counter, sep = ""))
+      message("Island ", counter)
     }
   }
   return(island_replicates)
diff --git a/R/DAISIE_sim_relaxed_rate.R b/R/DAISIE_sim_relaxed_rate.R
index 1c2271df..451632d6 100644
--- a/R/DAISIE_sim_relaxed_rate.R
+++ b/R/DAISIE_sim_relaxed_rate.R
@@ -149,7 +149,7 @@ DAISIE_sim_relaxed_rate <- function(
     }
     island_replicates[[rep]] <- full_list
     if (verbose == TRUE) {
-      print(paste("Island replicate ", rep, sep = ""))
+      message("Island replicate ", rep)
     }
   }
   island_replicates <- DAISIE_format_CS(
diff --git a/R/DAISIE_sim_time_dep_cs.R b/R/DAISIE_sim_time_dep_cs.R
index 61991812..d54814ba 100644
--- a/R/DAISIE_sim_time_dep_cs.R
+++ b/R/DAISIE_sim_time_dep_cs.R
@@ -53,7 +53,7 @@ DAISIE_sim_time_dep_cs <- function(total_time,
     }
     island_replicates[[rep]] <- full_list
     if (verbose == TRUE) {
-      print(paste("Island replicate ", rep, sep = ""))
+      message("Island replicate ", rep)
     }
   }
   island_replicates <- DAISIE_format_CS(
diff --git a/R/DAISIE_sim_time_dep_gw.R b/R/DAISIE_sim_time_dep_gw.R
index ccd57bcd..4891b7eb 100644
--- a/R/DAISIE_sim_time_dep_gw.R
+++ b/R/DAISIE_sim_time_dep_gw.R
@@ -49,7 +49,7 @@ DAISIE_sim_time_dep_gw <- function(total_time,
     }
     island_replicates[[rep]] <- full_list
     if (verbose == TRUE) {
-      print(paste("Island replicate ", rep, sep = ""))
+      message("Island replicate ", rep)
     }
   }
   island_replicates <- DAISIE_format_GW(
diff --git a/R/DAISIE_sim_time_dep_iw.R b/R/DAISIE_sim_time_dep_iw.R
index 18863a2b..bd91a10b 100644
--- a/R/DAISIE_sim_time_dep_iw.R
+++ b/R/DAISIE_sim_time_dep_iw.R
@@ -48,7 +48,7 @@ DAISIE_sim_time_dep_iw <- function(total_time,
       number_present <- length(present)
     }
     if (verbose == TRUE) {
-      print(paste("Island replicate ", rep, sep = ""))
+      message("Island replicate ", rep)
     }
   }
   island_replicates <- DAISIE_format_IW(
diff --git a/R/DAISIE_sim_trait_dep.R b/R/DAISIE_sim_trait_dep.R
index 4beeb503..4f575444 100644
--- a/R/DAISIE_sim_trait_dep.R
+++ b/R/DAISIE_sim_trait_dep.R
@@ -91,7 +91,7 @@ DAISIE_sim_trait_dep <- function(
         trait_pars = trait_pars
       )
       if (verbose == TRUE) {
-        print(paste("Island replicate ", rep, sep = ""))
+        message("Island replicate ", rep)
       }
     }
     island_replicates <- DAISIE_format_IW(
@@ -168,7 +168,7 @@ DAISIE_sim_trait_dep <- function(
       }
       island_replicates[[rep]] <- full_list
       if (verbose == TRUE) {
-        print(paste("Island replicate ", rep, sep = ""))
+        message("Island replicate ", rep)
       }
     }
     island_replicates <- DAISIE_format_CS(
diff --git a/R/DAISIE_sim_trait_dep_2K.R b/R/DAISIE_sim_trait_dep_2K.R
index 5496884e..24e98a5a 100644
--- a/R/DAISIE_sim_trait_dep_2K.R
+++ b/R/DAISIE_sim_trait_dep_2K.R
@@ -92,7 +92,7 @@ DAISIE_sim_trait_dep_2K <- function(
         trait_pars = trait_pars
       )
       if (verbose == TRUE) {
-        print(paste("Island replicate ", rep, sep = ""))
+        message("Island replicate ", rep)
       }
     }
     island_replicates <- DAISIE_format_IW(
@@ -171,7 +171,7 @@ DAISIE_sim_trait_dep_2K <- function(
       }
       island_replicates[[rep]] <- full_list
       if (verbose == TRUE) {
-        print(paste("Island replicate ", rep, sep = ""))
+        message("Island replicate ", rep)
       }
     }
     island_replicates <- DAISIE_format_CS(
diff --git a/R/DAISIE_sumstats_rates.R b/R/DAISIE_sumstats_rates.R
index ae9ebdc6..062945e3 100644
--- a/R/DAISIE_sumstats_rates.R
+++ b/R/DAISIE_sumstats_rates.R
@@ -5,38 +5,8 @@
 #'
 #' @inheritParams default_params_doc
 #' @author Pedro Neves
-#' @keywords internal
+#' @noRd
 #' @return A named list with mean and median values of specified parameters
-#' @examples
-#' pars <- c(0.01, 1, 20, 0.01, 1)
-#' area_pars <- create_area_pars(
-#'   max_area = 13500,
-#'   current_area = 3500,
-#'   proportional_peak_t = 0.1,
-#'   total_island_age = 15,
-#'   sea_level_amplitude = 0,
-#'   sea_level_frequency = 0,
-#'   island_gradient_angle = 0
-#' )
-#' hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
-#' island_ontogeny <- 1
-#' sea_level <- 0
-#' extcutoff <- 1100
-#' resol <- 100
-#' total_time <- 10
-#' mainland_n <- 1000
-#'
-#' mean_med <- DAISIE:::DAISIE_calc_sumstats_pcrates(
-#'   pars = pars,
-#'   total_time = total_time,
-#'   area_pars = area_pars,
-#'   hyper_pars = hyper_pars,
-#'   island_ontogeny = island_ontogeny,
-#'   sea_level = sea_level,
-#'   extcutoff = extcutoff,
-#'   mainland_n = mainland_n,
-#'   resol = resol
-#' )
 DAISIE_calc_sumstats_pcrates <- function(
   pars,
   total_time,
diff --git a/R/DAISIE_utils.R b/R/DAISIE_utils.R
index 8c34aa30..35bc8d67 100644
--- a/R/DAISIE_utils.R
+++ b/R/DAISIE_utils.R
@@ -279,8 +279,7 @@ sample_relaxed_rate <- function(pars,
 #' @inheritParams default_params_doc
 #'
 #' @return Numeric, 0 for null-ontogeny, 1 for beta function
-#' @keywords internal
-#' @examples translated_ontogeny <- DAISIE:::translate_island_ontogeny("const")
+#' @noRd
 translate_island_ontogeny <- function(island_ontogeny) {
 
   if (island_ontogeny == "const" || island_ontogeny == 0) {
@@ -297,8 +296,7 @@ translate_island_ontogeny <- function(island_ontogeny) {
 #' @inheritParams default_params_doc
 #'
 #' @return Numeric, 0 for null-sea-level, 1 for sine function
-#' @keywords internal
-#' @examples translated_sea_level <- DAISIE:::translate_sea_level("const")
+#' @noRd
 translate_sea_level <- function(sea_level) {
 
   if (sea_level == "const" || sea_level == 0) {
@@ -321,11 +319,7 @@ translate_sea_level <- function(sea_level) {
 #'
 #' @return A list of non-endemic species, endemic species and the new
 #' mainland species pool
-#' @examples DAISIE:::DAISIE_nonoceanic_spec(
-#' prob_samp = 0.1,
-#' prob_nonend = 0.9,
-#' mainland_n = 1000)
-#' @keywords internal
+#' @noRd
 DAISIE_nonoceanic_spec <- function(prob_samp, prob_nonend, mainland_n) {
   testit::assert(prob_samp <= 1)
   testit::assert(prob_samp >= 0)
@@ -453,3 +447,75 @@ add_column_to_dataframe <- function(df, position, column_to_insert) {
   names(df)[names(df) == 'nc'] <- names(column_to_insert)
   return(df)
 }
+
+
+#' Print optimisation settings
+#'
+#' @inheritParams default_params_doc
+#' @param all_no_shift numeric vector with the standard no shifted values
+#' depending on a model. Internal parameter to DAISIE_ML1, set to NA upstream
+#' if not needed to prevent shift message being generated.
+#'
+#' @return Invisible `NULL`. Prints a `message()` to the console with the parameters
+#'   that are to be optimized, fixed, and shifted if `verbose >= 1`.
+#' @noRd
+print_ml_par_settings <- function(namepars,
+                                  idparsopt,
+                                  idparsfix,
+                                  idparsnoshift,
+                                  all_no_shift,
+                                  verbose) {
+  if (isTRUE(verbose >= 1)) {
+
+    if (length(namepars[idparsopt]) == 0) {
+      optstr <- "nothing"
+    } else {
+      optstr <- namepars[idparsopt]
+    }
+
+    opt_print <- paste0("You are optimizing: ", paste(optstr, collapse = " "))
+    if (length(namepars[idparsfix]) == 0) {
+      fixstr <- "nothing"
+    } else {
+      fixstr <- namepars[idparsfix]
+    }
+    fix_print <- paste0("You are fixing: ", paste(fixstr, collapse = " "))
+
+    if (any(is.numeric(idparsnoshift)) &&
+        sum(idparsnoshift %in% (all_no_shift)) != 5) {
+      noshiftstring <- namepars[idparsnoshift]
+      shift_prt <- paste0(
+        "You are not shifting: ",
+        paste(noshiftstring, collapse = " ")
+      )
+      message(paste(opt_print, fix_print, shift_prt, sep = "\n"))
+    } else {
+      message(paste(opt_print, fix_print, sep = "\n"))
+    }
+
+  }
+
+  invisible(NULL)
+}
+
+#' Print likelihood for initial parameters
+#'
+#' @inheritParams default_params_doc
+#' @param initloglik A numeric with the value of loglikehood obtained prior to
+#'   optimisation. Only used internally.
+#'
+#' @return Invisible `NULL`. Prints a `message()` to the console with the
+#'   initial loglikelihood if `verbose >= 1`
+#' @noRd
+print_init_ll <- function(initloglik,
+                          verbose) {
+  if (isTRUE(verbose >= 1)) {
+    init_ll_msg1 <- "Calculating the likelihood for the initial parameters."
+    init_ll_msg2 <- paste0("The loglikelihood for the initial parameter values is ", initloglik)
+    init_ll_msg3 <- c("Optimizing the likelihood - this may take a while.")
+    message(paste(init_ll_msg1, init_ll_msg2, init_ll_msg3, sep = "\n"))
+
+  }
+
+  invisible(NULL)
+}
diff --git a/R/RcppExports.R b/R/RcppExports.R
index 5d754b1e..6b86ed04 100644
--- a/R/RcppExports.R
+++ b/R/RcppExports.R
@@ -1,16 +1,21 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+#' Driver for the boost::odeint solver for the CS model
+#'
+#' @name daisie_odeint_cs
 #' @export daisie_odeint_cs
+#' @return Object of type `state_type`, which itself is
+#' `vector_t`<double>, with the result of the
+#' integration depending on the runmod chosen.
 NULL
 
-#' Driver for the boost::odeint solver
-#'
-#' @name daisie_odeint_cs
+#' @export daisie_odeint_iw
 NULL
 
-#' Driver for the boost::odeint solver
+#' Driver for the boost::odeint solver for the IW model
 #'
 #' @name daisie_odeint_iw
+#' @export daisie_odeint_iw
 NULL
 
diff --git a/R/create_pars.R b/R/create_pars.R
index 19eac88e..56a022bb 100644
--- a/R/create_pars.R
+++ b/R/create_pars.R
@@ -33,10 +33,8 @@ create_pars <- function(clado_rate,
 #' @export
 #' @author Richel J.C Bilderbeek, Joshua Lambert, Pedro Neves
 #'
-#'
 #' @examples
-#' testit::assert(DAISIE:::are_area_pars(
-#' create_area_pars(
+#' area_pars <- create_area_pars(
 #'   max_area = 10,
 #'   current_area = 1,
 #'   proportional_peak_t = 0.5,
@@ -44,9 +42,9 @@ create_pars <- function(clado_rate,
 #'   sea_level_amplitude = 5,
 #'   sea_level_frequency = 10,
 #'   island_gradient_angle = 0
-#'       )
-#'     )
-#'   )
+#'
+#'
+#' )
 create_area_pars <- function(max_area,
                              current_area,
                              proportional_peak_t,
@@ -105,15 +103,15 @@ create_hyper_pars <- function(d, x) {
 #' @export
 #'
 #' @examples
-#' testit::assert(DAISIE:::are_trait_pars(
-#'   create_trait_pars(
-#'     trans_rate = 0.5,
-#'     immig_rate2 = 0.1,
-#'     ext_rate2 = 0.2,
-#'     ana_rate2 = 0.3,
-#'     clado_rate2 = 0.4,
-#'     trans_rate2 = 0.5,
-#'     M2 = 1000)) == TRUE)
+#' trait_pars <- create_trait_pars(
+#'    trans_rate = 0.5,
+#'    immig_rate2 = 0.1,
+#'    ext_rate2 = 0.2,
+#'    ana_rate2 = 0.3,
+#'    clado_rate2 = 0.4,
+#'    trans_rate2 = 0.5,
+#'    M2 = 1000
+#'  )
 create_trait_pars <- function(trans_rate,
                               immig_rate2,
                               ext_rate2,
diff --git a/R/default_params_doc.R b/R/default_params_doc.R
index e205477a..1cc094b0 100644
--- a/R/default_params_doc.R
+++ b/R/default_params_doc.R
@@ -73,12 +73,15 @@
 #'   of species is present, STT is plotted for all species. If two types are
 #'   present, three plots are produced: STT for all, STT for type 1 and STT for
 #'   type 2.
-#' @param verbose In simulation and dataprep functions a logical,
-#'   \code{Default = TRUE} gives intermediate output should be printed.
+#' @param verbose A numeric vector of length 1, which in simulations and
+#'   `DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+#'   should be printed.
 #'   For ML functions a numeric determining if intermediate output should be
-#'   printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-#'   intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-#'   means also intermediate progress during loglikelihood computation is shown.
+#'   printed. The default: `0` does not print, `1` prints the initial
+#'   likelihood and the settings that were selected (which parameters are
+#'   to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+#'   intermediate output of the parameters and loglikelihood, while `3` the
+#'   same as `2` and prints intermediate progress during likelihood computation.
 #' @param area_pars A named list containing area and sea level parameters as
 #'   created by \code{\link{create_area_pars}()}:
 #'   \itemize{
@@ -101,8 +104,7 @@
 #' @param island_ontogeny In \code{\link{DAISIE_sim_time_dep}()},
 #'   \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 #'   island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-#'   describing area through time. String checked by
-#'   \code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+#'   describing area through time. \cr In all other functions a
 #'   numeric describing the type of island ontogeny. Can be \code{0} for
 #'   constant, \code{1} for a beta function describing area through time. In ML
 #'   functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -110,8 +112,7 @@
 #'   Will return an error if called in that case.
 #' @param sea_level In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 #'   string describing the type of sea level. Can be \code{"const"} or
-#'   \code{"sine"} for a sine function describing area through time. String
-#'   checked by \code{\link{is_sea_level_input}()}.
+#'   \code{"sine"} for a sine function describing area through time.
 #'   \cr In all other functions a numeric describing the type of sea level. Can
 #'   be \code{0} for constant, \code{1} for a sine function describing area
 #'   through time.
diff --git a/inst/COPYRIGHTS b/inst/COPYRIGHTS
new file mode 100644
index 00000000..30e48cc6
--- /dev/null
+++ b/inst/COPYRIGHTS
@@ -0,0 +1,31 @@
+Files: src/DAISIE_CS.cpp src/DAISIE_IW.cpp src/DAISIE_odeint.h src/DAISIE_types.h
+Copyright: 2023 Hanno Hildenbrandt
+License: BSL-1.0
+
+Files: src/DAISIE_loglik_rhs_FORTRAN.95
+Copyright: 2023 Rampal S. Etienne
+License: BSL-1.0
+
+Boost Software License - Version 1.0 - August 17th, 2003
+
+Permission is hereby granted, free of charge, to any person or organization
+obtaining a copy of the software and accompanying documentation covered by
+this license (the "Software") to use, reproduce, display, distribute,
+execute, and transmit the Software, and to prepare derivative works of the
+Software, and to permit third-parties to whom the Software is furnished to
+do so, all subject to the following:
+
+The copyright notices in the Software and this entire statement, including
+the above license grant, this restriction and the following disclaimer,
+must be included in all copies of the Software, in whole or in part, and
+all derivative works of the Software, unless such copies or derivative
+works are solely in the form of machine-executable object code generated by
+a source language processor.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
diff --git a/inst/LICENSE_1_0.txt b/inst/LICENSE_1_0.txt
new file mode 100644
index 00000000..36b7cd93
--- /dev/null
+++ b/inst/LICENSE_1_0.txt
@@ -0,0 +1,23 @@
+Boost Software License - Version 1.0 - August 17th, 2003
+
+Permission is hereby granted, free of charge, to any person or organization
+obtaining a copy of the software and accompanying documentation covered by
+this license (the "Software") to use, reproduce, display, distribute,
+execute, and transmit the Software, and to prepare derivative works of the
+Software, and to permit third-parties to whom the Software is furnished to
+do so, all subject to the following:
+
+The copyright notices in the Software and this entire statement, including
+the above license grant, this restriction and the following disclaimer,
+must be included in all copies of the Software, in whole or in part, and
+all derivative works of the Software, unless such copies or derivative
+works are solely in the form of machine-executable object code generated by
+a source language processor.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
diff --git a/man/DAISIE_ML.Rd b/man/DAISIE_ML.Rd
index 057774ac..098d672d 100644
--- a/man/DAISIE_ML.Rd
+++ b/man/DAISIE_ML.Rd
@@ -122,8 +122,7 @@ on the island. This last option is not yet available for the IW model \cr}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -182,12 +181,15 @@ model, for a relaxed-rate model a list with the following elements:
 \code{"immigration"}, or \code{"anagenesis"}.}
   }}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{tolint}{Vector of two elements containing the absolute and relative
 tolerance of the integration.}
diff --git a/man/DAISIE_ML1.Rd b/man/DAISIE_ML1.Rd
index a908afc6..158de7c1 100644
--- a/man/DAISIE_ML1.Rd
+++ b/man/DAISIE_ML1.Rd
@@ -154,12 +154,15 @@ model, for a relaxed-rate model a list with the following elements:
 \code{"immigration"}, or \code{"anagenesis"}.}
   }}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{tolint}{Vector of two elements containing the absolute and relative
 tolerance of the integration.}
@@ -167,8 +170,7 @@ tolerance of the integration.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
diff --git a/man/DAISIE_ML2.Rd b/man/DAISIE_ML2.Rd
index d7c726c7..1521dfe1 100644
--- a/man/DAISIE_ML2.Rd
+++ b/man/DAISIE_ML2.Rd
@@ -105,8 +105,7 @@ on the island. This last option is not yet available for the IW model \cr}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -136,12 +135,15 @@ and \code{"ode45"} from \code{\link[deSolve]{ode}()} for
 `subplex` (see `\link[subplex]{subplex}()` for full details).
 Alternative is \code{"simplex"} which was the method in previous versions.}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{tolint}{Vector of two elements containing the absolute and relative
 tolerance of the integration.}
diff --git a/man/DAISIE_ML4.Rd b/man/DAISIE_ML4.Rd
index b30ae271..e31fc101 100644
--- a/man/DAISIE_ML4.Rd
+++ b/man/DAISIE_ML4.Rd
@@ -129,12 +129,15 @@ model, for a relaxed-rate model a list with the following elements:
 \code{"immigration"}, or \code{"anagenesis"}.}
   }}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{tolint}{Vector of two elements containing the absolute and relative
 tolerance of the integration.}
@@ -142,8 +145,7 @@ tolerance of the integration.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
diff --git a/man/DAISIE_ML_IW.Rd b/man/DAISIE_ML_IW.Rd
index 50ef9088..51b53994 100644
--- a/man/DAISIE_ML_IW.Rd
+++ b/man/DAISIE_ML_IW.Rd
@@ -115,12 +115,15 @@ and \code{"ode45"} from \code{\link[deSolve]{ode}()} for
 `subplex` (see `\link[subplex]{subplex}()` for full details).
 Alternative is \code{"simplex"} which was the method in previous versions.}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{tolint}{Vector of two elements containing the absolute and relative
 tolerance of the integration.}
diff --git a/man/DAISIE_SR_ML.Rd b/man/DAISIE_SR_ML.Rd
index 288c28c4..f4e0f720 100644
--- a/man/DAISIE_SR_ML.Rd
+++ b/man/DAISIE_SR_ML.Rd
@@ -166,10 +166,13 @@ used, otherwise the information in the data is overruled.
 }
 \examples{
 
-\dontrun{
-### When all species have the same rates, and we want to optimize all 5 parameters,
-# we use:
-
+\donttest{
+## In all following DAISIE_ML calls very high tolerances and low system size
+## are used  for fast computation for this example. Use default or better
+## tol, tolint an res values in actual analyses.
+##################
+### When all species have the same rates, and we want to optimize all 5
+### parameters, we use:
 utils::data(Galapagos_datalist)
 DAISIE_ML(
    datalist = Galapagos_datalist,
@@ -177,7 +180,10 @@ DAISIE_ML(
    ddmodel = 11,
    idparsopt = 1:5,
    parsfix = NULL,
-   idparsfix = NULL
+   idparsfix = NULL,
+   tol = c(0.1, 0.02, 0.01),
+   tolint = c(1e-4, 1e-2),
+   res = 50
 )
 
 ### When all species have the same rates, and we want to optimize all parameters
@@ -189,7 +195,10 @@ DAISIE_ML(
    initparsopt = c(2.5,2.7,0.009,1.01),
    idparsopt = c(1,2,4,5),
    parsfix = Inf,
-   idparsfix = 3
+   idparsfix = 3,
+   tol = c(0.1, 0.02, 0.01),
+   tolint = c(1e-4, 1e-2),
+   res = 50
    )
 
 ### When all species have the same rates except that the finches have a different
@@ -203,7 +212,10 @@ DAISIE_ML(
    idparsopt = c(1,2,4,5,6),
    parsfix = c(Inf,Inf,0.163),
    idparsfix = c(3,8,11),
-   idparsnoshift = c(7,9,10)
+   idparsnoshift = c(7,9,10),
+   tol = c(0.1, 0.02, 0.01),
+   tolint = c(1e-4, 1e-2),
+   res = 50
    )
 
 ### When all species have the same rates except that the finches have a different
@@ -218,7 +230,10 @@ DAISIE_ML(
    idparsopt = c(1,2,4,5,6,7,8),
    parsfix = c(Inf,0.163),
    idparsfix = c(3,11),
-   idparsnoshift = c(9,10)
+   idparsnoshift = c(9,10),
+   tol = c(0.1, 0.02, 0.01),
+   tolint = c(1e-4, 1e-2),
+   res = 50
    )
 
 
@@ -234,7 +249,10 @@ DAISIE_ML(
    idparsopt = c(1,2,4,5,7,11),
    parsfix = c(Inf,Inf),
    idparsfix = c(3,8),
-   idparsnoshift = c(6,9,10)
+   idparsnoshift = c(6,9,10),
+   tol = c(0.1, 0.02, 0.01),
+   tolint = c(1e-4, 1e-2),
+   res = 50
    )
 
 ### When we have two islands with the same rates except for immigration and anagenesis rate,
@@ -248,7 +266,10 @@ DAISIE_ML(
    idparsmat = rbind(1:5,c(1:3,6,7)),
    idparsopt = 1:7,
    parsfix = NULL,
-   idparsfix = NULL
+   idparsfix = NULL,
+   tol = c(0.1, 0.02, 0.01),
+   tolint = c(1e-4, 1e-2),
+   res = 50
 )
 
 ### When we consider the four Macaronesia archipelagoes and set all parameters the same
@@ -265,7 +286,10 @@ DAISIE_ML(
    idparsmat = rbind(1:5,c(6,2,3,7,5),1:5,1:5),
    idparsopt = c(2,4,5,6,7),
    parsfix = c(0,Inf),
-   idparsfix = c(1,3)
+   idparsfix = c(1,3),
+   tol = c(0.1, 0.02, 0.01),
+   tolint = c(1e-4, 1e-2),
+   res = 50
 )
 
 }
diff --git a/man/DAISIE_SR_loglik_CS.Rd b/man/DAISIE_SR_loglik_CS.Rd
index 31eb60fb..63064fba 100644
--- a/man/DAISIE_SR_loglik_CS.Rd
+++ b/man/DAISIE_SR_loglik_CS.Rd
@@ -14,8 +14,7 @@ DAISIE_SR_loglik_CS(
   methode = "lsodes",
   CS_version = 1,
   abstolint = 1e-16,
-  reltolint = 1e-10,
-  verbose = FALSE
+  reltolint = 1e-10
 )
 }
 \arguments{
@@ -104,8 +103,6 @@ model, for a relaxed-rate model a list with the following elements:
 \item{abstolint}{Absolute tolerance of the integration}
 
 \item{reltolint}{Relative tolerance of the integration}
-
-\item{verbose}{Logical controling if progress is printed to console.}
 }
 \value{
 The loglikelihood
diff --git a/man/DAISIE_SR_sim.Rd b/man/DAISIE_SR_sim.Rd
deleted file mode 100644
index e275045f..00000000
--- a/man/DAISIE_SR_sim.Rd
+++ /dev/null
@@ -1,129 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_SR_sim.R
-\name{DAISIE_SR_sim}
-\alias{DAISIE_SR_sim}
-\title{DEPRECATED - Simulate islands with given parameters.}
-\usage{
-DAISIE_SR_sim(
-  time,
-  M,
-  pars,
-  replicates,
-  sample_freq = 25,
-  plot_sims = TRUE,
-  ddep = 11,
-  verbose = FALSE,
-  ...
-)
-}
-\arguments{
-\item{time}{Length of the simulation in time units. For example, if an
-island is know to be 4 million years old, setting time = 4 will simulate
-entire life span of the island; setting time = 2 will stop the simulation at
-the mid-life of the island.}
-
-\item{M}{The size of the mainland pool, i.e the number of species that can
-potentially colonize the island}
-
-\item{pars}{Contains the model parameters: \cr \cr \code{pars[1]}
-corresponds to lambda^c (cladogenesis rate) before the shift \cr \code{pars[2]} corresponds
-to mu (extinction rate) before the shift \cr \code{pars[3]} corresponds to K (clade-level
-carrying capacity) before the shift. Set K=Inf for non-diversity dependence.\cr
-\code{pars[4]} corresponds to gamma (immigration rate) before the shift \cr \code{pars[5]}
-corresponds to lambda^a (anagenesis rate) before the shift \cr \code{pars[6]} corresponds to
-lambda^c (cladogenesis rate) after the shift \cr \code{pars[7]}
-corresponds to mu (extinction rate) after the shift \cr \code{pars[8]}
-corresponds to K (clade-level carrying capacity) after the shift.  Set
-K=Inf for non-diversity dependence. \cr \code{pars[9]} corresponds to gamma
-(immigration rate)  after the shift \cr \code{pars[10]} corresponds to
-lambda^a (anagenesis rate) after the shift \cr \code{pars[11]} corresponds to
-the time of shift. This is defined as time before the end of the simulation. For example,
-setting time = 4 and pars[11] = 1.5 will simulate with pars[1:5] from 4 to 1.5 and
-with pars[6:10] from 1.5 to 0.}
-
-\item{replicates}{Number of island replicates to be simulated.}
-
-\item{sample_freq}{Specifies the number of units time should be divided by
-for plotting purposes. Larger values will lead to plots with higher
-resolution, but will also run slower.}
-
-\item{plot_sims}{Default=TRUE plots species-through-time (STT) plots. It
-detects how many types of species are present. If only one type of species
-is present, STT is plotted for all species. If two types are present, three
-plots are produced: STT for all, STT for type 1 and STT for type 2.}
-
-\item{ddep}{= diversity-dependent model,mode of diversity-dependence \cr \cr
-\code{ddep == 0} no diversity-dependence
-\code{ddep == 1} linear dependence in speciation rate (anagenesis and cladogenesis)
-\code{ddep == 11} linear dependence in speciation rate and immigration rate
-\code{ddep == 3} linear dependence in extinction rate}
-
-\item{verbose}{\code{Default=TRUE} Give intermediate output, also if
-everything goes OK.}
-
-\item{...}{Any arguments to pass on to plotting functions.}
-}
-\value{
-Each simulated dataset is an element of the list, which can be
-called using [[x]]. For example if the object is called island_replicates,
-the 1st replicate can be called using island_replicates[[1]] Each of the
-island replicates is a list in itself. The first (e.g.
-island_replicates[[x]][[1]]) element of that list has the following
-components: \cr \code{$island_age} - the island age \cr Then, we have:\cr \code{$not_present}
-- the number of mainland lineages that are not present on the island \cr
-\code{$stt_all} - STT table for all species on the island (nI - number of
-non-endemic species; nA - number of anagenetic species, nC - number of
-cladogenetic species, present - number of independent colonisations present)\cr
-The subsequent elements of the list each contain information on a single
-colonist lineage on the island and has 4 components:\cr
-\code{$branching_times} - island age and stem age of the population/species
-in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic
-species. For cladogenetic species these should be island age and branching
-times of the radiation including the stem age of the radiation.\cr
-\code{$stac} - the status of the colonist \cr * Non_endemic_MaxAge: 1 \cr *
-Endemic: 2 \cr * Endemic&Non_Endemic: 3 \cr * Non_endemic: 4 \cr
-\code{$missing_species} - number of island species that were not sampled for
-particular clade (only applicable for endemic clades) \cr \code{$type_1or2}
-- whether the colonist belongs to type 1 or type 2 \cr
-}
-\description{
-This function simulates islands with given cladogenesis, extinction, Kprime,
-immigration and anagenesis parameters that shift at some time.
-Runs the function with clade-specific
-carrying capacity, where diversity-dependence operates only within single
-clades, i.e. only among species originating from the same mainland
-colonist.
-
-Returns R list object that contains the simulated islands.
-}
-\details{
-This function's use has been deprecated in favor
-of \code{\link{DAISIE_sim_cr_shift}()}. Please use that
-function instead.
-}
-\examples{
-# Simulate 15 islands for 4 million years with a shift in immigration rate
-# at 0.195 Ma, and plot the species-through-time plot. Pool size 296.
-
-pars_before_shift = c(0.079, 0.973, Inf, 0.136, 0.413)
-pars_after_shift = c(0.079, 0.973, Inf, 0.652, 0.413)
-tshift = 0.195
-island_shift_replicates = DAISIE:::DAISIE_SR_sim(
-   time = 4,
-   M = 296,
-   pars = c(pars_before_shift, pars_after_shift, tshift),
-   replicates = 15
- )
-}
-\references{
-Hauffe, T., D. Delicado, R.S. Etienne and L. Valente (2020).
-Lake expansion increases equilibrium diversity via the target effect of
-island biogeography
-}
-\seealso{
-\code{\link{DAISIE_plot_sims}()}
-}
-\author{
-Luis Valente, Albert Phillimore, and Torsten Hauffe
-}
-\keyword{internal}
diff --git a/man/DAISIE_calc_sumstats_pcrates.Rd b/man/DAISIE_calc_sumstats_pcrates.Rd
deleted file mode 100644
index 4f8d70d5..00000000
--- a/man/DAISIE_calc_sumstats_pcrates.Rd
+++ /dev/null
@@ -1,141 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_sumstats_rates.R
-\name{DAISIE_calc_sumstats_pcrates}
-\alias{DAISIE_calc_sumstats_pcrates}
-\title{Calculate summary statistics of per capita rates}
-\usage{
-DAISIE_calc_sumstats_pcrates(
-  pars,
-  total_time,
-  area_pars,
-  hyper_pars,
-  island_ontogeny = 1,
-  sea_level = 0,
-  extcutoff = 100,
-  mainland_n = 1000,
-  resol = 100
-)
-}
-\arguments{
-\item{pars}{A numeric vector containing the model parameters:
-\itemize{
-  \item{\code{pars[1]}: lambda^c (cladogenesis rate)}
-  \item{\code{pars[2]}: mu (extinction rate)}
-  \item{\code{pars[3]}: K (carrying capacity), set K=Inf for diversity
-  independence.}
-  \item{\code{pars[4]}: gamma (immigration rate)}
-  \item{\code{pars[5]}: lambda^a (anagenesis rate)}
-  \item{\code{pars[6]}: lambda^c (cladogenesis rate) for either type 2 species
-  or rate set 2 in rate shift model}
-  \item{\code{pars[7]}: mu (extinction rate) for either type 2 species or rate
-  set 2 in rate shift model}
-  \item{\code{pars[8]}: K (carrying capacity) for either type 2 species or rate
-  set 2 in rate shift model, set K=Inf for diversity independence.}
-  \item{\code{pars[9]}: gamma (immigration rate) for either type 2 species
-  or rate set 2 in rate shift model}
-  \item{\code{pars[10]}: lambda^a (anagenesis rate) for either type 2
-  species or rate set 2 in rate shift model}
-}
-Elements 6:10 are required only when type 2 species are included
-or in the rate shift model. For \code{\link{DAISIE_sim_relaxed_rate}()}
-\code{pars[6]} is the standard deviation of the gamma distribution for the
-relaxed parameter and the parameter chosen by the \code{relaxed_par}
-argument is the mean of the gamma distribution for the relaxed parameter.}
-
-\item{total_time}{Numeric defining the length of the simulation in time
-units.}
-
-\item{area_pars}{A named list containing area and sea level parameters as
-created by \code{\link{create_area_pars}()}:
-\itemize{
-  \item{[1]: maximum area}
-  \item{[2]: current area}
-  \item{[3]: value from 0 to 1 indicating where in the island's history the
-  peak area is achieved}
-  \item{[4]: total island age}
-  \item{[5]: amplitude of area fluctuation from sea level}
-  \item{[6]: frequency of sine wave of area change from sea level}
-  \item{[7]: angle of the slope of the island}
-}}
-
-\item{hyper_pars}{A named list of numeric hyperparameters for the rate
-calculations as returned by \code{\link{create_hyper_pars}()}:
-\itemize{
-  \item{[1]: is d the scaling parameter for exponent for calculating
-  cladogenesis rate}
-  \item{[2]: is x the exponent for calculating extinction rate}
-}}
-
-\item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
-\code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
-island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
-numeric describing the type of island ontogeny. Can be \code{0} for
-constant, \code{1} for a beta function describing area through time. In ML
-functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
-dependent estimation is not yet available as development is still ongoing.
-Will return an error if called in that case.}
-
-\item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
-string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
-\cr In all other functions a numeric describing the type of sea level. Can
-be \code{0} for constant, \code{1} for a sine function describing area
-through time.}
-
-\item{extcutoff}{A numeric with the cutoff for the the maximum extinction
-rate preventing it from being too large and slowing down simulation.}
-
-\item{mainland_n}{A numeric stating the number of mainland species, that
-is the number of species that can potentially colonize the island.
-If using a clade-specific diversity dependence, this value is set to 1.
-If using an island-wide diversity dependence, this value is set to the
-number of mainland species.}
-
-\item{resol}{numeric for resolution of summary stats calculation. Should be
-> 1.}
-}
-\value{
-A named list with mean and median values of specified parameters
-}
-\description{
-Calculates the summary statistics of per capita rates throught an ontogeny
-simulation
-}
-\examples{
-pars <- c(0.01, 1, 20, 0.01, 1)
-area_pars <- create_area_pars(
-  max_area = 13500,
-  current_area = 3500,
-  proportional_peak_t = 0.1,
-  total_island_age = 15,
-  sea_level_amplitude = 0,
-  sea_level_frequency = 0,
-  island_gradient_angle = 0
-)
-hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
-island_ontogeny <- 1
-sea_level <- 0
-extcutoff <- 1100
-resol <- 100
-total_time <- 10
-mainland_n <- 1000
-
-mean_med <- DAISIE:::DAISIE_calc_sumstats_pcrates(
-  pars = pars,
-  total_time = total_time,
-  area_pars = area_pars,
-  hyper_pars = hyper_pars,
-  island_ontogeny = island_ontogeny,
-  sea_level = sea_level,
-  extcutoff = extcutoff,
-  mainland_n = mainland_n,
-  resol = resol
-)
-}
-\author{
-Pedro Neves
-}
-\keyword{internal}
diff --git a/man/DAISIE_convert_to_classic_plot.Rd b/man/DAISIE_convert_to_classic_plot.Rd
deleted file mode 100644
index 01a2872d..00000000
--- a/man/DAISIE_convert_to_classic_plot.Rd
+++ /dev/null
@@ -1,44 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_plot_stt.R
-\name{DAISIE_convert_to_classic_plot}
-\alias{DAISIE_convert_to_classic_plot}
-\title{Prepare input for DAISIE_stt}
-\usage{
-DAISIE_convert_to_classic_plot(simulation_outputs, trait_pars = NULL)
-}
-\arguments{
-\item{simulation_outputs}{A list with matrices and vectors of simulation
-produced by DAISIE_sim functions.}
-
-\item{trait_pars}{A named list containing diversification rates considering
-  two trait states created by \code{\link{create_trait_pars}}:
-\itemize{
-  \item{[1]:A numeric with the per capita transition rate with state1}
-  \item{[2]:A numeric with the per capita immigration rate with state2}
-  \item{[3]:A numeric with the per capita extinction rate with state2}
-  \item{[4]:A numeric with the per capita anagenesis rate with state2}
-  \item{[5]:A numeric with the per capita cladogenesis rate with state2}
-  \item{[6]:A numeric with the per capita transition rate with state2}
-  \item{[7]:A numeric with the number of species with trait state 2 on
-   mainland}
-}}
-}
-\value{
-a list with wrangled data to be used for plotting STT plots with
-DAISIE_plot_stt
-}
-\description{
-Prepare input for DAISIE_stt
-}
-\examples{
-utils::data("islands_1type_1000reps", package = "DAISIE")
-simulation_outuputs <- DAISIE:::DAISIE_convert_to_classic_plot(
-islands_1type_1000reps
-)
-
-
-}
-\seealso{
-\code{\link{DAISIE_plot_stt}}, \code{\link{DAISIE_plot_sims}}
-}
-\keyword{internal}
diff --git a/man/DAISIE_format_CS.Rd b/man/DAISIE_format_CS.Rd
index 84773fb1..e5101da8 100644
--- a/man/DAISIE_format_CS.Rd
+++ b/man/DAISIE_format_CS.Rd
@@ -37,12 +37,15 @@ species that can potentially colonize the island.}
 divided by for plotting purposes. Larger values will lead to plots with
 higher resolution, but will also run slower.}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{trait_pars}{A named list containing diversification rates considering
   two trait states created by \code{\link{create_trait_pars}}:
diff --git a/man/DAISIE_format_CS_full_stt.Rd b/man/DAISIE_format_CS_full_stt.Rd
index 811b3e56..28b99beb 100644
--- a/man/DAISIE_format_CS_full_stt.Rd
+++ b/man/DAISIE_format_CS_full_stt.Rd
@@ -32,12 +32,15 @@ will stop the simulation at the mid-life of the island.}
 \item{M}{Numeric defining the size of mainland pool, i.e. the number of
 species that can potentially colonize the island.}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{trait_pars}{A named list containing diversification rates considering
   two trait states created by \code{\link{create_trait_pars}}:
diff --git a/man/DAISIE_format_CS_sampled_stt.Rd b/man/DAISIE_format_CS_sampled_stt.Rd
index 2d6e2f28..844c2b9a 100644
--- a/man/DAISIE_format_CS_sampled_stt.Rd
+++ b/man/DAISIE_format_CS_sampled_stt.Rd
@@ -37,12 +37,15 @@ species that can potentially colonize the island.}
 divided by for plotting purposes. Larger values will lead to plots with
 higher resolution, but will also run slower.}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{trait_pars}{A named list containing diversification rates considering
   two trait states created by \code{\link{create_trait_pars}}:
diff --git a/man/DAISIE_format_GW.Rd b/man/DAISIE_format_GW.Rd
index 8c4b8e38..6da3ee03 100644
--- a/man/DAISIE_format_GW.Rd
+++ b/man/DAISIE_format_GW.Rd
@@ -41,12 +41,15 @@ higher resolution, but will also run slower.}
 mainland species is divided by the number of guilds when
 \code{divdepmodel = "GW"}}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 }
 \value{
 List with GW DAISIE simulation output
diff --git a/man/DAISIE_format_IW.Rd b/man/DAISIE_format_IW.Rd
deleted file mode 100644
index 75b1972b..00000000
--- a/man/DAISIE_format_IW.Rd
+++ /dev/null
@@ -1,99 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_format_IW.R
-\name{DAISIE_format_IW}
-\alias{DAISIE_format_IW}
-\title{Formats island-wide simulation output into
-standard DAISIE list output}
-\usage{
-DAISIE_format_IW(
-  island_replicates,
-  time,
-  M,
-  sample_freq = 25,
-  verbose = TRUE,
-  trait_pars = NULL
-)
-}
-\arguments{
-\item{island_replicates}{List output from
-\code{\link{DAISIE_sim_core_cr}()},
-\code{\link{DAISIE_sim_core_time_dep}()},
-\code{\link{DAISIE_sim_core_cr_shift}()} or
-\code{\link{DAISIE_sim_min_type2}()} functions. Minimally, this must be a
-list that has as many elements as replicates. Each element must be a list
-with the elements \code{island_age}, \code{not_present} and \code{stt_all}.
-\code{stt_all} must be a data frame with the column names \code{Time},
-\code{nI}, \code{nA}, \code{nC} and \code{present}.}
-
-\item{time}{Numeric defining the length of the simulation in time units.
-For example, if an island is known to be 4 million years old, setting
-time = 4 will simulate the entire life span of the island; setting time = 2
-will stop the simulation at the mid-life of the island.}
-
-\item{M}{Numeric defining the size of mainland pool, i.e. the number of
-species that can potentially colonize the island.}
-
-\item{sample_freq}{Numeric specifing the number of units times should be
-divided by for plotting purposes. Larger values will lead to plots with
-higher resolution, but will also run slower.}
-
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
-For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
-
-\item{trait_pars}{A named list containing diversification rates considering
-  two trait states created by \code{\link{create_trait_pars}}:
-\itemize{
-  \item{[1]:A numeric with the per capita transition rate with state1}
-  \item{[2]:A numeric with the per capita immigration rate with state2}
-  \item{[3]:A numeric with the per capita extinction rate with state2}
-  \item{[4]:A numeric with the per capita anagenesis rate with state2}
-  \item{[5]:A numeric with the per capita cladogenesis rate with state2}
-  \item{[6]:A numeric with the per capita transition rate with state2}
-  \item{[7]:A numeric with the number of species with trait state 2 on
-   mainland}
-}}
-}
-\value{
-List with CS DAISIE simulation output
-}
-\description{
-Formats island-wide simulation output into
-standard DAISIE list output
-}
-\examples{
-island_replicates <- list()
-island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_cr(
-  time = 5,
-  mainland_n = 1000,
-  pars = c(2, 2, 40, 0.1, 1),
-  area_pars = DAISIE::create_area_pars(
-    max_area = 1,
-    current_area = 1,
-    proportional_peak_t = 0,
-    total_island_age = 0,
-    sea_level_amplitude = 0,
-    sea_level_frequency = 0,
-    island_gradient_angle = 0),
-  hyper_pars = create_hyper_pars(d = 0.2, x = 0.1),
-  nonoceanic_pars = c(0, 0)
-)
-formatted_island_sampled <- DAISIE:::DAISIE_format_IW(
-  island_replicates = island_replicates,
-  time = 5,
-  M = 1000,
-  sample_freq = 25,
-  verbose = FALSE
-)
-formatted_island_full <- DAISIE:::DAISIE_format_IW(
-  island_replicates = island_replicates,
-  time = 5,
-  M = 1000,
-  sample_freq = Inf,
-  verbose = FALSE
-)
-}
-\keyword{internal}
diff --git a/man/DAISIE_format_IW_full_stt.Rd b/man/DAISIE_format_IW_full_stt.Rd
index 88f07bb4..280ef37f 100644
--- a/man/DAISIE_format_IW_full_stt.Rd
+++ b/man/DAISIE_format_IW_full_stt.Rd
@@ -24,12 +24,15 @@ units.}
 \item{M}{Numeric defining the size of mainland pool, i.e. the number of
 species that can potentially colonize the island.}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 }
 \value{
 List with IW DAISIE simulation output
diff --git a/man/DAISIE_format_IW_sampled_stt.Rd b/man/DAISIE_format_IW_sampled_stt.Rd
index 91e0cfe9..602cbbad 100644
--- a/man/DAISIE_format_IW_sampled_stt.Rd
+++ b/man/DAISIE_format_IW_sampled_stt.Rd
@@ -34,12 +34,15 @@ species that can potentially colonize the island.}
 divided by for plotting purposes. Larger values will lead to plots with
 higher resolution, but will also run slower.}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 }
 \value{
 List with IW DAISIE simulation output
diff --git a/man/DAISIE_loglik_integrand.Rd b/man/DAISIE_loglik_integrand.Rd
index aec1eaee..f85af8e1 100644
--- a/man/DAISIE_loglik_integrand.Rd
+++ b/man/DAISIE_loglik_integrand.Rd
@@ -61,12 +61,15 @@ and \code{"ode45"} from \code{\link[deSolve]{ode}()} for
 
 \item{reltolint}{Numeric relative tolerance of the integration}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{pick}{Numeric determining which parameter is selected for the
 relaxed-rate model}
diff --git a/man/DAISIE_loglik_integrate.Rd b/man/DAISIE_loglik_integrate.Rd
index 80ba5b8f..e5b7a6c8 100644
--- a/man/DAISIE_loglik_integrate.Rd
+++ b/man/DAISIE_loglik_integrate.Rd
@@ -66,12 +66,15 @@ and \code{"ode45"} from \code{\link[deSolve]{ode}()} for
 
 \item{reltolint}{Numeric relative tolerance of the integration}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 }
 \value{
 A loglikelihood value
diff --git a/man/DAISIE_nonoceanic_spec.Rd b/man/DAISIE_nonoceanic_spec.Rd
deleted file mode 100644
index 57d9a1d4..00000000
--- a/man/DAISIE_nonoceanic_spec.Rd
+++ /dev/null
@@ -1,32 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_utils.R
-\name{DAISIE_nonoceanic_spec}
-\alias{DAISIE_nonoceanic_spec}
-\title{Calculates the species on the island initially when \code{nonoceanic_pars[1]
-!= 0}}
-\usage{
-DAISIE_nonoceanic_spec(prob_samp, prob_nonend, mainland_n)
-}
-\arguments{
-\item{prob_samp}{probability of a species being sampled
-from the mainland pool}
-
-\item{prob_nonend}{probability of a species sampled being non-endemic}
-
-\item{mainland_n}{number of species in the mainland pool}
-}
-\value{
-A list of non-endemic species, endemic species and the new
-mainland species pool
-}
-\description{
-Calculates the species on the island initially when \code{nonoceanic_pars[1]
-!= 0}
-}
-\examples{
-DAISIE:::DAISIE_nonoceanic_spec(
-prob_samp = 0.1,
-prob_nonend = 0.9,
-mainland_n = 1000)
-}
-\keyword{internal}
diff --git a/man/DAISIE_plot_area.Rd b/man/DAISIE_plot_area.Rd
index f0330d36..94b48ce8 100644
--- a/man/DAISIE_plot_area.Rd
+++ b/man/DAISIE_plot_area.Rd
@@ -38,8 +38,7 @@ present and the \code{area_pars}.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -50,8 +49,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
diff --git a/man/DAISIE_plot_cladogenesis.Rd b/man/DAISIE_plot_cladogenesis.Rd
index 79f95847..3a8481f2 100644
--- a/man/DAISIE_plot_cladogenesis.Rd
+++ b/man/DAISIE_plot_cladogenesis.Rd
@@ -46,8 +46,7 @@ present and the \code{area_pars}.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -56,8 +55,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
diff --git a/man/DAISIE_plot_comparison_stts.Rd b/man/DAISIE_plot_comparison_stts.Rd
deleted file mode 100644
index 3d108871..00000000
--- a/man/DAISIE_plot_comparison_stts.Rd
+++ /dev/null
@@ -1,51 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_plot_comparison_stts.R
-\name{DAISIE_plot_comparison_stts}
-\alias{DAISIE_plot_comparison_stts}
-\title{Plot STT and overlay additional STT curves.}
-\usage{
-DAISIE_plot_comparison_stts(
-  time,
-  plot_lists_simulations,
-  plot_lists_simulations_MLE,
-  type,
-  kind_of_plot = "line"
-)
-}
-\arguments{
-\item{time}{Numeric defining the length of the simulation in time units.
-For example, if an island is known to be 4 million years old, setting
-time = 4 will simulate the entire life span of the island; setting time = 2
-will stop the simulation at the mid-life of the island.}
-
-\item{plot_lists_simulations}{List with simulation output after parsing by
-\code{DAISIE_prepare_data_plotting}.}
-
-\item{plot_lists_simulations_MLE}{List with simulation output after parsing
-by \code{DAISIE_prepare_data_plotting}, but obtained by simulating MLE
-output.}
-
-\item{type}{String to indicate if stt of all species or all possible stt
-should be plotted. Default is \code{"all_species"}, \code{"type1_species"}
-or \code{"type2_species"} should be plotted.}
-
-\item{kind_of_plot}{Character vector stating how STT plot resulting from MLE
-based simulations should be plotted. Default is \code{"line"} for multiple
-individual lines. Can also be \code{"shade"} for the 5\% quantile.}
-}
-\value{
-Standard \code{\link{DAISIE_plot_stt}} with overlaid additional
-  STT curves for comparison.
-}
-\description{
-Plot STT and overlay additional STT curves.
-}
-\seealso{
-\code{\link{DAISIE_plot_sims}}, \code{\link{DAISIE_plot_stt}},
-  \code{\link{DAISIE_convert_to_classic_plot}}
-}
-\author{
-Pedro Neves
-}
-\concept{plotting}
-\keyword{internal}
diff --git a/man/DAISIE_plot_extinction.Rd b/man/DAISIE_plot_extinction.Rd
index 9562e0dd..837f1d30 100644
--- a/man/DAISIE_plot_extinction.Rd
+++ b/man/DAISIE_plot_extinction.Rd
@@ -52,8 +52,7 @@ calculations as returned by \code{\link{create_hyper_pars}()}:
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -62,8 +61,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
diff --git a/man/DAISIE_plot_immigration.Rd b/man/DAISIE_plot_immigration.Rd
index f74e4a57..dc1a5b79 100644
--- a/man/DAISIE_plot_immigration.Rd
+++ b/man/DAISIE_plot_immigration.Rd
@@ -61,8 +61,7 @@ calculations as returned by \code{\link{create_hyper_pars}()}:
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -71,8 +70,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
diff --git a/man/DAISIE_plot_pc_rates.Rd b/man/DAISIE_plot_pc_rates.Rd
index d7758da5..d793f82c 100644
--- a/man/DAISIE_plot_pc_rates.Rd
+++ b/man/DAISIE_plot_pc_rates.Rd
@@ -49,8 +49,7 @@ argument is the mean of the gamma distribution for the relaxed parameter.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -59,8 +58,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
diff --git a/man/DAISIE_sim.Rd b/man/DAISIE_sim.Rd
index f46a0e23..f058e824 100644
--- a/man/DAISIE_sim.Rd
+++ b/man/DAISIE_sim.Rd
@@ -138,12 +138,15 @@ conditioning on island age and non-extinction of the island biota \cr.
 cond > 1 : conditioning on island age and having at least cond colonizations
 on the island. This last option is not yet available for the IW model \cr}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{...}{Any arguments to pass on to plotting functions.}
 }
diff --git a/man/DAISIE_sim_core_time_dep.Rd b/man/DAISIE_sim_core_time_dep.Rd
index f2ba6171..40f1f75a 100644
--- a/man/DAISIE_sim_core_time_dep.Rd
+++ b/man/DAISIE_sim_core_time_dep.Rd
@@ -66,8 +66,7 @@ argument is the mean of the gamma distribution for the relaxed parameter.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -76,8 +75,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
diff --git a/man/DAISIE_sim_core_trait_dep.Rd b/man/DAISIE_sim_core_trait_dep.Rd
index 36faea6f..5c665b20 100644
--- a/man/DAISIE_sim_core_trait_dep.Rd
+++ b/man/DAISIE_sim_core_trait_dep.Rd
@@ -56,8 +56,7 @@ argument is the mean of the gamma distribution for the relaxed parameter.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -66,8 +65,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
diff --git a/man/DAISIE_sim_cr_cs.Rd b/man/DAISIE_sim_cr_cs.Rd
index c65e1af2..4befd59b 100644
--- a/man/DAISIE_sim_cr_cs.Rd
+++ b/man/DAISIE_sim_cr_cs.Rd
@@ -111,12 +111,15 @@ conditioning on island age and non-extinction of the island biota \cr.
 cond > 1 : conditioning on island age and having at least cond colonizations
 on the island. This last option is not yet available for the IW model \cr}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 }
 \value{
 A list. The highest level of the least corresponds to each individual
diff --git a/man/DAISIE_sim_cr_gw.Rd b/man/DAISIE_sim_cr_gw.Rd
index 93c267f6..f23853c9 100644
--- a/man/DAISIE_sim_cr_gw.Rd
+++ b/man/DAISIE_sim_cr_gw.Rd
@@ -89,12 +89,15 @@ created by \code{\link{create_area_pars}()}:
   \item{[7]: angle of the slope of the island}
 }}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 }
 \value{
 A list. The highest level of the least corresponds to each individual
diff --git a/man/DAISIE_sim_cr_iw.Rd b/man/DAISIE_sim_cr_iw.Rd
index 09a8e647..456184c9 100644
--- a/man/DAISIE_sim_cr_iw.Rd
+++ b/man/DAISIE_sim_cr_iw.Rd
@@ -90,12 +90,15 @@ conditioning on island age and non-extinction of the island biota \cr.
 cond > 1 : conditioning on island age and having at least cond colonizations
 on the island. This last option is not yet available for the IW model \cr}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 }
 \value{
 A list. The highest level of the least corresponds to each individual
diff --git a/man/DAISIE_sim_cr_shift.Rd b/man/DAISIE_sim_cr_shift.Rd
index 2b4a9893..8a45c848 100644
--- a/man/DAISIE_sim_cr_shift.Rd
+++ b/man/DAISIE_sim_cr_shift.Rd
@@ -120,12 +120,15 @@ conditioning on island age and non-extinction of the island biota \cr.
 cond > 1 : conditioning on island age and having at least cond colonizations
 on the island. This last option is not yet available for the IW model \cr}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{...}{Any arguments to pass on to plotting functions.}
 }
diff --git a/man/DAISIE_sim_min_type2.Rd b/man/DAISIE_sim_min_type2.Rd
index c5be7d4f..12e98058 100644
--- a/man/DAISIE_sim_min_type2.Rd
+++ b/man/DAISIE_sim_min_type2.Rd
@@ -81,12 +81,15 @@ calculations as returned by \code{\link{create_hyper_pars}()}:
   \item{[2]: is x the exponent for calculating extinction rate}
 }}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 }
 \description{
 Internal function of the DAISIE simulation
diff --git a/man/DAISIE_sim_relaxed_rate.Rd b/man/DAISIE_sim_relaxed_rate.Rd
index fc62a68b..685f9175 100644
--- a/man/DAISIE_sim_relaxed_rate.Rd
+++ b/man/DAISIE_sim_relaxed_rate.Rd
@@ -106,12 +106,15 @@ conditioning on island age and non-extinction of the island biota \cr.
 cond > 1 : conditioning on island age and having at least cond colonizations
 on the island. This last option is not yet available for the IW model \cr}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{...}{Any arguments to pass on to plotting functions.}
 }
diff --git a/man/DAISIE_sim_time_dep.Rd b/man/DAISIE_sim_time_dep.Rd
index 00f29ee9..20e2c258 100644
--- a/man/DAISIE_sim_time_dep.Rd
+++ b/man/DAISIE_sim_time_dep.Rd
@@ -115,8 +115,7 @@ type 2.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -125,8 +124,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
@@ -139,12 +137,15 @@ conditioning on island age and non-extinction of the island biota \cr.
 cond > 1 : conditioning on island age and having at least cond colonizations
 on the island. This last option is not yet available for the IW model \cr}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{...}{Any arguments to pass on to plotting functions.}
 }
diff --git a/man/DAISIE_sim_time_dep_cs.Rd b/man/DAISIE_sim_time_dep_cs.Rd
index 66b8180c..101556c9 100644
--- a/man/DAISIE_sim_time_dep_cs.Rd
+++ b/man/DAISIE_sim_time_dep_cs.Rd
@@ -94,8 +94,7 @@ higher resolution, but will also run slower.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -104,8 +103,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
@@ -127,12 +125,15 @@ conditioning on island age and non-extinction of the island biota \cr.
 cond > 1 : conditioning on island age and having at least cond colonizations
 on the island. This last option is not yet available for the IW model \cr}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 }
 \value{
 A list. The highest level of the least corresponds to each individual
diff --git a/man/DAISIE_sim_time_dep_gw.Rd b/man/DAISIE_sim_time_dep_gw.Rd
index 9afbf070..56f83128 100644
--- a/man/DAISIE_sim_time_dep_gw.Rd
+++ b/man/DAISIE_sim_time_dep_gw.Rd
@@ -98,8 +98,7 @@ higher resolution, but will also run slower.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -108,8 +107,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
@@ -126,12 +124,15 @@ present and the \code{area_pars}.}
 \item{extcutoff}{A numeric with the cutoff for the the maximum extinction
 rate preventing it from being too large and slowing down simulation.}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 }
 \value{
 A list. The highest level of the least corresponds to each individual
diff --git a/man/DAISIE_sim_time_dep_iw.Rd b/man/DAISIE_sim_time_dep_iw.Rd
index 602576e8..a5ee8e7a 100644
--- a/man/DAISIE_sim_time_dep_iw.Rd
+++ b/man/DAISIE_sim_time_dep_iw.Rd
@@ -94,8 +94,7 @@ higher resolution, but will also run slower.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -104,8 +103,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
@@ -127,12 +125,15 @@ conditioning on island age and non-extinction of the island biota \cr.
 cond > 1 : conditioning on island age and having at least cond colonizations
 on the island. This last option is not yet available for the IW model \cr}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 }
 \value{
 A list. The highest level of the least corresponds to each individual
diff --git a/man/DAISIE_sim_trait_dep.Rd b/man/DAISIE_sim_trait_dep.Rd
index 6e082fe5..1a3cb8e7 100644
--- a/man/DAISIE_sim_trait_dep.Rd
+++ b/man/DAISIE_sim_trait_dep.Rd
@@ -83,8 +83,7 @@ type 2.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -93,8 +92,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
@@ -128,12 +126,15 @@ conditioning on island age and non-extinction of the island biota \cr.
 cond > 1 : conditioning on island age and having at least cond colonizations
 on the island. This last option is not yet available for the IW model \cr}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{trait_pars}{A named list containing diversification rates considering
   two trait states created by \code{\link{create_trait_pars}}:
diff --git a/man/DAISIE_sim_trait_dep_2K.Rd b/man/DAISIE_sim_trait_dep_2K.Rd
index 414661a5..c2d86e39 100644
--- a/man/DAISIE_sim_trait_dep_2K.Rd
+++ b/man/DAISIE_sim_trait_dep_2K.Rd
@@ -83,8 +83,7 @@ type 2.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -93,8 +92,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
@@ -128,12 +126,15 @@ conditioning on island age and non-extinction of the island biota \cr.
 cond > 1 : conditioning on island age and having at least cond colonizations
 on the island. This last option is not yet available for the IW model \cr}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{trait_pars}{A named list containing diversification rates considering
   two trait states created by \code{\link{create_trait_pars}}:
diff --git a/man/are_area_pars.Rd b/man/are_area_pars.Rd
deleted file mode 100644
index db25ed7f..00000000
--- a/man/are_area_pars.Rd
+++ /dev/null
@@ -1,44 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_check_format.R
-\name{are_area_pars}
-\alias{are_area_pars}
-\title{Test if list has area parameters}
-\usage{
-are_area_pars(area_pars)
-}
-\arguments{
-\item{area_pars}{A named list containing area and sea level parameters as
-created by \code{\link{create_area_pars}()}:
-\itemize{
-  \item{[1]: maximum area}
-  \item{[2]: current area}
-  \item{[3]: value from 0 to 1 indicating where in the island's history the
-  peak area is achieved}
-  \item{[4]: total island age}
-  \item{[5]: amplitude of area fluctuation from sea level}
-  \item{[6]: frequency of sine wave of area change from sea level}
-  \item{[7]: angle of the slope of the island}
-}}
-}
-\value{
-Boolean that indicates if list conforms to expected area parameters
-as created by \link{create_area_pars}
-}
-\description{
-Test if list has area parameters
-}
-\examples{
-testit::assert(DAISIE:::are_area_pars(
-  create_area_pars(
-    max_area = 10,
-    current_area = 4,
-    proportional_peak_t = 0.5,
-    total_island_age = 5,
-    sea_level_amplitude = 5,
-    sea_level_frequency = 10,
-    island_gradient_angle = 0)))
-}
-\author{
-Richel J.C Bilderbeek, Joshua Lambert, Pedro Neves
-}
-\keyword{internal}
diff --git a/man/are_hyper_pars.Rd b/man/are_hyper_pars.Rd
deleted file mode 100644
index 3fa55fe2..00000000
--- a/man/are_hyper_pars.Rd
+++ /dev/null
@@ -1,32 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_check_format.R
-\name{are_hyper_pars}
-\alias{are_hyper_pars}
-\title{Test if a list has hyperparameters}
-\usage{
-are_hyper_pars(hyper_pars)
-}
-\arguments{
-\item{hyper_pars}{A named list of numeric hyperparameters for the rate
-calculations as returned by \code{\link{create_hyper_pars}()}:
-\itemize{
-  \item{[1]: is d the scaling parameter for exponent for calculating
-  cladogenesis rate}
-  \item{[2]: is x the exponent for calculating extinction rate}
-}}
-}
-\value{
-\code{TRUE} if list contains hyperparameters, \code{FALSE} otherwise.
-}
-\description{
-Test if a list has hyperparameters
-}
-\examples{
-testit::assert(
-  DAISIE:::are_hyper_pars(create_hyper_pars(d = 0.027, x = 0.15))
-)
-}
-\author{
-Pedro Neves, Joshua Lambert
-}
-\keyword{internal}
diff --git a/man/are_max_rates.Rd b/man/are_max_rates.Rd
deleted file mode 100644
index 7d16471f..00000000
--- a/man/are_max_rates.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_check_format.R
-\name{are_max_rates}
-\alias{are_max_rates}
-\title{Determines if object max_rates are max_rates}
-\usage{
-are_max_rates(max_rates)
-}
-\arguments{
-\item{max_rates}{named list of numeric max rates as returned by
-\code{\link{update_max_rates}()}.}
-}
-\value{
-\code{TRUE} if object max_rates is a list of rates,
-\code{FALSE} otherwise.
-}
-\description{
-Determines if object max_rates are max_rates
-}
-\keyword{internal}
diff --git a/man/are_max_rates_gt_rates.Rd b/man/are_max_rates_gt_rates.Rd
deleted file mode 100644
index 8565c9e1..00000000
--- a/man/are_max_rates_gt_rates.Rd
+++ /dev/null
@@ -1,49 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_check_format.R
-\name{are_max_rates_gt_rates}
-\alias{are_max_rates_gt_rates}
-\title{Check if maximum rates are greater or equal to rates}
-\usage{
-are_max_rates_gt_rates(rates, max_rates)
-}
-\arguments{
-\item{rates}{named list of numeric rates as returned by
-\code{\link{update_rates}()}.}
-
-\item{max_rates}{named list of numeric max rates as returned by
-\code{\link{update_max_rates}()}.}
-}
-\value{
-\code{TRUE} if maximum rates are greater or equal than rates,
-\code{FALSE} otherwise.
-}
-\description{
-Check if maximum rates are greater or equal to rates
-}
-\examples{
-rates <- list(
-  ext_rate = 0.1,
-  immig_rate = 0.1,
-  ana_rate = 0.1,
-  clado_rate = 0.1
-)
-max_rates <- list(
-  ext_max_rate = 1,
-  immig_max_rate = 1,
-  ana_max_rate = 1,
-  clado_max_rate = 1
-)
-testthat::expect_true(
-  DAISIE:::are_max_rates_gt_rates(
-    rates = rates,
-    max_rates = max_rates
-  )
-)
-}
-\seealso{
-\code{\link{are_rates}}, \code{\link{are_max_rates}}
-}
-\author{
-Joshua Lambert, Pedro Neves
-}
-\keyword{internal}
diff --git a/man/are_trait_pars.Rd b/man/are_trait_pars.Rd
deleted file mode 100644
index e4b47591..00000000
--- a/man/are_trait_pars.Rd
+++ /dev/null
@@ -1,41 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_check_format.R
-\name{are_trait_pars}
-\alias{are_trait_pars}
-\title{Test if list has trait state parameters}
-\usage{
-are_trait_pars(trait_pars)
-}
-\arguments{
-\item{trait_pars}{A named list containing diversification rates considering
-  two trait states created by \code{\link{create_trait_pars}}:
-\itemize{
-  \item{[1]:A numeric with the per capita transition rate with state1}
-  \item{[2]:A numeric with the per capita immigration rate with state2}
-  \item{[3]:A numeric with the per capita extinction rate with state2}
-  \item{[4]:A numeric with the per capita anagenesis rate with state2}
-  \item{[5]:A numeric with the per capita cladogenesis rate with state2}
-  \item{[6]:A numeric with the per capita transition rate with state2}
-  \item{[7]:A numeric with the number of species with trait state 2 on
-   mainland}
-}}
-}
-\value{
-Boolean that indicates if list conforms to expected area parameters
-as created by \link{create_trait_pars}
-}
-\description{
-Test if list has trait state parameters
-}
-\examples{
-testit::assert(DAISIE:::are_trait_pars(
-  create_trait_pars(
-    trans_rate = 0.5,
-    immig_rate2 = 0.1,
-    ext_rate2 = 0.2,
-    ana_rate2 = 0.3,
-    clado_rate2 = 0.4,
-    trans_rate2 = 0.5,
-    M2 = 1000)) == TRUE)
-}
-\keyword{internal}
diff --git a/man/create_area_pars.Rd b/man/create_area_pars.Rd
index c0e623be..34002ab7 100644
--- a/man/create_area_pars.Rd
+++ b/man/create_area_pars.Rd
@@ -42,8 +42,7 @@ for island ontogeny simulation
 Create named list of area parameters
 }
 \examples{
-testit::assert(DAISIE:::are_area_pars(
-create_area_pars(
+area_pars <- create_area_pars(
   max_area = 10,
   current_area = 1,
   proportional_peak_t = 0.5,
@@ -51,9 +50,9 @@ create_area_pars(
   sea_level_amplitude = 5,
   sea_level_frequency = 10,
   island_gradient_angle = 0
-      )
-    )
-  )
+
+
+)
 }
 \author{
 Richel J.C Bilderbeek, Joshua Lambert, Pedro Neves
diff --git a/man/create_trait_pars.Rd b/man/create_trait_pars.Rd
index c8cba6b5..e17d089b 100644
--- a/man/create_trait_pars.Rd
+++ b/man/create_trait_pars.Rd
@@ -36,13 +36,13 @@ list of numerical values containing trait state parameters
 Create named list of trait state parameters
 }
 \examples{
-testit::assert(DAISIE:::are_trait_pars(
-  create_trait_pars(
-    trans_rate = 0.5,
-    immig_rate2 = 0.1,
-    ext_rate2 = 0.2,
-    ana_rate2 = 0.3,
-    clado_rate2 = 0.4,
-    trans_rate2 = 0.5,
-    M2 = 1000)) == TRUE)
+trait_pars <- create_trait_pars(
+   trans_rate = 0.5,
+   immig_rate2 = 0.1,
+   ext_rate2 = 0.2,
+   ana_rate2 = 0.3,
+   clado_rate2 = 0.4,
+   trans_rate2 = 0.5,
+   M2 = 1000
+ )
 }
diff --git a/man/daisie_odeint_cs.Rd b/man/daisie_odeint_cs.Rd
index 71435a9e..71af420a 100644
--- a/man/daisie_odeint_cs.Rd
+++ b/man/daisie_odeint_cs.Rd
@@ -2,7 +2,12 @@
 % Please edit documentation in R/RcppExports.R
 \name{daisie_odeint_cs}
 \alias{daisie_odeint_cs}
-\title{Driver for the boost::odeint solver}
+\title{Driver for the boost::odeint solver for the CS model}
+\value{
+Object of type `state_type`, which itself is
+`vector_t`<double>, with the result of the
+integration depending on the runmod chosen.
+}
 \description{
-Driver for the boost::odeint solver
+Driver for the boost::odeint solver for the CS model
 }
diff --git a/man/daisie_odeint_iw.Rd b/man/daisie_odeint_iw.Rd
index 8a8af05b..87e6efaa 100644
--- a/man/daisie_odeint_iw.Rd
+++ b/man/daisie_odeint_iw.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/RcppExports.R
 \name{daisie_odeint_iw}
 \alias{daisie_odeint_iw}
-\title{Driver for the boost::odeint solver}
+\title{Driver for the boost::odeint solver for the IW model}
 \description{
-Driver for the boost::odeint solver
+Driver for the boost::odeint solver for the IW model
 }
diff --git a/man/default_params_doc.Rd b/man/default_params_doc.Rd
index 3c74d4a7..a352fc87 100644
--- a/man/default_params_doc.Rd
+++ b/man/default_params_doc.Rd
@@ -219,12 +219,15 @@ of species is present, STT is plotted for all species. If two types are
 present, three plots are produced: STT for all, STT for type 1 and STT for
 type 2.}
 
-\item{verbose}{In simulation and dataprep functions a logical,
-\code{Default = TRUE} gives intermediate output should be printed.
+\item{verbose}{A numeric vector of length 1, which in simulations and
+`DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
+should be printed.
 For ML functions a numeric determining if intermediate output should be
-printed, \code{Default = 0} does not print, \code{verbose = 1} prints
-intermediate output of the parameters and loglikelihood, \code{verbose = 2}
-means also intermediate progress during loglikelihood computation is shown.}
+printed. The default: `0` does not print, `1` prints the initial
+likelihood and the settings that were selected (which parameters are
+to be optimised, fixed or shifted), `2` prints the same as `1 and also the
+intermediate output of the parameters and loglikelihood, while `3` the
+same as `2` and prints intermediate progress during likelihood computation.}
 
 \item{area_pars}{A named list containing area and sea level parameters as
 created by \code{\link{create_area_pars}()}:
@@ -250,8 +253,7 @@ calculations as returned by \code{\link{create_hyper_pars}()}:
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -260,8 +262,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
diff --git a/man/get_clado_rate_per_capita.Rd b/man/get_clado_rate_per_capita.Rd
deleted file mode 100644
index 66c08deb..00000000
--- a/man/get_clado_rate_per_capita.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_rates.R
-\name{get_clado_rate_per_capita}
-\alias{get_clado_rate_per_capita}
-\title{Calculate per-capita cladogenesis rate}
-\usage{
-get_clado_rate_per_capita(lac, d, num_spec, K, A = 1)
-}
-\arguments{
-\item{lac}{A numeric with the per capita cladogenesis rate.}
-
-\item{d}{Numeric defining the scaling parameter for exponent for
-calculating cladogenesis rate.}
-
-\item{num_spec}{A numeric with the current number of species.}
-
-\item{K}{A numeric with carrying capacity.}
-
-\item{A}{A numeric value for island area at a given point in time.}
-}
-\value{
-Numeric with the per-capita cladogenesis rate given a base
-cladogenesis rate, K, A and the d hyperparameter.
-}
-\description{
-This function is only called directly inside the RHS of the ontogeny
-likelihood functions. In all other cases \code{\link{get_clado_rate}()} is to
-be called instead.
-}
-\examples{
-lac <- 0.4
-d <- 0
-num_spec <- 2
-K <- 10
-A <- 1
-clado_rate_pc <- DAISIE:::get_clado_rate_per_capita(lac, d, num_spec, K, A)
-}
-\keyword{internal}
diff --git a/man/get_ext_rate_per_capita.Rd b/man/get_ext_rate_per_capita.Rd
deleted file mode 100644
index 66018299..00000000
--- a/man/get_ext_rate_per_capita.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_rates.R
-\name{get_ext_rate_per_capita}
-\alias{get_ext_rate_per_capita}
-\title{Function to describe per-capita changes in extinction rate through time}
-\usage{
-get_ext_rate_per_capita(mu, x, extcutoff = 1000, A = 1)
-}
-\arguments{
-\item{mu}{A numeric with the per capita extinction rate.}
-
-\item{x}{Numeric defining the exponent for calculating extinction rate.}
-
-\item{extcutoff}{A numeric with the cutoff for the the maximum extinction
-rate preventing it from being too large and slowing down simulation.}
-
-\item{A}{A numeric value for island area at a given point in time.}
-}
-\value{
-Numeric with per capita extinction rate, given A(t), x, and mu0.
-}
-\description{
-This function is only called directly inside the RHS of the ontogeny
-likelihood functions. In all other cases \code{\link{get_ext_rate}()} is to
-be called instead.
-}
-\examples{
-ext_rate_per_capita <- DAISIE:::get_ext_rate_per_capita(
-  mu = 0.5,
-  x = 1,
-  A = 1000
-)
-}
-\keyword{internal}
diff --git a/man/get_global_max_area.Rd b/man/get_global_max_area.Rd
deleted file mode 100644
index 76685f40..00000000
--- a/man/get_global_max_area.Rd
+++ /dev/null
@@ -1,85 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_max_rates.R
-\name{get_global_max_area}
-\alias{get_global_max_area}
-\title{Get the maximum area}
-\usage{
-get_global_max_area(total_time, area_pars, peak, island_ontogeny, sea_level)
-}
-\arguments{
-\item{total_time}{Numeric defining the length of the simulation in time
-units.}
-
-\item{area_pars}{A named list containing area and sea level parameters as
-created by \code{\link{create_area_pars}()}:
-\itemize{
-  \item{[1]: maximum area}
-  \item{[2]: current area}
-  \item{[3]: value from 0 to 1 indicating where in the island's history the
-  peak area is achieved}
-  \item{[4]: total island age}
-  \item{[5]: amplitude of area fluctuation from sea level}
-  \item{[6]: frequency of sine wave of area change from sea level}
-  \item{[7]: angle of the slope of the island}
-}}
-
-\item{peak}{A numeric value specifying the peakiness (or shaprness) of the
-ontogeny curve. Higher values imply peakier ontogeny. This value is
-internally calculated by \code{\link{calc_peak}()} given the area at the
-present and the \code{area_pars}.}
-
-\item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
-\code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
-island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
-numeric describing the type of island ontogeny. Can be \code{0} for
-constant, \code{1} for a beta function describing area through time. In ML
-functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
-dependent estimation is not yet available as development is still ongoing.
-Will return an error if called in that case.}
-
-\item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
-string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
-\cr In all other functions a numeric describing the type of sea level. Can
-be \code{0} for constant, \code{1} for a sine function describing area
-through time.}
-}
-\value{
-Numeric maximum area during the simulation.
-}
-\description{
-Get the maximum area
-}
-\examples{
-timeval <- 1
-total_time <- 10
-area_pars <- DAISIE::create_area_pars(
-  max_area = 5000,
-  current_area = 4000,
-  proportional_peak_t = 0.5,
-  total_island_age = 15,
-  sea_level_amplitude = 0,
-  sea_level_frequency = 0,
-  island_gradient_angle = 0
-)
-island_ontogeny <- 1
-sea_level <- 0
-peak <- DAISIE:::calc_peak(total_time = total_time, area_pars = area_pars)
-testthat::expect_silent(
-  global_max_area_time <- DAISIE:::get_global_max_area(
-    total_time = total_time,
-    peak = peak,
-    area_pars = area_pars,
-    island_ontogeny = island_ontogeny,
-    sea_level = sea_level
-  )
-)
-
-}
-\author{
-Pedro Neves, Joshua Lambert, Shu Xie
-}
-\keyword{internal}
diff --git a/man/get_global_min_area.Rd b/man/get_global_min_area.Rd
deleted file mode 100644
index bfb80a7d..00000000
--- a/man/get_global_min_area.Rd
+++ /dev/null
@@ -1,86 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_max_rates.R
-\name{get_global_min_area}
-\alias{get_global_min_area}
-\title{Get the minimum area}
-\usage{
-get_global_min_area(total_time, area_pars, peak, island_ontogeny, sea_level)
-}
-\arguments{
-\item{total_time}{Numeric defining the length of the simulation in time
-units.}
-
-\item{area_pars}{A named list containing area and sea level parameters as
-created by \code{\link{create_area_pars}()}:
-\itemize{
-  \item{[1]: maximum area}
-  \item{[2]: current area}
-  \item{[3]: value from 0 to 1 indicating where in the island's history the
-  peak area is achieved}
-  \item{[4]: total island age}
-  \item{[5]: amplitude of area fluctuation from sea level}
-  \item{[6]: frequency of sine wave of area change from sea level}
-  \item{[7]: angle of the slope of the island}
-}}
-
-\item{peak}{A numeric value specifying the peakiness (or shaprness) of the
-ontogeny curve. Higher values imply peakier ontogeny. This value is
-internally calculated by \code{\link{calc_peak}()} given the area at the
-present and the \code{area_pars}.}
-
-\item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
-\code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
-island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
-numeric describing the type of island ontogeny. Can be \code{0} for
-constant, \code{1} for a beta function describing area through time. In ML
-functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
-dependent estimation is not yet available as development is still ongoing.
-Will return an error if called in that case.}
-
-\item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
-string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
-\cr In all other functions a numeric describing the type of sea level. Can
-be \code{0} for constant, \code{1} for a sine function describing area
-through time.}
-}
-\value{
-Numeric with time at which area is minimum during the simulation
-}
-\description{
-Get the minimum area
-}
-\examples{
-timeval <- 1
-total_time <- 10
-area_pars <- DAISIE::create_area_pars(
-  max_area = 5000,
-  current_area = 4000,
-  proportional_peak_t = 0.5,
-  total_island_age = 15,
-  sea_level_amplitude = 0,
-  sea_level_frequency = 0,
-  island_gradient_angle = 0
-)
-island_ontogeny <- 1
-sea_level <- 0
-peak <- DAISIE:::calc_peak(total_time = total_time, area_pars = area_pars)
-
-testthat::expect_silent(
-  DAISIE:::get_global_min_area(
-    total_time = total_time,
-    area_pars = area_pars,
-    peak = peak,
-    island_ontogeny = island_ontogeny,
-    sea_level = sea_level
-  )
-)
-
-}
-\author{
-Pedro Neves, Joshua Lambert, Shu Xie
-}
-\keyword{internal}
diff --git a/man/get_immig_rate_per_capita.Rd b/man/get_immig_rate_per_capita.Rd
deleted file mode 100644
index 2340f481..00000000
--- a/man/get_immig_rate_per_capita.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_rates.R
-\name{get_immig_rate_per_capita}
-\alias{get_immig_rate_per_capita}
-\title{Calculate per-capita immigration rate}
-\usage{
-get_immig_rate_per_capita(gam, num_spec, K, A = 1)
-}
-\arguments{
-\item{gam}{A numeric with the per capita immigration rate.}
-
-\item{num_spec}{A numeric with the current number of species.}
-
-\item{K}{A numeric with carrying capacity.}
-
-\item{A}{A numeric value for island area at a given point in time.}
-}
-\value{
-A numeric with the per-capita immigration rate given A(t) and K.
-}
-\description{
-This function is only called directly inside the RHS of the ontogeny
-likelihood functions. In all other cases \code{\link{get_immig_rate}()} is to
-be called instead.
-}
-\examples{
-immig_rate_per_capita <- DAISIE:::get_immig_rate_per_capita(
-  gam = 0.001,
-  num_spec = 5,
-  K = 20,
-  A = 1000
-)
-}
-\keyword{internal}
diff --git a/man/is_island_ontogeny_input.Rd b/man/is_island_ontogeny_input.Rd
deleted file mode 100644
index 847b6877..00000000
--- a/man/is_island_ontogeny_input.Rd
+++ /dev/null
@@ -1,30 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_check_format.R
-\name{is_island_ontogeny_input}
-\alias{is_island_ontogeny_input}
-\title{Check if island_ontogeny is correct after user input}
-\usage{
-is_island_ontogeny_input(island_ontogeny)
-}
-\arguments{
-\item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
-\code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
-island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
-numeric describing the type of island ontogeny. Can be \code{0} for
-constant, \code{1} for a beta function describing area through time. In ML
-functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
-dependent estimation is not yet available as development is still ongoing.
-Will return an error if called in that case.}
-}
-\value{
-Boolean stating if island_ontogeny is correct.
-}
-\description{
-Check if island_ontogeny is correct after user input
-}
-\seealso{
-is_island_ontogeny_runtime
-}
-\keyword{internal}
diff --git a/man/is_sea_level_input.Rd b/man/is_sea_level_input.Rd
deleted file mode 100644
index 67321f2c..00000000
--- a/man/is_sea_level_input.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_check_format.R
-\name{is_sea_level_input}
-\alias{is_sea_level_input}
-\title{Check if sea_level is correct after user input}
-\usage{
-is_sea_level_input(sea_level)
-}
-\arguments{
-\item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
-string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
-\cr In all other functions a numeric describing the type of sea level. Can
-be \code{0} for constant, \code{1} for a sine function describing area
-through time.}
-}
-\value{
-Boolean stating if sea_level is correct.
-}
-\description{
-Check if sea_level is correct after user input
-}
-\seealso{
-is_sea_level_runtime
-}
-\keyword{internal}
diff --git a/man/is_simulation_outputs.Rd b/man/is_simulation_outputs.Rd
deleted file mode 100644
index 3139dbc1..00000000
--- a/man/is_simulation_outputs.Rd
+++ /dev/null
@@ -1,37 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_check_format.R
-\name{is_simulation_outputs}
-\alias{is_simulation_outputs}
-\title{Measures if the input is a valid collection of simulation
-outputs.}
-\usage{
-is_simulation_outputs(simulation_outputs)
-}
-\arguments{
-\item{simulation_outputs}{A list with matrices and vectors of simulation
-produced by DAISIE_sim functions.}
-}
-\value{
-TRUE if the input is a valid collection of simulation
-outputs.
-}
-\description{
-Measures if the input is a valid collection of simulation
-outputs.
-}
-\examples{
-testthat::expect_false(DAISIE:::is_simulation_outputs("nonsense"))
-
-simulation_outputs <- DAISIE_sim_cr(
-  time = 2,
-  M = 1000,
-  pars = c(2, 1, 20, 0.0001, 1),
-  replicates = 1,
-  plot_sims = FALSE
- )
-testthat::expect_true(DAISIE:::is_simulation_outputs(simulation_outputs))
-}
-\author{
-Richel J.C Bilderbeek, Pedro Neves
-}
-\keyword{internal}
diff --git a/man/island_area.Rd b/man/island_area.Rd
index d0ca12f9..1da2d969 100644
--- a/man/island_area.Rd
+++ b/man/island_area.Rd
@@ -33,8 +33,7 @@ present and the \code{area_pars}.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -43,8 +42,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
diff --git a/man/translate_island_ontogeny.Rd b/man/translate_island_ontogeny.Rd
deleted file mode 100644
index b491a2e6..00000000
--- a/man/translate_island_ontogeny.Rd
+++ /dev/null
@@ -1,30 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_utils.R
-\name{translate_island_ontogeny}
-\alias{translate_island_ontogeny}
-\title{Translate user-friendly ontogeny codes to numerics}
-\usage{
-translate_island_ontogeny(island_ontogeny)
-}
-\arguments{
-\item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
-\code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
-island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
-numeric describing the type of island ontogeny. Can be \code{0} for
-constant, \code{1} for a beta function describing area through time. In ML
-functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
-dependent estimation is not yet available as development is still ongoing.
-Will return an error if called in that case.}
-}
-\value{
-Numeric, 0 for null-ontogeny, 1 for beta function
-}
-\description{
-Translate user-friendly ontogeny codes to numerics
-}
-\examples{
-translated_ontogeny <- DAISIE:::translate_island_ontogeny("const")
-}
-\keyword{internal}
diff --git a/man/translate_sea_level.Rd b/man/translate_sea_level.Rd
deleted file mode 100644
index a486c9be..00000000
--- a/man/translate_sea_level.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/DAISIE_utils.R
-\name{translate_sea_level}
-\alias{translate_sea_level}
-\title{Translate user-friendly sea-level codes to numerics}
-\usage{
-translate_sea_level(sea_level)
-}
-\arguments{
-\item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
-string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
-\cr In all other functions a numeric describing the type of sea level. Can
-be \code{0} for constant, \code{1} for a sine function describing area
-through time.}
-}
-\value{
-Numeric, 0 for null-sea-level, 1 for sine function
-}
-\description{
-Translate user-friendly sea-level codes to numerics
-}
-\examples{
-translated_sea_level <- DAISIE:::translate_sea_level("const")
-}
-\keyword{internal}
diff --git a/man/update_rates.Rd b/man/update_rates.Rd
index 0e9c3b2f..b20a6154 100644
--- a/man/update_rates.Rd
+++ b/man/update_rates.Rd
@@ -68,8 +68,7 @@ present and the \code{area_pars}.}
 \item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
 \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
 island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
-describing area through time. String checked by
-\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+describing area through time. \cr In all other functions a
 numeric describing the type of island ontogeny. Can be \code{0} for
 constant, \code{1} for a beta function describing area through time. In ML
 functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
@@ -78,8 +77,7 @@ Will return an error if called in that case.}
 
 \item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
 string describing the type of sea level. Can be \code{"const"} or
-\code{"sine"} for a sine function describing area through time. String
-checked by \code{\link{is_sea_level_input}()}.
+\code{"sine"} for a sine function describing area through time.
 \cr In all other functions a numeric describing the type of sea level. Can
 be \code{0} for constant, \code{1} for a sine function describing area
 through time.}
diff --git a/src/DAISIE_CS.cpp b/src/DAISIE_CS.cpp
index 8afa8f8d..07373dd1 100644
--- a/src/DAISIE_CS.cpp
+++ b/src/DAISIE_CS.cpp
@@ -1,7 +1,14 @@
-// [[Rcpp::plugins(cpp14)]]
+//
+//  Copyright (c) 2023, Hanno Hildenbrandt
+//
+//  Distributed under the Boost Software License, Version 1.0. (See
+//  accompanying file LICENSE_1_0.txt or copy at
+//  http://www.boost.org/LICENSE_1_0.txt)
+//
+
 // [[Rcpp::depends(BH)]]
 
-//' @export daisie_odeint_cs
+
 
 #include "config.h"
 #include "DAISIE_odeint.h"
@@ -18,9 +25,11 @@ namespace {
   static constexpr int default_max_cs_steps = 1000000;
   static int max_cs_steps = default_max_cs_steps;
 
+
   // step-size factor for adams_bashforth_moulton integration
   static constexpr double default_abm_factor = 0.0001;
-  static double abm_factor = default_abm_factor;
+  double abm_factor = default_abm_factor;
+
 
   // common parameter
   struct param_t
@@ -48,9 +57,11 @@ namespace {
     }
 
     // odeint interface
-    void operator()(const state_type& x, state_type& dx, double t) const
+    void operator()(const state_type& x, state_type& dx, double /*t*/) const
     {
-      if (++p_.steps > max_cs_steps) throw std::runtime_error("cpp_daisie_cs_runmod: too many steps");
+      if (++p_.steps > max_cs_steps) {
+        throw std::runtime_error("cpp_daisie_cs_runmod: too many steps");
+      }
 
       const auto xx1 = padded_vector_view<2>(x.data().begin(), p_.lx);
       const auto xx2 = padded_vector_view<2>(x.data().begin() + p_.lx, p_.lx);
@@ -113,9 +124,11 @@ namespace {
     }
 
     // odeint interface
-    void operator()(const state_type& x, state_type& dx, double) const
+    void operator()(const state_type& x, state_type& dx, double /*t*/) const
     {
-      if (++p_.steps > max_cs_steps) throw std::runtime_error("cpp_daisie_cs_runmod_1: too many steps");
+      if (++p_.steps > max_cs_steps) {
+        throw std::runtime_error("cpp_daisie_cs_runmod_1: too many steps");
+      }
 
       const auto xx1 = padded_vector_view<2>(x.data().begin(), p_.lx);
       const auto xx2 = padded_vector_view<2>(x.data().begin() + p_.lx, p_.lx);
@@ -196,9 +209,11 @@ namespace {
     }
 
     // odeint interface
-    void operator()(const state_type& x, state_type& dx, double) const
+    void operator()(const state_type& x, state_type& dx, double /*t*/) const
     {
-      if (++p_.steps > max_cs_steps) throw std::runtime_error("cpp_daisie_cs_runmod_2: too many steps");
+      if (++p_.steps > max_cs_steps) {
+        throw std::runtime_error("cpp_daisie_cs_runmod_2: too many steps");
+      }
 
       const auto xx1 = padded_vector_view<2>(x.data().begin(), p_.lx);
       const auto xx2 = padded_vector_view<2>(x.data().begin() + p_.lx, p_.lx);
@@ -262,9 +277,13 @@ namespace {
 } // anonymous namespace
 
 
-//' Driver for the boost::odeint solver
+//' Driver for the boost::odeint solver for the CS model
 //'
 //' @name daisie_odeint_cs
+//' @export daisie_odeint_cs
+//' @return Object of type `state_type`, which itself is
+//' `vector_t`<double>, with the result of the
+//' integration depending on the runmod chosen.
 RcppExport SEXP daisie_odeint_cs(SEXP rrunmod, SEXP ry, SEXP rtimes, SEXP rlx, SEXP rkk, SEXP rpar, SEXP Stepper, SEXP ratol, SEXP rrtol) {
 BEGIN_RCPP
   Rcpp::RObject rcpp_result_gen;
diff --git a/src/DAISIE_IW.cpp b/src/DAISIE_IW.cpp
index ae84a11a..e46f8939 100644
--- a/src/DAISIE_IW.cpp
+++ b/src/DAISIE_IW.cpp
@@ -1,6 +1,13 @@
+//
+//  Copyright (c) 2023, Hanno Hildenbrandt
+//
+//  Distributed under the Boost Software License, Version 1.0. (See
+//  accompanying file LICENSE_1_0.txt or copy at
+//  http://www.boost.org/LICENSE_1_0.txt)
+//
+
 //' @export daisie_odeint_iw
 
-// [[Rcpp::plugins(cpp14)]]
 // [[Rcpp::plugins(openmp)]]
 // [[Rcpp::depends(BH)]]
 // [[Rcpp::depends(RcppEigen)]]
@@ -216,9 +223,13 @@ namespace {
 } // anonymous namespace
 
 
-//' Driver for the boost::odeint solver
+//' Driver for the boost::odeint solver for the IW model
 //'
 //' @name daisie_odeint_iw
+//' @export daisie_odeint_iw
+ //' @return Object of type `state_type`, which itself is
+ //' `vector_t`<double>, with the result of the
+ //' integration depending on the runmod chosen.
 RcppExport SEXP daisie_odeint_iw(SEXP ry, SEXP rtimes, SEXP rpars, SEXP Stepper, SEXP atolint, SEXP reltolint) {
 BEGIN_RCPP
   Rcpp::RObject rcpp_result_gen;
diff --git a/src/DAISIE_loglik_rhs_FORTRAN.f95 b/src/DAISIE_loglik_rhs_FORTRAN.f95
index 5c121830..e7ffdc93 100644
--- a/src/DAISIE_loglik_rhs_FORTRAN.f95
+++ b/src/DAISIE_loglik_rhs_FORTRAN.f95
@@ -1,3 +1,10 @@
+!
+!  Copyright (c) 2023, Rampal S. Etienne
+!
+!  Distributed under the Boost Software License, Version 1.0. (See
+!  accompanying file LICENSE_1_0.txt or copy at
+!  http://www.boost.org/LICENSE_1_0.txt)
+!
 !==========================================================================
 ! Helper function:
 ! fill vec with N elements from parms, starting at position ii
diff --git a/src/DAISIE_odeint.h b/src/DAISIE_odeint.h
index 20fa9fa2..088c8141 100644
--- a/src/DAISIE_odeint.h
+++ b/src/DAISIE_odeint.h
@@ -1,25 +1,47 @@
-// [[Rcpp::plugins(cpp14)]]
+//
+//  Copyright (c) 2023, Hanno Hildenbrandt
+//
+//  Distributed under the Boost Software License, Version 1.0. (See
+//  accompanying file LICENSE_1_0.txt or copy at
+//  http://www.boost.org/LICENSE_1_0.txt)
+//
 
-#pragma once
 #ifndef DAISIE_ODEINT_H_INCLUDED
 #define DAISIE_ODEINT_H_INCLUDED
 
 #include "config.h"
-#include "ublas_types.h"
-#include "patched_bulrisch_stoer.h"   // shadow buggy boost header
+#include "DAISIE_types.h"
 #include <boost/numeric/odeint.hpp>
 #include <algorithm>
 #include <stdexcept>
 #include <memory>
 
+
+#ifdef USE_BULRISCH_STOER_PATCH
+
+#include <boost/units/quantity.hpp>
+#include <boost/units/systems/si/dimensionless.hpp>
+
+using bstime_t = boost::units::quantity<boost::units::si::dimensionless, double>;
+
+#else // USE_BULRISCH_STOER_PATCH
+
+// The default. Causes unitialized member m_last_dt in
+// boost::odeint::bulrisch_stoer<>, declared in
+// boost/numreic/odeint/stepper/bulrisch_stoer.hpp
+using bstime_t = double;
+
+#endif // USE_BULRISCH_STOER_PATCH
+
+
 using namespace Rcpp;
 using namespace boost::numeric::odeint;
 
-
 // type of the ode state
 using state_type = vector_t<double>;
 
 
+
 // zero-value padded view into vector
 template <int Pad>
 class padded_vector_view
@@ -44,7 +66,7 @@ class padded_vector_view
 
 namespace daisie_odeint {
 
-  extern double abm_factor;
+  extern double abm_factor;   // defined in DAISIE_CS.cpp
 
 
   template <typename Stepper, typename Rhs>
@@ -133,8 +155,8 @@ namespace daisie_odeint {
     }
     else if ("odeint::bulirsch_stoer" == stepper) {
       // outlier in calling convention
-      using stepper_t = bulirsch_stoer<state_type>;
-      integrate_adaptive(stepper_t(atol, rtol), rhs, y, t0, t1, 0.1 * (t1 - t0));
+      using stepper_t = bulirsch_stoer<state_type, double, state_type, bstime_t>;
+      integrate_adaptive(stepper_t(atol, rtol), rhs, y, bstime_t{t0}, bstime_t{t1}, bstime_t{0.1 * (t1 - t0)});
     }
     else if (0 == stepper.compare(0, stepper.size() - 2, "odeint::adams_bashforth")) {
       const char steps = stepper.back();
diff --git a/src/DAISIE_types.h b/src/DAISIE_types.h
index 78ae8f2f..2a0eb312 100644
--- a/src/DAISIE_types.h
+++ b/src/DAISIE_types.h
@@ -1,3 +1,124 @@
-#pragma once
+//
+//  Copyright (c) 2023, Hanno Hildenbrandt
+//
+//  Distributed under the Boost Software License, Version 1.0. (See
+//  accompanying file LICENSE_1_0.txt or copy at
+//  http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef DAISIE_TYPES_H_INCLUDED
+#define DAISIE_TYPES_H_INCLUDED
+
 #include "config.h"
-#include "odeint_types.h"
+#include <RcppCommon.h>
+#include <boost/numeric/ublas/vector.hpp>
+#include <boost/numeric/ublas/matrix.hpp>
+
+
+namespace ublas = boost::numeric::ublas;
+
+
+template <typename T> using vector_t = ublas::vector<T>;
+template <typename T> using matrix_t = ublas::matrix<T>;
+
+
+// forward declarations Rcpp <-> boost::numeric::ublas
+namespace Rcpp {
+
+  namespace traits {
+
+    template <typename T> SEXP wrap(const vector_t<T>&);
+    template <typename T> SEXP wrap(const matrix_t<T>&);
+
+    template <typename T> vector_t<T> as(SEXP);
+    template <typename T> matrix_t<T> as(SEXP);
+
+    template <typename T> class Exporter<vector_t<T>>;
+    template <typename T> class Exporter<matrix_t<T>>;
+
+  }
+
+}
+
+
+#include <Rcpp.h>
+
+
+namespace Rcpp {
+
+  namespace traits {
+
+    template <typename T> inline SEXP wrap(const vector_t<T>& obj) {
+      const int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
+      return Rcpp::Vector<RTYPE>(obj.begin(), obj.end());
+    }
+
+
+    template <typename T> inline SEXP wrap(const matrix_t<T>& obj) {
+      const size_t nr = static_cast<size_t>(obj.size1());
+      const size_t nc = static_cast<size_t>(obj.size2());
+      const int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
+      Rcpp::Matrix<RTYPE> rmat(nr, nc);
+      for (size_t i = 0; i < nr; ++i) {
+        for (size_t j = 0; j < nc; ++j) {
+          rmat(i, j) = obj(i, j);
+        }
+      }
+      return rmat;
+    }
+
+
+    template<typename T>
+    class Exporter<vector_t<T>>
+    {
+    private:
+      static constexpr int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
+      Rcpp::Vector<RTYPE> rvec;
+
+    public:
+      Exporter(SEXP x) : rvec(x) {
+        if (TYPEOF(x) != RTYPE) {
+          throw std::invalid_argument("Wrong R type for mapped 1D array");
+        }
+      }
+
+      vector_t<T> get() {
+        vector_t<T> x(rvec.size());
+        std::copy(rvec.begin(), rvec.end(), x.begin());
+        return x;
+      }
+    };
+
+
+    template<typename T>
+    class Exporter<matrix_t<T>>
+    {
+    private:
+      static constexpr int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
+      Rcpp::Matrix<RTYPE> rmat;
+
+    public:
+      Exporter(SEXP x) : rmat(x) {
+        if (TYPEOF(x) != RTYPE) {
+          throw std::invalid_argument("Wrong R type for mapped 2D array");
+        }
+      }
+
+      matrix_t<T> get() {
+        const size_t nr = static_cast<size_t>(rmat.rows());
+        const size_t nc = static_cast<size_t>(rmat.cols());
+        matrix_t<T> x(nr, nc);
+        for (size_t i = 0; i < nr; ++i) {
+          for (size_t j = 0; j < nc; ++j) {
+            x(i, j) = rmat(i, j);
+          }
+        }
+        return x;
+      }
+    };
+
+  }
+
+}
+
+#endif
diff --git a/src/R_init_DAISIE.c b/src/R_init_DAISIE.c
index e5fd4b78..450941a3 100644
--- a/src/R_init_DAISIE.c
+++ b/src/R_init_DAISIE.c
@@ -1,3 +1,11 @@
+//
+//  Copyright (c) 2023, Hanno Hildenbrandt
+//
+//  Distributed under the Boost Software License, Version 1.0. (See
+//  accompanying file LICENSE_1_0.txt or copy at
+//  http://www.boost.org/LICENSE_1_0.txt)
+//
+
 // [[Rcpp::plugins(cpp14)]]
 
 #include"config.h"
diff --git a/src/config.h b/src/config.h
index 32cfa85b..c74d5afd 100644
--- a/src/config.h
+++ b/src/config.h
@@ -1,28 +1,29 @@
+//
+//  Copyright (c) 2023, Hanno Hildenbrandt
+//
+//  Distributed under the Boost Software License, Version 1.0. (See
+//  accompanying file LICENSE_1_0.txt or copy at
+//  http://www.boost.org/LICENSE_1_0.txt)
+//
+
 #ifndef ODEINT_CONFIG_H_INCLUDED
 #define ODEINT_CONFIG_H_INCLUDED
 
 // [[Rcpp::plugins(cpp14)]]
 
-// Special case to make use of some steppers that would include
-// boost/functional.hpp
-// moved to Makevars[.win]
-/*
-#if __cplusplus >= 201703L
-# ifdef _HAS_AUTO_PTR_ETC
-#  undef _HAS_AUTO_PTR_ETC
-# endif
-# define _HAS_AUTO_PTR_ETC 0
-#endif
- */
-
 // Special case to make use of some steppers that would include
 // boost/get_pointer.hpp
 #ifndef BOOST_NO_AUTO_PTR
 # define BOOST_NO_AUTO_PTR
 #endif
 
-// uncomment if unitialized member variable bulirsch_stoer::m_dt_last
-// is fixed in boost (BH)
+// Addresses unitialized member variable bulirsch_stoer<>::m_dt_last.
+//
+// The issue is *not* fixed in BOOST_VERSION 1.81.1.
+// We need to check for fixes in upcomming boost (BH) releases.
+//
+// Uncomment if unitialized member variable bulirsch_stoer::m_dt_last
+// is fixed in boost (BH):
 #define USE_BULRISCH_STOER_PATCH
 
 #endif
diff --git a/src/patched_bulrisch_stoer.h b/src/patched_bulrisch_stoer.h
deleted file mode 100644
index cad4f521..00000000
--- a/src/patched_bulrisch_stoer.h
+++ /dev/null
@@ -1,661 +0,0 @@
-/*
-  Patched version of
-  boost/numeric/odeint/stepper/bulirsch_stoer.hpp
-
-  Addresses unitialized member variable bulirsch_stoer<>::m_dt_last.
-
-  Include this header before boost/numeric/odeint to shadow
-  boost/numeriuc/odeint/stepper/bulrisch_stoer.hpp
-
-  The issue is *not* fixed in BOOST_VERSION == 1.81.0.
-  We need to check for fixes in upcomming boost (BH) releases.
-
-  Hanno Hildenbrandt 2023
-*/
-
-/*
-  [auto_generated]
-  boost/numeric/odeint/stepper/bulirsch_stoer.hpp
-
-  [begin_description]
-  Implementation of the Burlish-Stoer method. As described in
-  Ernst Hairer, Syvert Paul Norsett, Gerhard Wanner
-  Solving Ordinary Differential Equations I. Nonstiff Problems.
-  Springer Series in Comput. Mathematics, Vol. 8, Springer-Verlag 1987, Second revised edition 1993.
-  [end_description]
-
-  Copyright 2011-2013 Mario Mulansky
-  Copyright 2011-2013 Karsten Ahnert
-  Copyright 2012 Christoph Koke
-
-  Distributed under the Boost Software License, Version 1.0.
-  (See accompanying file LICENSE_1_0.txt or
-  copy at http://www.boost.org/LICENSE_1_0.txt)
-*/
-
-#ifdef USE_BULRISCH_STOER_PATCH
-
-#ifndef BOOST_NUMERIC_ODEINT_STEPPER_BULIRSCH_STOER_HPP_INCLUDED
-#define BOOST_NUMERIC_ODEINT_STEPPER_BULIRSCH_STOER_HPP_INCLUDED
-
-
-#include <iostream>
-
-#include <algorithm>
-
-#include <boost/config.hpp> // for min/max guidelines
-
-#include <boost/numeric/odeint/util/bind.hpp>
-#include <boost/numeric/odeint/util/unwrap_reference.hpp>
-
-#include <boost/numeric/odeint/stepper/controlled_runge_kutta.hpp>
-#include <boost/numeric/odeint/stepper/modified_midpoint.hpp>
-#include <boost/numeric/odeint/stepper/controlled_step_result.hpp>
-#include <boost/numeric/odeint/algebra/range_algebra.hpp>
-#include <boost/numeric/odeint/algebra/default_operations.hpp>
-#include <boost/numeric/odeint/algebra/algebra_dispatcher.hpp>
-#include <boost/numeric/odeint/algebra/operations_dispatcher.hpp>
-
-#include <boost/numeric/odeint/util/state_wrapper.hpp>
-#include <boost/numeric/odeint/util/is_resizeable.hpp>
-#include <boost/numeric/odeint/util/resizer.hpp>
-#include <boost/numeric/odeint/util/unit_helper.hpp>
-#include <boost/numeric/odeint/util/detail/less_with_sign.hpp>
-
-namespace boost {
-namespace numeric {
-namespace odeint {
-
-template<
-    class State ,
-    class Value = double ,
-    class Deriv = State ,
-    class Time = Value ,
-    class Algebra = typename algebra_dispatcher< State >::algebra_type ,
-    class Operations = typename operations_dispatcher< State >::operations_type ,
-    class Resizer = initially_resizer
-    >
-class bulirsch_stoer {
-
-public:
-
-    typedef State state_type;
-    typedef Value value_type;
-    typedef Deriv deriv_type;
-    typedef Time time_type;
-    typedef Algebra algebra_type;
-    typedef Operations operations_type;
-    typedef Resizer resizer_type;
-#ifndef DOXYGEN_SKIP
-    typedef state_wrapper< state_type > wrapped_state_type;
-    typedef state_wrapper< deriv_type > wrapped_deriv_type;
-    typedef controlled_stepper_tag stepper_category;
-
-    typedef bulirsch_stoer< State , Value , Deriv , Time , Algebra , Operations , Resizer > controlled_error_bs_type;
-
-    typedef typename inverse_time< time_type >::type inv_time_type;
-
-    typedef std::vector< value_type > value_vector;
-    typedef std::vector< time_type > time_vector;
-    typedef std::vector< inv_time_type > inv_time_vector;  //should be 1/time_type for boost.units
-    typedef std::vector< value_vector > value_matrix;
-    typedef std::vector< size_t > int_vector;
-    typedef std::vector< wrapped_state_type > state_table_type;
-#endif //DOXYGEN_SKIP
-    const static size_t m_k_max = 8;
-
-    bulirsch_stoer(
-        value_type eps_abs = 1E-6 , value_type eps_rel = 1E-6 ,
-        value_type factor_x = 1.0 , value_type factor_dxdt = 1.0 ,
-        time_type max_dt = static_cast<time_type>(0))
-        : m_error_checker( eps_abs , eps_rel , factor_x, factor_dxdt ) , m_midpoint() ,
-          m_last_step_rejected( false ) , m_first( true ) ,
-          m_dt_last(static_cast<time_type>(-1)) ,    // !!! patched !!!
-          m_max_dt(max_dt) ,
-          m_interval_sequence( m_k_max+1 ) ,
-          m_coeff( m_k_max+1 ) ,
-          m_cost( m_k_max+1 ) ,
-          m_facmin_table( m_k_max+1 ) ,
-          m_table( m_k_max ) ,
-          STEPFAC1( 0.65 ) , STEPFAC2( 0.94 ) , STEPFAC3( 0.02 ) , STEPFAC4( 4.0 ) , KFAC1( 0.8 ) , KFAC2( 0.9 )
-    {
-        BOOST_USING_STD_MIN();
-        BOOST_USING_STD_MAX();
-        /* initialize sequence of stage numbers and work */
-        for( unsigned short i = 0; i < m_k_max+1; i++ )
-        {
-            m_interval_sequence[i] = 2 * (i+1);
-            if( i == 0 )
-                m_cost[i] = m_interval_sequence[i];
-            else
-                m_cost[i] = m_cost[i-1] + m_interval_sequence[i];
-            m_coeff[i].resize(i);
-            m_facmin_table[i] = pow BOOST_PREVENT_MACRO_SUBSTITUTION( STEPFAC3 , static_cast< value_type >(1) / static_cast< value_type >( 2*i+1 ) );
-            for( size_t k = 0 ; k < i ; ++k  )
-            {
-                const value_type r = static_cast< value_type >( m_interval_sequence[i] ) / static_cast< value_type >( m_interval_sequence[k] );
-                m_coeff[i][k] = 1.0 / ( r*r - static_cast< value_type >( 1.0 ) ); // coefficients for extrapolation
-            }
-        }
-        reset();
-    }
-
-
-    /*
-     * Version 1 : try_step( sys , x , t , dt )
-     *
-     * The overloads are needed to solve the forwarding problem
-     */
-    template< class System , class StateInOut >
-    controlled_step_result try_step( System system , StateInOut &x , time_type &t , time_type &dt )
-    {
-        return try_step_v1( system , x , t, dt );
-    }
-
-    /**
-     * \brief Second version to solve the forwarding problem, can be used with Boost.Range as StateInOut.
-     */
-    template< class System , class StateInOut >
-    controlled_step_result try_step( System system , const StateInOut &x , time_type &t , time_type &dt )
-    {
-        return try_step_v1( system , x , t, dt );
-    }
-
-    /*
-     * Version 2 : try_step( sys , x , dxdt , t , dt )
-     *
-     * this version does not solve the forwarding problem, boost.range can not be used
-     */
-    template< class System , class StateInOut , class DerivIn >
-    controlled_step_result try_step( System system , StateInOut &x , const DerivIn &dxdt , time_type &t , time_type &dt )
-    {
-        m_xnew_resizer.adjust_size( x , detail::bind( &controlled_error_bs_type::template resize_m_xnew< StateInOut > , detail::ref( *this ) , detail::_1 ) );
-        controlled_step_result res = try_step( system , x , dxdt , t , m_xnew.m_v , dt );
-        if( res == success )
-        {
-            boost::numeric::odeint::copy( m_xnew.m_v , x );
-        }
-        return res;
-    }
-
-    /*
-     * Version 3 : try_step( sys , in , t , out , dt )
-     *
-     * this version does not solve the forwarding problem, boost.range can not be used
-     */
-    template< class System , class StateIn , class StateOut >
-    typename boost::disable_if< boost::is_same< StateIn , time_type > , controlled_step_result >::type
-    try_step( System system , const StateIn &in , time_type &t , StateOut &out , time_type &dt )
-    {
-        typename odeint::unwrap_reference< System >::type &sys = system;
-        m_dxdt_resizer.adjust_size( in , detail::bind( &controlled_error_bs_type::template resize_m_dxdt< StateIn > , detail::ref( *this ) , detail::_1 ) );
-        sys( in , m_dxdt.m_v , t );
-        return try_step( system , in , m_dxdt.m_v , t , out , dt );
-    }
-
-
-    /*
-     * Full version : try_step( sys , in , dxdt_in , t , out , dt )
-     *
-     * contains the actual implementation
-     */
-    template< class System , class StateIn , class DerivIn , class StateOut >
-    controlled_step_result try_step( System system , const StateIn &in , const DerivIn &dxdt , time_type &t , StateOut &out , time_type &dt )
-    {
-        if( m_max_dt != static_cast<time_type>(0) && detail::less_with_sign(m_max_dt, dt, dt) )
-        {
-            // given step size is bigger then max_dt
-            // set limit and return fail
-            dt = m_max_dt;
-            return fail;
-        }
-
-        BOOST_USING_STD_MIN();
-        BOOST_USING_STD_MAX();
-
-        static const value_type val1( 1.0 );
-
-        if( m_resizer.adjust_size( in , detail::bind( &controlled_error_bs_type::template resize_impl< StateIn > , detail::ref( *this ) , detail::_1 ) ) )
-        {
-            reset(); // system resized -> reset
-        }
-
-        if( dt != m_dt_last )
-        {
-            reset(); // step size changed from outside -> reset
-        }
-
-        bool reject( true );
-
-        time_vector h_opt( m_k_max+1 );
-        inv_time_vector work( m_k_max+1 );
-
-        time_type new_h = dt;
-
-        /* m_current_k_opt is the estimated current optimal stage number */
-        for( size_t k = 0 ; k <= m_current_k_opt+1 ; k++ )
-        {
-            /* the stage counts are stored in m_interval_sequence */
-            m_midpoint.set_steps( m_interval_sequence[k] );
-            if( k == 0 )
-            {
-                m_midpoint.do_step( system , in , dxdt , t , out , dt );
-                /* the first step, nothing more to do */
-            }
-            else
-            {
-                m_midpoint.do_step( system , in , dxdt , t , m_table[k-1].m_v , dt );
-                extrapolate( k , m_table , m_coeff , out );
-                // get error estimate
-                m_algebra.for_each3( m_err.m_v , out , m_table[0].m_v ,
-                                     typename operations_type::template scale_sum2< value_type , value_type >( val1 , -val1 ) );
-                const value_type error = m_error_checker.error( m_algebra , in , dxdt , m_err.m_v , dt );
-                h_opt[k] = calc_h_opt( dt , error , k );
-                work[k] = static_cast<value_type>( m_cost[k] ) / h_opt[k];
-
-                if( (k == m_current_k_opt-1) || m_first )
-                { // convergence before k_opt ?
-                    if( error < 1.0 )
-                    {
-                        //convergence
-                        reject = false;
-                        if( (work[k] < KFAC2*work[k-1]) || (m_current_k_opt <= 2) )
-                        {
-                            // leave order as is (except we were in first round)
-                            m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max)-1 , max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(k)+1 ) );
-                            new_h = h_opt[k];
-                            new_h *= static_cast<value_type>( m_cost[k+1] ) / static_cast<value_type>( m_cost[k] );
-                        } else {
-                            m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max)-1 , max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(k) ) );
-                            new_h = h_opt[k];
-                        }
-                        break;
-                    }
-                    else if( should_reject( error , k ) && !m_first )
-                    {
-                        reject = true;
-                        new_h = h_opt[k];
-                        break;
-                    }
-                }
-                if( k == m_current_k_opt )
-                { // convergence at k_opt ?
-                    if( error < 1.0 )
-                    {
-                        //convergence
-                        reject = false;
-                        if( (work[k-1] < KFAC2*work[k]) )
-                        {
-                            m_current_k_opt = max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(m_current_k_opt)-1 );
-                            new_h = h_opt[m_current_k_opt];
-                        }
-                        else if( (work[k] < KFAC2*work[k-1]) && !m_last_step_rejected )
-                        {
-                            m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max-1) , static_cast<int>(m_current_k_opt)+1 );
-                            new_h = h_opt[k];
-                            new_h *= static_cast<value_type>(m_cost[m_current_k_opt])/static_cast<value_type>(m_cost[k]);
-                        } else
-                            new_h = h_opt[m_current_k_opt];
-                        break;
-                    }
-                    else if( should_reject( error , k ) )
-                    {
-                        reject = true;
-                        new_h = h_opt[m_current_k_opt];
-                        break;
-                    }
-                }
-                if( k == m_current_k_opt+1 )
-                { // convergence at k_opt+1 ?
-                    if( error < 1.0 )
-                    {   //convergence
-                        reject = false;
-                        if( work[k-2] < KFAC2*work[k-1] )
-                            m_current_k_opt = max BOOST_PREVENT_MACRO_SUBSTITUTION( 2 , static_cast<int>(m_current_k_opt)-1 );
-                        if( (work[k] < KFAC2*work[m_current_k_opt]) && !m_last_step_rejected )
-                            m_current_k_opt = min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<int>(m_k_max)-1 , static_cast<int>(k) );
-                        new_h = h_opt[m_current_k_opt];
-                    } else
-                    {
-                        reject = true;
-                        new_h = h_opt[m_current_k_opt];
-                    }
-                    break;
-                }
-            }
-        }
-
-        if( !reject )
-        {
-            t += dt;
-        }
-
-        if( !m_last_step_rejected || boost::numeric::odeint::detail::less_with_sign(new_h, dt, dt) )
-        {
-            // limit step size
-            if( m_max_dt != static_cast<time_type>(0) )
-            {
-                new_h = detail::min_abs(m_max_dt, new_h);
-            }
-            m_dt_last = new_h;
-            dt = new_h;
-        }
-
-        m_last_step_rejected = reject;
-        m_first = false;
-
-        if( reject )
-            return fail;
-        else
-            return success;
-    }
-
-    /** \brief Resets the internal state of the stepper */
-    void reset()
-    {
-        m_first = true;
-        m_last_step_rejected = false;
-        // crude estimate of optimal order
-        m_current_k_opt = 4;
-        /* no calculation because log10 might not exist for value_type!
-        const value_type logfact( -log10( max BOOST_PREVENT_MACRO_SUBSTITUTION( eps_rel , static_cast< value_type >(1.0E-12) ) ) * 0.6 + 0.5 );
-        m_current_k_opt = max BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<value_type>( 1 ) , min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<value_type>( m_k_max-1 ) , logfact ));
-        */
-    }
-
-
-    /* Resizer methods */
-
-    template< class StateIn >
-    void adjust_size( const StateIn &x )
-    {
-        resize_m_dxdt( x );
-        resize_m_xnew( x );
-        resize_impl( x );
-        m_midpoint.adjust_size( x );
-    }
-
-
-private:
-
-    template< class StateIn >
-    bool resize_m_dxdt( const StateIn &x )
-    {
-        return adjust_size_by_resizeability( m_dxdt , x , typename is_resizeable<deriv_type>::type() );
-    }
-
-    template< class StateIn >
-    bool resize_m_xnew( const StateIn &x )
-    {
-        return adjust_size_by_resizeability( m_xnew , x , typename is_resizeable<state_type>::type() );
-    }
-
-    template< class StateIn >
-    bool resize_impl( const StateIn &x )
-    {
-        bool resized( false );
-        for( size_t i = 0 ; i < m_k_max ; ++i )
-            resized |= adjust_size_by_resizeability( m_table[i] , x , typename is_resizeable<state_type>::type() );
-        resized |= adjust_size_by_resizeability( m_err , x , typename is_resizeable<state_type>::type() );
-        return resized;
-    }
-
-
-    template< class System , class StateInOut >
-    controlled_step_result try_step_v1( System system , StateInOut &x , time_type &t , time_type &dt )
-    {
-        typename odeint::unwrap_reference< System >::type &sys = system;
-        m_dxdt_resizer.adjust_size( x , detail::bind( &controlled_error_bs_type::template resize_m_dxdt< StateInOut > , detail::ref( *this ) , detail::_1 ) );
-        sys( x , m_dxdt.m_v ,t );
-        return try_step( system , x , m_dxdt.m_v , t , dt );
-    }
-
-
-    template< class StateInOut >
-    void extrapolate( size_t k , state_table_type &table , const value_matrix &coeff , StateInOut &xest )
-    /* polynomial extrapolation, see http://www.nr.com/webnotes/nr3web21.pdf
-       uses the obtained intermediate results to extrapolate to dt->0 
-    */
-    {
-        static const value_type val1 = static_cast< value_type >( 1.0 );
-        for( int j=k-1 ; j>0 ; --j )
-        {
-            m_algebra.for_each3( table[j-1].m_v , table[j].m_v , table[j-1].m_v ,
-                                 typename operations_type::template scale_sum2< value_type , value_type >( val1 + coeff[k][j] , -coeff[k][j] ) );
-        }
-        m_algebra.for_each3( xest , table[0].m_v , xest ,
-                             typename operations_type::template scale_sum2< value_type , value_type >( val1 + coeff[k][0] , -coeff[k][0]) );
-    }
-
-    time_type calc_h_opt( time_type h , value_type error , size_t k ) const
-    /* calculates the optimal step size for a given error and stage number */
-    {
-        BOOST_USING_STD_MIN();
-        BOOST_USING_STD_MAX();
-        using std::pow;
-        value_type expo( 1.0/(2*k+1) );
-        value_type facmin = m_facmin_table[k];
-        value_type fac;
-        if (error == 0.0)
-            fac=1.0/facmin;
-        else
-        {
-            fac = STEPFAC2 / pow BOOST_PREVENT_MACRO_SUBSTITUTION( error / STEPFAC1 , expo );
-            fac = max BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<value_type>(facmin/STEPFAC4) , min BOOST_PREVENT_MACRO_SUBSTITUTION( static_cast<value_type>(1.0/facmin) , fac ) );
-        }
-        return h*fac;
-    }
-
-    controlled_step_result set_k_opt( size_t k , const inv_time_vector &work , const time_vector &h_opt , time_type &dt )
-    /* calculates the optimal stage number */
-    {
-        if( k == 1 )
-        {
-            m_current_k_opt = 2;
-            return success;
-        }
-        if( (work[k-1] < KFAC1*work[k]) || (k == m_k_max) )
-        {   // order decrease
-            m_current_k_opt = k-1;
-            dt = h_opt[ m_current_k_opt ];
-            return success;
-        }
-        else if( (work[k] < KFAC2*work[k-1]) || m_last_step_rejected || (k == m_k_max-1) )
-        {   // same order - also do this if last step got rejected
-            m_current_k_opt = k;
-            dt = h_opt[ m_current_k_opt ];
-            return success;
-        }
-        else
-        {   // order increase - only if last step was not rejected
-            m_current_k_opt = k+1;
-            dt = h_opt[ m_current_k_opt-1 ] * m_cost[ m_current_k_opt ] / m_cost[ m_current_k_opt-1 ] ;
-            return success;
-        }
-    }
-
-    bool in_convergence_window( size_t k ) const
-    {
-        if( (k == m_current_k_opt-1) && !m_last_step_rejected )
-            return true; // decrease stepsize only if last step was not rejected
-        return ( (k == m_current_k_opt) || (k == m_current_k_opt+1) );
-    }
-
-    bool should_reject( value_type error , size_t k ) const
-    {
-        if( k == m_current_k_opt-1 )
-        {
-            const value_type d = m_interval_sequence[m_current_k_opt] * m_interval_sequence[m_current_k_opt+1] /
-                (m_interval_sequence[0]*m_interval_sequence[0]);
-            //step will fail, criterion 17.3.17 in NR
-            return ( error > d*d );
-        }
-        else if( k == m_current_k_opt )
-        {
-            const value_type d = m_interval_sequence[m_current_k_opt] / m_interval_sequence[0];
-            return ( error > d*d );
-        } else
-            return error > 1.0;
-    }
-
-    default_error_checker< value_type, algebra_type , operations_type > m_error_checker;
-    modified_midpoint< state_type , value_type , deriv_type , time_type , algebra_type , operations_type , resizer_type > m_midpoint;
-
-    bool m_last_step_rejected;
-    bool m_first;
-
-    time_type m_dt_last;
-    time_type m_t_last;
-    time_type m_max_dt;
-
-    size_t m_current_k_opt;
-
-    algebra_type m_algebra;
-
-    resizer_type m_dxdt_resizer;
-    resizer_type m_xnew_resizer;
-    resizer_type m_resizer;
-
-    wrapped_state_type m_xnew;
-    wrapped_state_type m_err;
-    wrapped_deriv_type m_dxdt;
-
-    int_vector m_interval_sequence; // stores the successive interval counts
-    value_matrix m_coeff;
-    int_vector m_cost; // costs for interval count
-    value_vector m_facmin_table; // for precomputed facmin to save pow calls
-
-    state_table_type m_table; // sequence of states for extrapolation
-
-    value_type STEPFAC1 , STEPFAC2 , STEPFAC3 , STEPFAC4 , KFAC1 , KFAC2;
-};
-
-
-/******** DOXYGEN ********/
-/**
- * \class bulirsch_stoer
- * \brief The Bulirsch-Stoer algorithm.
- * 
- * The Bulirsch-Stoer is a controlled stepper that adjusts both step size
- * and order of the method. The algorithm uses the modified midpoint and
- * a polynomial extrapolation compute the solution.
- *
- * \tparam State The state type.
- * \tparam Value The value type.
- * \tparam Deriv The type representing the time derivative of the state.
- * \tparam Time The time representing the independent variable - the time.
- * \tparam Algebra The algebra type.
- * \tparam Operations The operations type.
- * \tparam Resizer The resizer policy type.
- */
-
-    /**
-     * \fn bulirsch_stoer::bulirsch_stoer( value_type eps_abs , value_type eps_rel , value_type factor_x , value_type factor_dxdt )
-     * \brief Constructs the bulirsch_stoer class, including initialization of 
-     * the error bounds.
-     *
-     * \param eps_abs Absolute tolerance level.
-     * \param eps_rel Relative tolerance level.
-     * \param factor_x Factor for the weight of the state.
-     * \param factor_dxdt Factor for the weight of the derivative.
-     */
-
-    /**
-     * \fn bulirsch_stoer::try_step( System system , StateInOut &x , time_type &t , time_type &dt )
-     * \brief Tries to perform one step.
-     *
-     * This method tries to do one step with step size dt. If the error estimate
-     * is to large, the step is rejected and the method returns fail and the 
-     * step size dt is reduced. If the error estimate is acceptably small, the
-     * step is performed, success is returned and dt might be increased to make 
-     * the steps as large as possible. This method also updates t if a step is
-     * performed. Also, the internal order of the stepper is adjusted if required.
-     *
-     * \param system The system function to solve, hence the r.h.s. of the ODE. 
-     * It must fulfill the Simple System concept.
-     * \param x The state of the ODE which should be solved. Overwritten if 
-     * the step is successful.
-     * \param t The value of the time. Updated if the step is successful.
-     * \param dt The step size. Updated.
-     * \return success if the step was accepted, fail otherwise.
-     */
-
-    /**
-     * \fn bulirsch_stoer::try_step( System system , StateInOut &x , const DerivIn &dxdt , time_type &t , time_type &dt )
-     * \brief Tries to perform one step.
-     *
-     * This method tries to do one step with step size dt. If the error estimate
-     * is to large, the step is rejected and the method returns fail and the 
-     * step size dt is reduced. If the error estimate is acceptably small, the
-     * step is performed, success is returned and dt might be increased to make 
-     * the steps as large as possible. This method also updates t if a step is
-     * performed. Also, the internal order of the stepper is adjusted if required.
-     *
-     * \param system The system function to solve, hence the r.h.s. of the ODE. 
-     * It must fulfill the Simple System concept.
-     * \param x The state of the ODE which should be solved. Overwritten if 
-     * the step is successful.
-     * \param dxdt The derivative of state.
-     * \param t The value of the time. Updated if the step is successful.
-     * \param dt The step size. Updated.
-     * \return success if the step was accepted, fail otherwise.
-     */
-
-    /**
-     * \fn bulirsch_stoer::try_step( System system , const StateIn &in , time_type &t , StateOut &out , time_type &dt )
-     * \brief Tries to perform one step.
-     *
-     * \note This method is disabled if state_type=time_type to avoid ambiguity.
-     *
-     * This method tries to do one step with step size dt. If the error estimate
-     * is to large, the step is rejected and the method returns fail and the 
-     * step size dt is reduced. If the error estimate is acceptably small, the
-     * step is performed, success is returned and dt might be increased to make 
-     * the steps as large as possible. This method also updates t if a step is
-     * performed. Also, the internal order of the stepper is adjusted if required.
-     *
-     * \param system The system function to solve, hence the r.h.s. of the ODE. 
-     * It must fulfill the Simple System concept.
-     * \param in The state of the ODE which should be solved.
-     * \param t The value of the time. Updated if the step is successful.
-     * \param out Used to store the result of the step.
-     * \param dt The step size. Updated.
-     * \return success if the step was accepted, fail otherwise.
-     */
-
-
-    /**
-     * \fn bulirsch_stoer::try_step( System system , const StateIn &in , const DerivIn &dxdt , time_type &t , StateOut &out , time_type &dt )
-     * \brief Tries to perform one step.
-     *
-     * This method tries to do one step with step size dt. If the error estimate
-     * is to large, the step is rejected and the method returns fail and the 
-     * step size dt is reduced. If the error estimate is acceptably small, the
-     * step is performed, success is returned and dt might be increased to make 
-     * the steps as large as possible. This method also updates t if a step is
-     * performed. Also, the internal order of the stepper is adjusted if required.
-     *
-     * \param system The system function to solve, hence the r.h.s. of the ODE. 
-     * It must fulfill the Simple System concept.
-     * \param in The state of the ODE which should be solved.
-     * \param dxdt The derivative of state.
-     * \param t The value of the time. Updated if the step is successful.
-     * \param out Used to store the result of the step.
-     * \param dt The step size. Updated.
-     * \return success if the step was accepted, fail otherwise.
-     */
-
-
-    /**
-     * \fn bulirsch_stoer::adjust_size( const StateIn &x )
-     * \brief Adjust the size of all temporaries in the stepper manually.
-     * \param x A state from which the size of the temporaries to be resized is deduced.
-     */
-
-}
-}
-}
-
-#endif // BOOST_NUMERIC_ODEINT_STEPPER_BULIRSCH_STOER_HPP_INCLUDED
-
-#endif // USE_BULRISCH_STOER_PATCH
diff --git a/src/ublas_types.h b/src/ublas_types.h
deleted file mode 100644
index 750b7056..00000000
--- a/src/ublas_types.h
+++ /dev/null
@@ -1,119 +0,0 @@
-// [[Rcpp::plugins(cpp14)]]
-
-#pragma once
-#ifndef UBLAS_TYPES_H_INCLUDED
-#define UBLAS_TYPES_H_INCLUDED
-
-#include "config.h"
-#include <RcppCommon.h>
-#include <boost/numeric/ublas/vector.hpp>
-#include <boost/numeric/ublas/matrix.hpp>
-
-
-namespace ublas = boost::numeric::ublas;
-
-
-template <typename T> using vector_t = ublas::vector<T>;
-template <typename T> using matrix_t = ublas::matrix<T>;
-
-
-// forward declarations Rcpp <-> boost::numeric::ublas
-namespace Rcpp {
-
-  namespace traits {
-
-    template <typename T> SEXP wrap(const vector_t<T>&);
-    template <typename T> SEXP wrap(const matrix_t<T>&);
-
-    template <typename T> vector_t<T> as(SEXP);
-    template <typename T> matrix_t<T> as(SEXP);
-
-    template <typename T> class Exporter<vector_t<T>>;
-    template <typename T> class Exporter<matrix_t<T>>;
-
-  }
-
-}
-
-
-#include <Rcpp.h>
-
-
-namespace Rcpp {
-
-  namespace traits {
-
-    template <typename T> inline SEXP wrap(const vector_t<T>& obj) {
-      const int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
-      return Rcpp::Vector<RTYPE>(obj.begin(), obj.end());
-    }
-
-
-    template <typename T> inline SEXP wrap(const matrix_t<T>& obj) {
-      const size_t nr = static_cast<size_t>(obj.size1());
-      const size_t nc = static_cast<size_t>(obj.size2());
-      const int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
-      Rcpp::Matrix<RTYPE> rmat(nr, nc);
-      for (size_t i = 0; i < nr; ++i) {
-        for (size_t j = 0; j < nc; ++j) {
-          rmat(i, j) = obj(i, j);
-        }
-      }
-      return rmat;
-    }
-
-
-    template<typename T>
-    class Exporter<vector_t<T>>
-    {
-    private:
-      static constexpr int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
-      Rcpp::Vector<RTYPE> rvec;
-
-    public:
-      Exporter(SEXP x) : rvec(x) {
-        if (TYPEOF(x) != RTYPE) {
-          throw std::invalid_argument("Wrong R type for mapped 1D array");
-        }
-      }
-
-      vector_t<T> get() {
-        vector_t<T> x(rvec.size());
-        std::copy(rvec.begin(), rvec.end(), x.begin());
-        return x;
-      }
-    };
-
-
-    template<typename T>
-    class Exporter<matrix_t<T>>
-    {
-    private:
-      static constexpr int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
-      Rcpp::Matrix<RTYPE> rmat;
-
-    public:
-      Exporter(SEXP x) : rmat(x) {
-        if (TYPEOF(x) != RTYPE) {
-          throw std::invalid_argument("Wrong R type for mapped 2D array");
-        }
-      }
-
-      matrix_t<T> get() {
-        const size_t nr = static_cast<size_t>(rmat.rows());
-        const size_t nc = static_cast<size_t>(rmat.cols());
-        matrix_t<T> x(nr, nc);
-        for (size_t i = 0; i < nr; ++i) {
-          for (size_t j = 0; j < nc; ++j) {
-            x(i, j) = rmat(i, j);
-          }
-        }
-        return x;
-      }
-    };
-
-  }
-
-}
-
-#endif
diff --git a/tests/testthat/test-DAISIE_ML1.R b/tests/testthat/test-DAISIE_ML1.R
index 4aa7def5..58c56872 100644
--- a/tests/testthat/test-DAISIE_ML1.R
+++ b/tests/testthat/test-DAISIE_ML1.R
@@ -10,7 +10,6 @@ test_that("use", {
   idparsopt <- 1:5
   parsfix <- NULL
   idparsfix <- NULL
-  invisible(capture.output(
     tested_MLE <- DAISIE_ML1(
       datalist = datalist,
       initparsopt = initparsopt,
@@ -23,7 +22,6 @@ test_that("use", {
       res = 15,
       tolint = c(0.1, 0.01)
     )
-  ))
   expected_MLE <- data.frame(
     lambda_c = 3.689104200780465,
     mu = 4.31030299415995,
@@ -48,7 +46,7 @@ test_that("abuse", {
   parsfix <- NULL
   idparsfix <- NULL
   expect_error(
-    DAISIE:::DAISIE_ML1(
+    DAISIE_ML1(
       datalist = "nonsense",
       initparsopt = initparsopt,
       idparsopt = idparsopt,
diff --git a/tests/testthat/test-DAISIE_ML2.R b/tests/testthat/test-DAISIE_ML2.R
index 0d64954e..58af6660 100644
--- a/tests/testthat/test-DAISIE_ML2.R
+++ b/tests/testthat/test-DAISIE_ML2.R
@@ -2,7 +2,6 @@ test_that("use", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
   skip_on_cran()
   utils::data(Macaronesia_datalist, package = "DAISIE")
-  invisible(capture.output(
     tested_MLE <- DAISIE_ML2(
       datalist = Macaronesia_datalist,
       initparsopt = c(
@@ -22,9 +21,9 @@ test_that("use", {
       idparsfix = c(1, 3),
       tol = c(0.01, 0.1, 0.001),
       res = 15,
-      tolint = c(0.1, 0.01)
+      tolint = c(0.1, 0.01),
+      verbose = 0
     )
-  ))
   expected_MLE <- data.frame(
     lambda_c = c(0.0,
                  0.315015693879739,
@@ -60,7 +59,7 @@ test_that("use", {
 test_that("abuse", {
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
   skip_on_cran()
-  expect_error(tested_MLE <- DAISIE:::DAISIE_ML2(
+  expect_error(tested_MLE <- DAISIE_ML2(
     datalist = "nonsense",
     initparsopt = c(
       1.053151832,
diff --git a/tests/testthat/test-DAISIE_ML4.R b/tests/testthat/test-DAISIE_ML4.R
index 435ec184..f5aec0ab 100644
--- a/tests/testthat/test-DAISIE_ML4.R
+++ b/tests/testthat/test-DAISIE_ML4.R
@@ -7,6 +7,7 @@ test_that("DAISIE_ML4 is silent and produces correct output", {
     idparsopt = 1:6,
     parsfix = NULL,
     idparsfix = NULL,
+    verbose = 0,
     methode = 'lsodes',
     optimmethod = 'simplex',
     CS_version = create_CS_version(model = 2,
diff --git a/tests/testthat/test-DAISIE_MW_ML.R b/tests/testthat/test-DAISIE_MW_ML.R
index 23b55798..fd52d34c 100644
--- a/tests/testthat/test-DAISIE_MW_ML.R
+++ b/tests/testthat/test-DAISIE_MW_ML.R
@@ -7,7 +7,7 @@ test_that("DAISIE_MW_ML produces correct output", {
   utils::data(archipelagos41)
 
   invisible(capture.output(
-    M19_tested <- DAISIE::DAISIE_MW_ML(
+    M19_tested <- DAISIE_MW_ML(
       datalist = archipelagos41,
       initparsopt = c(
         0.040073803,
@@ -81,7 +81,7 @@ test_that("DAISIE_MW_ML produces correct output when in parallel", {
   )
 
   invisible(capture.output(
-    M19_computation <- DAISIE::DAISIE_MW_ML(
+    M19_computation <- DAISIE_MW_ML(
       datalist = archipelagos41,
       initparsopt = c(
         0.040073803,
diff --git a/tests/testthat/test-DAISIE_ONEcolonist.R b/tests/testthat/test-DAISIE_ONEcolonist.R
index c0437b11..86319784 100644
--- a/tests/testthat/test-DAISIE_ONEcolonist.R
+++ b/tests/testthat/test-DAISIE_ONEcolonist.R
@@ -7,7 +7,7 @@ test_that("DAISIE_ONEcolonist works on an oceanic DAISIE_sim_core", {
   imm_rate <- 1.0
   ana_rate <- 1.0
   set.seed(1)
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -17,7 +17,7 @@ test_that("DAISIE_ONEcolonist works on an oceanic DAISIE_sim_core", {
     island_gradient_angle = 0)
   hyper_pars <- create_hyper_pars(d = 0, x = 0)
   nonoceanic_pars <- c(0, 0)
-  sim <- DAISIE:::DAISIE_sim_core_cr(
+  sim <- DAISIE_sim_core_cr(
     time = sim_time,
     mainland_n = n_mainland_species,
     pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate),
@@ -51,7 +51,7 @@ test_that("DAISIE_ONEcolonist works on an oceanic DAISIE_sim_core", {
   init_nonend_spec <- sim$init_nonend_spec
   init_end_spec <- sim$init_end_spec
   carrying_capacity <- sim$carrying_capacity
-  result <- DAISIE:::DAISIE_ONEcolonist(
+  result <- DAISIE_ONEcolonist(
     time = sim_time,
     island_spec = island_spec,
     stt_table = stt_table
@@ -77,7 +77,7 @@ test_that("DAISIE_ONEcolonist works with >=2 cladogenetic with same ancestor", {
   carr_cap <- 4
   imm_rate <- 1
   ana_rate <- 0.000001
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -87,7 +87,7 @@ test_that("DAISIE_ONEcolonist works with >=2 cladogenetic with same ancestor", {
     island_gradient_angle = 0)
   hyper_pars <- create_hyper_pars(d = 0, x = 0)
   nonoceanic_pars <- c(0, 0)
-  expect_silent(out <- DAISIE:::DAISIE_sim_core_cr(
+  expect_silent(out <- DAISIE_sim_core_cr(
     time = sim_time,
     mainland_n = n_mainland_species,
     pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate),
@@ -108,7 +108,7 @@ test_that("DAISIE_ONEcolonist works with >=2 anagenetic with same ancestor", {
   carr_cap <- 4
   imm_rate <- 1
   ana_rate <- 2
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -118,7 +118,7 @@ test_that("DAISIE_ONEcolonist works with >=2 anagenetic with same ancestor", {
     island_gradient_angle = 0)
   hyper_pars <- create_hyper_pars(d = 0, x = 0)
   nonoceanic_pars <- c(0, 0)
-  expect_silent(out <- DAISIE:::DAISIE_sim_core_cr(
+  expect_silent(out <- DAISIE_sim_core_cr(
     time = sim_time,
     mainland_n = n_mainland_species,
     pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate),
@@ -137,7 +137,7 @@ test_that("DAISIE_ONEcolonist works with >=2 nonendemic with same ancestor", {
   carr_cap <- 4
   imm_rate <- 3
   ana_rate <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -147,7 +147,7 @@ test_that("DAISIE_ONEcolonist works with >=2 nonendemic with same ancestor", {
     island_gradient_angle = 0)
   hyper_pars <- create_hyper_pars(d = 0, x = 0)
   nonoceanic_pars <- c(0, 0)
-  expect_silent(out <- DAISIE:::DAISIE_sim_core_cr(
+  expect_silent(out <- DAISIE_sim_core_cr(
     time = sim_time,
     mainland_n = n_mainland_species,
     pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate),
@@ -185,7 +185,7 @@ test_that("DAISIE_ONEcolonist stac and brts works for single colonist", {
     "Anagenetic_origin"
   )
   stt_table <- NULL
-  result <- DAISIE:::DAISIE_ONEcolonist(
+  result <- DAISIE_ONEcolonist(
     time = sim_time,
     island_spec = island_spec,
     stt_table = stt_table
@@ -221,7 +221,7 @@ test_that("DAISIE_ONEcolonist stac and brts works for 1 nonendemic colonist", {
     "Anagenetic_origin"
   )
   stt_table <- NULL
-  result <- DAISIE:::DAISIE_ONEcolonist(
+  result <- DAISIE_ONEcolonist(
     time = sim_time,
     island_spec = island_spec,
     stt_table = stt_table
@@ -266,7 +266,7 @@ test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic colonists,
     "Anagenetic_origin"
   )
   stt_table <- NULL
-  result <- DAISIE:::DAISIE_ONEcolonist(
+  result <- DAISIE_ONEcolonist(
     time = sim_time,
     island_spec = island_spec,
     stt_table = stt_table
@@ -312,7 +312,7 @@ test_that("DAISIE_ONEcolonist stac and brts works for 3 endemic colonists", {
     "Anagenetic_origin"
   )
   stt_table <- NULL
-  result <- DAISIE:::DAISIE_ONEcolonist(
+  result <- DAISIE_ONEcolonist(
     time = sim_time,
     island_spec = island_spec,
     stt_table = stt_table
@@ -380,7 +380,7 @@ test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic clades", {
     "Anagenetic_origin"
   )
   stt_table <- NULL
-  result <- DAISIE:::DAISIE_ONEcolonist(
+  result <- DAISIE_ONEcolonist(
     time = sim_time,
     island_spec = island_spec,
     stt_table = stt_table
@@ -461,7 +461,7 @@ test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic clades,
     "Anagenetic_origin"
   )
   stt_table <- NULL
-  result <- DAISIE:::DAISIE_ONEcolonist(
+  result <- DAISIE_ONEcolonist(
     time = sim_time,
     island_spec = island_spec,
     stt_table = stt_table
@@ -548,7 +548,7 @@ test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic clades,
     "Anagenetic_origin"
   )
   stt_table <- NULL
-  result <- DAISIE:::DAISIE_ONEcolonist(
+  result <- DAISIE_ONEcolonist(
     time = sim_time,
     island_spec = island_spec,
     stt_table = stt_table
@@ -597,7 +597,7 @@ test_that("DAISIE_ONEcolonist stac and brts works for 1 anagenetic clade from
             imm_rate <- 1.0
             ana_rate <- 0
             set.seed(3)
-            area_pars <- DAISIE::create_area_pars(
+            area_pars <- create_area_pars(
               max_area = 1,
               current_area = 1,
               proportional_peak_t = 0,
@@ -607,7 +607,7 @@ test_that("DAISIE_ONEcolonist stac and brts works for 1 anagenetic clade from
               island_gradient_angle = 0)
             hyper_pars <- create_hyper_pars(d = 0, x = 0)
             nonoceanic_pars <- c(0, 0)
-            result <- DAISIE:::DAISIE_sim_core_cr(
+            result <- DAISIE_sim_core_cr(
               time = sim_time,
               mainland_n = n_mainland_species,
               pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate),
diff --git a/tests/testthat/test-DAISIE_convert_to_classic_plot.R b/tests/testthat/test-DAISIE_convert_to_classic_plot.R
index 2cae9ca3..1ca8c389 100644
--- a/tests/testthat/test-DAISIE_convert_to_classic_plot.R
+++ b/tests/testthat/test-DAISIE_convert_to_classic_plot.R
@@ -8,7 +8,7 @@ test_that("abuse", {
 
 # test_that("use", {
 #   utils::data("islands_1type_1000reps", package = "DAISIE")
-#   simulation_outputs <- DAISIE::DAISIE_convert_to_classic_plot(
+#   simulation_outputs <- DAISIE_convert_to_classic_plot(
 #     islands_1type_1000reps
 #   )
 #   expect_true(is_simulation_outputs(simulation_outuputs))
diff --git a/tests/testthat/test-DAISIE_format_CS.R b/tests/testthat/test-DAISIE_format_CS.R
index f8f54722..ba91e0a0 100644
--- a/tests/testthat/test-DAISIE_format_CS.R
+++ b/tests/testthat/test-DAISIE_format_CS.R
@@ -7,7 +7,7 @@ test_that("silent with empty island with correct output", {
   set.seed(1)
   island_replicates <- list()
   out <- list()
-  out[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  out[[1]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
@@ -25,7 +25,7 @@ test_that("silent with empty island with correct output", {
   )
   island_replicates[[1]] <- out
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
+    formatted_CS_sim <- DAISIE_format_CS(
     island_replicates = island_replicates,
     time = time,
     M = mainland_n,
@@ -54,13 +54,13 @@ test_that("silent with non-empty island with correct output", {
   set.seed(1)
   island_replicates <- list()
   out <- list()
-  out[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  out[[1]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
     nonoceanic_pars = c(0, 0),
     hyper_pars = create_hyper_pars(d = 0, x = 0),
-    area_pars = DAISIE::create_area_pars(
+    area_pars = create_area_pars(
       max_area = 1,
       current_area = 1,
       proportional_peak_t = 0,
@@ -71,7 +71,7 @@ test_that("silent with non-empty island with correct output", {
   )
   island_replicates[[1]] <- out
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS( # nolint
+    formatted_CS_sim <- DAISIE_format_CS( # nolint
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -106,13 +106,13 @@ test_that("output with empty island and verbose = TRUE", {
   set.seed(1)
   island_replicates <- list()
   out <- list()
-  out[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  out[[1]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
     nonoceanic_pars = c(0, 0),
     hyper_pars = create_hyper_pars(d = 0, x = 0),
-    area_pars = DAISIE::create_area_pars(
+    area_pars = create_area_pars(
       max_area = 1,
       current_area = 1,
       proportional_peak_t = 0,
@@ -123,7 +123,7 @@ test_that("output with empty island and verbose = TRUE", {
   )
   island_replicates[[1]] <- out
   expect_message(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
+    formatted_CS_sim <- DAISIE_format_CS(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -145,14 +145,14 @@ test_that("silent with non-empty 2 type island", {
   set.seed(1)
   island_replicates <- list()
   prop_type2_pool <- 0.4
-  island_replicates <- DAISIE:::DAISIE_sim_min_type2(
+  island_replicates <- DAISIE_sim_min_type2(
     time = total_time,
     M = M,
     pars = pars,
     replicates = replicates,
     prop_type2_pool = prop_type2_pool,
     hyper_pars = create_hyper_pars(d = 0, x = 0),
-    area_pars = DAISIE::create_area_pars(
+    area_pars = create_area_pars(
       max_area = 1,
       current_area = 1,
       proportional_peak_t = 0,
@@ -162,7 +162,7 @@ test_that("silent with non-empty 2 type island", {
       island_gradient_angle = 0),
     verbose = FALSE)
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
+    formatted_CS_sim <- DAISIE_format_CS(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -183,7 +183,7 @@ test_that("silent with non-empty 2 type island full stt", {
   set.seed(1)
   island_replicates <- list()
   prop_type2_pool <- 0.4
-  island_replicates <- DAISIE:::DAISIE_sim_min_type2(
+  island_replicates <- DAISIE_sim_min_type2(
     time = total_time,
     M = M,
     pars = pars,
@@ -191,7 +191,7 @@ test_that("silent with non-empty 2 type island full stt", {
     prop_type2_pool = prop_type2_pool,
     verbose = FALSE,
     hyper_pars = create_hyper_pars(d = 0, x = 0),
-    area_pars = DAISIE::create_area_pars(
+    area_pars = create_area_pars(
       max_area = 1,
       current_area = 1,
       proportional_peak_t = 0,
@@ -201,7 +201,7 @@ test_that("silent with non-empty 2 type island full stt", {
       island_gradient_angle = 0)
   )
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
+    formatted_CS_sim <- DAISIE_format_CS(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -212,7 +212,7 @@ test_that("silent with non-empty 2 type island full stt", {
 
 test_that("abuse", {
   expect_error(
-    DAISIE:::DAISIE_format_CS(
+    DAISIE_format_CS(
       island_replicates = "nonsense",
       time = "nonsense",
       M = "nonsense",
@@ -232,13 +232,13 @@ test_that("use full stt", {
   set.seed(1)
   island_replicates <- list()
   out <- list()
-  out[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  out[[1]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
     nonoceanic_pars = c(0, 0),
     hyper_pars = create_hyper_pars(d = 0, x = 0),
-    area_pars = DAISIE::create_area_pars(
+    area_pars = create_area_pars(
       max_area = 1,
       current_area = 1,
       proportional_peak_t = 0,
@@ -249,7 +249,7 @@ test_that("use full stt", {
   )
   island_replicates[[1]] <- out
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
+    formatted_CS_sim <- DAISIE_format_CS(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -333,21 +333,21 @@ test_that("use complete stt with ontogeny", {
   )
   hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
   nonoceanic_pars <- c(0, 0)
-  island_ontogeny = DAISIE:::translate_island_ontogeny("beta")
-  sea_level = DAISIE:::translate_sea_level("const")
-  peak <- DAISIE:::calc_peak(total_time = total_time,
+  island_ontogeny = translate_island_ontogeny("beta")
+  sea_level = translate_sea_level("const")
+  peak <- calc_peak(total_time = total_time,
                              area_pars = area_pars)
-  Amax <- DAISIE:::get_global_max_area(total_time = total_time,
+  Amax <- get_global_max_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
-  Amin <- DAISIE:::get_global_min_area(total_time = total_time,
+  Amin <- get_global_min_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
-  out[[1]] <- DAISIE:::DAISIE_sim_core_time_dep(
+  out[[1]] <- DAISIE_sim_core_time_dep(
     time = total_time,
     pars = pars,
     mainland_n = mainland_n,
@@ -363,7 +363,7 @@ test_that("use complete stt with ontogeny", {
   )
   island_replicates[[1]] <- out
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
+    formatted_CS_sim <- DAISIE_format_CS(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -417,7 +417,7 @@ test_that("full stt works with multiple replicates", {
   verbose <- FALSE
   sample_freq <- Inf
   set.seed(1)
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -430,7 +430,7 @@ test_that("full stt works with multiple replicates", {
   island_replicates <- list()
   island_replicates[[1]] <- island_replicates
   out <- list()
-  out[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  out[[1]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
@@ -438,7 +438,7 @@ test_that("full stt works with multiple replicates", {
     hyper_pars = hyper_pars,
     nonoceanic_pars = nonoceanic_pars
   )
-  out[[2]] <- DAISIE:::DAISIE_sim_core_cr(
+  out[[2]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
@@ -448,7 +448,7 @@ test_that("full stt works with multiple replicates", {
   )
   island_replicates[[1]] <- out
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
+    formatted_CS_sim <- DAISIE_format_CS(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -464,7 +464,7 @@ test_that("full stt works with empty island", {
   mainland_n <- 1
   verbose <- FALSE
   sample_freq <- Inf
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -483,7 +483,7 @@ test_that("full stt works with empty island", {
     out <- list()
     for (m_spec in 1:mainland_n) {
       out$branching_times <- c(10)
-        out <- DAISIE:::DAISIE_sim_core_cr(
+        out <- DAISIE_sim_core_cr(
           time = total_time,
           mainland_n = 1,
           pars = pars,
@@ -496,7 +496,7 @@ test_that("full stt works with empty island", {
     island_replicates[[rep]] <- full_list
   }
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
+    formatted_CS_sim <- DAISIE_format_CS(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -523,12 +523,12 @@ test_that("full stt with two trait states", {
   set.seed(1)
   island_replicates <- list()
   out <- list()
-  out[[1]] <- DAISIE:::DAISIE_sim_core_trait_dep(
+  out[[1]] <- DAISIE_sim_core_trait_dep(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
     hyper_pars = create_hyper_pars(d = 0, x = 0),
-    area_pars = DAISIE::create_area_pars(
+    area_pars = create_area_pars(
       max_area = 1,
       current_area = 1,
       proportional_peak_t = 0,
@@ -540,7 +540,7 @@ test_that("full stt with two trait states", {
   )
   island_replicates[[1]] <- out
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
+    formatted_CS_sim <- DAISIE_format_CS(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
diff --git a/tests/testthat/test-DAISIE_format_CS_full_stt.R b/tests/testthat/test-DAISIE_format_CS_full_stt.R
index 2b2bd8b5..e87ec03b 100644
--- a/tests/testthat/test-DAISIE_format_CS_full_stt.R
+++ b/tests/testthat/test-DAISIE_format_CS_full_stt.R
@@ -3,7 +3,7 @@ test_that("complete stt, 1 type, no geodynamics, oceanic island, one trait state
   pars <- c(0.4, 0.2, 10, 2, 0.5)
   total_time <- 1
   mainland_n <- 2
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -24,7 +24,7 @@ test_that("complete stt, 1 type, no geodynamics, oceanic island, one trait state
     for (m_spec in 1:mainland_n) {
       out$branching_times <- c(10)
       while (length(out$branching_times) == 1) {
-        out <- DAISIE:::DAISIE_sim_core_cr(
+        out <- DAISIE_sim_core_cr(
           time = total_time,
           mainland_n = 1,
           pars = pars,
@@ -40,7 +40,7 @@ test_that("complete stt, 1 type, no geodynamics, oceanic island, one trait state
 
 
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS_full_stt(
+    formatted_CS_sim <- DAISIE_format_CS_full_stt(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -119,14 +119,14 @@ test_that("complete stt, 1 type, geodynamics, oceanic island, one trait state
   )
   hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
   nonoceanic_pars <- c(0, 0)
-  peak <- DAISIE:::calc_peak(total_time = total_time,
+  peak <- calc_peak(total_time = total_time,
                              area_pars = area_pars)
-  Amax <- DAISIE:::get_global_max_area(total_time = total_time,
+  Amax <- get_global_max_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
-  Amin <- DAISIE:::get_global_min_area(total_time = total_time,
+  Amin <- get_global_min_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
@@ -138,7 +138,7 @@ test_that("complete stt, 1 type, geodynamics, oceanic island, one trait state
     for (m_spec in 1:mainland_n) {
       out$branching_times <- c(10)
       while (length(out$branching_times) == 1) {
-        out <- DAISIE:::DAISIE_sim_core_time_dep(
+        out <- DAISIE_sim_core_time_dep(
           island_ontogeny = 1,
           time = total_time,
           mainland_n = 1,
@@ -159,7 +159,7 @@ test_that("complete stt, 1 type, geodynamics, oceanic island, one trait state
   }
 
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS_full_stt(
+    formatted_CS_sim <- DAISIE_format_CS_full_stt(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -217,7 +217,7 @@ test_that("complete stt, 2 type, no geodynamics, oceanic island, one trait state
   mainland_n <- M
   verbose <- FALSE
   replicates <- 2
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -230,7 +230,7 @@ test_that("complete stt, 2 type, no geodynamics, oceanic island, one trait state
   island_replicates <- list()
   prop_type2_pool <- 0.4
 
-  island_replicates <- DAISIE:::DAISIE_sim_min_type2(
+  island_replicates <- DAISIE_sim_min_type2(
     time = total_time,
     M = M,
     pars = pars,
@@ -241,7 +241,7 @@ test_that("complete stt, 2 type, no geodynamics, oceanic island, one trait state
     verbose = FALSE
   )
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS_full_stt(
+    formatted_CS_sim <- DAISIE_format_CS_full_stt(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -366,7 +366,7 @@ test_that("complete stt, 1 type, no geodynamics, nonoceanic, one trait state
   ana_rate <- 1.010073119 # anagenesis rate
   pars <- c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate)
   replicates <- 3
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -386,7 +386,7 @@ test_that("complete stt, 1 type, no geodynamics, nonoceanic, one trait state
     for (m_spec in 1:mainland_n) {
       out$branching_times <- c(10)
       while (length(out$branching_times) == 1) {
-        out <- DAISIE:::DAISIE_sim_core_cr(
+        out <- DAISIE_sim_core_cr(
           time = total_time,
           mainland_n = 1,
           pars = pars,
@@ -400,7 +400,7 @@ test_that("complete stt, 1 type, no geodynamics, nonoceanic, one trait state
     island_replicates[[rep]] <- full_list
   }
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS_full_stt(
+    formatted_CS_sim <- DAISIE_format_CS_full_stt(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -415,7 +415,7 @@ test_that("complete stt, 1 type, no geodynamics, oceanic island, one trait state
   total_time <- 1
   mainland_n <- 2
   verbose <- TRUE
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -437,7 +437,7 @@ test_that("complete stt, 1 type, no geodynamics, oceanic island, one trait state
     for (m_spec in 1:mainland_n) {
       out$branching_times <- c(10)
       while (length(out$branching_times) == 1) {
-        out <- DAISIE:::DAISIE_sim_core_cr(
+        out <- DAISIE_sim_core_cr(
           time = total_time,
           mainland_n = 1,
           pars = pars,
@@ -451,7 +451,7 @@ test_that("complete stt, 1 type, no geodynamics, oceanic island, one trait state
     island_replicates[[rep]] <- full_list
   }
   expect_message(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS_full_stt(
+    formatted_CS_sim <- DAISIE_format_CS_full_stt(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -502,7 +502,7 @@ test_that("complete stt, 1 type, no geodynamics, oceanic,two trait states
         sea_level = sea_level,
         extcutoff = extcutoff,
         hyper_pars = create_hyper_pars(d = 0, x = 0),
-        area_pars = DAISIE::create_area_pars(
+        area_pars = create_area_pars(
           max_area = 1,
           current_area = 1,
           proportional_peak_t = 0,
@@ -530,7 +530,7 @@ test_that("complete stt, 1 type, no geodynamics, oceanic,two trait states
         sea_level = sea_level,
         extcutoff = extcutoff,
         hyper_pars = create_hyper_pars(d = 0, x = 0),
-        area_pars = DAISIE::create_area_pars(
+        area_pars = create_area_pars(
           max_area = 1,
           current_area = 1,
           proportional_peak_t = 0,
@@ -545,7 +545,7 @@ test_that("complete stt, 1 type, no geodynamics, oceanic,two trait states
     island_replicates[[rep]] <- full_list
   }
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS_full_stt(
+    formatted_CS_sim <- DAISIE_format_CS_full_stt(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -560,7 +560,7 @@ test_that("when no colonization happens returns 0", {
             pars <- c(0.4, 0.2, 10, 0.000001, 0.5)
             total_time <- 1
             mainland_n <- 1
-            area_pars <- DAISIE::create_area_pars(
+            area_pars <- create_area_pars(
               max_area = 1,
               current_area = 1,
               proportional_peak_t = 0,
@@ -578,7 +578,7 @@ test_that("when no colonization happens returns 0", {
               full_list <- list()
               out <- list()
               for (m_spec in 1:mainland_n) {
-                  out <- DAISIE:::DAISIE_sim_core_cr(
+                  out <- DAISIE_sim_core_cr(
                     time = total_time,
                     mainland_n = 1,
                     pars = pars,
@@ -594,7 +594,7 @@ test_that("when no colonization happens returns 0", {
 
 
             expect_silent(
-              formatted_CS_sim <- DAISIE:::DAISIE_format_CS_full_stt(
+              formatted_CS_sim <- DAISIE_format_CS_full_stt(
                 island_replicates = island_replicates,
                 time = total_time,
                 M = mainland_n,
diff --git a/tests/testthat/test-DAISIE_format_CS_sampled_stt.R b/tests/testthat/test-DAISIE_format_CS_sampled_stt.R
index 7544f826..3b8637b4 100644
--- a/tests/testthat/test-DAISIE_format_CS_sampled_stt.R
+++ b/tests/testthat/test-DAISIE_format_CS_sampled_stt.R
@@ -5,7 +5,7 @@ test_that("sampled stt, 1 type, no geodynamics, oceanic island (same arguments
   mainland_n <- 1
   verbose <- FALSE
   sample_freq <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -78,20 +78,20 @@ test_that("sampled stt, 1 type, geodynamics, oceanic island (same arguments as
     island_gradient_angle = 0
   )
   hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
-  peak <- DAISIE:::calc_peak(total_time = total_time,
+  peak <- calc_peak(total_time = total_time,
                     area_pars = area_pars)
-  Amax <- DAISIE:::get_global_max_area(total_time = total_time,
+  Amax <- get_global_max_area(total_time = total_time,
                               area_pars = area_pars,
                               peak = peak,
                               island_ontogeny = island_ontogeny,
                               sea_level = sea_level)
-  Amin <- DAISIE:::get_global_min_area(total_time = total_time,
+  Amin <- get_global_min_area(total_time = total_time,
                               area_pars = area_pars,
                               peak = peak,
                               island_ontogeny = island_ontogeny,
                               sea_level = sea_level)
   nonoceanic_pars <- c(0, 0)
-  out[[1]] <- DAISIE:::DAISIE_sim_core_time_dep(
+  out[[1]] <- DAISIE_sim_core_time_dep(
     time = total_time,
     pars = pars,
     mainland_n = mainland_n,
@@ -106,7 +106,7 @@ test_that("sampled stt, 1 type, geodynamics, oceanic island (same arguments as
   )
   island_replicates[[1]] <- out
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS_sampled_stt(
+    formatted_CS_sim <- DAISIE_format_CS_sampled_stt(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -161,7 +161,7 @@ test_that("sampled stt, 2 type, no geodynamics, oceanic island (same arguments
   verbose <- FALSE
   replicates <- 1
   sample_freq <- 25
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -173,7 +173,7 @@ test_that("sampled stt, 2 type, no geodynamics, oceanic island (same arguments
   set.seed(1)
   island_replicates <- list()
   prop_type2_pool <- 0.4
-  island_replicates <- DAISIE:::DAISIE_sim_min_type2(
+  island_replicates <- DAISIE_sim_min_type2(
     time = total_time,
     M = M,
     pars = pars,
@@ -184,7 +184,7 @@ test_that("sampled stt, 2 type, no geodynamics, oceanic island (same arguments
     verbose = FALSE
   )
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS_sampled_stt(
+    formatted_CS_sim <- DAISIE_format_CS_sampled_stt(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -242,7 +242,7 @@ test_that("sampled stt, 1 type, no geodynamics, nonoceanic (same arguments as
   imm_rate <- 0.00933207 # immigration rate
   ana_rate <- 1.010073119 # anagenesis rate
   pars <- c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate)
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -258,7 +258,7 @@ test_that("sampled stt, 1 type, no geodynamics, nonoceanic (same arguments as
   set.seed(1)
   island_replicates <- list()
   out <- list()
-  out[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  out[[1]] <- DAISIE_sim_core_cr(
     time = total_time,
     pars = pars,
     mainland_n = mainland_n,
@@ -268,7 +268,7 @@ test_that("sampled stt, 1 type, no geodynamics, nonoceanic (same arguments as
   )
   island_replicates[[1]] <- out
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS_sampled_stt(
+    formatted_CS_sim <- DAISIE_format_CS_sampled_stt(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
@@ -285,7 +285,7 @@ test_that("sampled stt, 1 type, no geodynamics, oceanic (same arguments as
   mainland_n <- 2
   verbose <- FALSE
   sample_freq <- 25
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -305,7 +305,7 @@ test_that("sampled stt, 1 type, no geodynamics, oceanic (same arguments as
     for (m_spec in 1:mainland_n) {
       out$branching_times <- c(10)
       while (length(out$branching_times) == 1) {
-        out <- DAISIE:::DAISIE_sim_core_cr(
+        out <- DAISIE_sim_core_cr(
           time = total_time,
           mainland_n = 1,
           pars = pars,
@@ -320,7 +320,7 @@ test_that("sampled stt, 1 type, no geodynamics, oceanic (same arguments as
   }
 
   expect_silent(
-    formatted_CS_sim <- DAISIE:::DAISIE_format_CS_sampled_stt(
+    formatted_CS_sim <- DAISIE_format_CS_sampled_stt(
       island_replicates = island_replicates,
       time = total_time,
       M = mainland_n,
diff --git a/tests/testthat/test-DAISIE_format_CS_trait.R b/tests/testthat/test-DAISIE_format_CS_trait.R
index 7db2a982..497c2c03 100644
--- a/tests/testthat/test-DAISIE_format_CS_trait.R
+++ b/tests/testthat/test-DAISIE_format_CS_trait.R
@@ -40,7 +40,7 @@ test_that("sampled stt, 1 type, no geodynamics, oceanic, two trait states
                   sea_level = sea_level,
                   extcutoff = extcutoff,
                   hyper_pars = create_hyper_pars(d = 0, x = 0),
-                  area_pars = DAISIE::create_area_pars(
+                  area_pars = create_area_pars(
                     max_area = 1,
                     current_area = 1,
                     proportional_peak_t = 0,
@@ -70,7 +70,7 @@ test_that("sampled stt, 1 type, no geodynamics, oceanic, two trait states
                   sea_level = sea_level,
                   extcutoff = extcutoff,
                   hyper_pars = create_hyper_pars(d = 0, x = 0),
-                  area_pars = DAISIE::create_area_pars(
+                  area_pars = create_area_pars(
                     max_area = 1,
                     current_area = 1,
                     proportional_peak_t = 0,
@@ -85,7 +85,7 @@ test_that("sampled stt, 1 type, no geodynamics, oceanic, two trait states
               island_replicates[[rep]] <- full_list
             }
             expect_silent(
-              formatted_CS_sim <- DAISIE:::DAISIE_format_CS_sampled_stt(
+              formatted_CS_sim <- DAISIE_format_CS_sampled_stt(
                 island_replicates = island_replicates,
                 time = total_time,
                 M = mainland_n,
diff --git a/tests/testthat/test-DAISIE_format_GW.R b/tests/testthat/test-DAISIE_format_GW.R
index 59e80f36..769e1bc1 100644
--- a/tests/testthat/test-DAISIE_format_GW.R
+++ b/tests/testthat/test-DAISIE_format_GW.R
@@ -5,7 +5,7 @@ test_that("silent with empty island with correct output", {
   num_guilds <- 1
   verbose <- FALSE
   sample_freq <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -18,7 +18,7 @@ test_that("silent with empty island with correct output", {
   set.seed(1)
   island_replicates <- list()
   out <- list()
-  out[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  out[[1]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
@@ -28,7 +28,7 @@ test_that("silent with empty island with correct output", {
   )
   island_replicates[[1]] <- out
   expect_silent(
-    formatted_GW_sim <- DAISIE:::DAISIE_format_GW(
+    formatted_GW_sim <- DAISIE_format_GW(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -56,7 +56,7 @@ test_that("silent with non-empty island with correct output", {
   num_guilds <- 1
   verbose <- FALSE
   sample_freq <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -69,7 +69,7 @@ test_that("silent with non-empty island with correct output", {
   set.seed(1)
   island_replicates <- list()
   out <- list()
-  out[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  out[[1]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
@@ -79,7 +79,7 @@ test_that("silent with non-empty island with correct output", {
   )
   island_replicates[[1]] <- out
   expect_silent(
-    formatted_GW_sim <- DAISIE:::DAISIE_format_GW(
+    formatted_GW_sim <- DAISIE_format_GW(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -98,7 +98,7 @@ test_that("output with empty island and verbose = TRUE", {
   verbose <- TRUE
   sample_freq <- 1
   set.seed(1)
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -110,7 +110,7 @@ test_that("output with empty island and verbose = TRUE", {
   nonoceanic_pars <- c(0, 0)
   island_replicates <- list()
   out <- list()
-  out[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  out[[1]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
@@ -119,8 +119,8 @@ test_that("output with empty island and verbose = TRUE", {
     nonoceanic_pars = nonoceanic_pars
   )
   island_replicates[[1]] <- out
-  expect_output(
-    formatted_GW_sim <- DAISIE:::DAISIE_format_GW(
+  expect_message(
+    formatted_GW_sim <- DAISIE_format_GW(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -133,5 +133,5 @@ test_that("output with empty island and verbose = TRUE", {
 })
 
 test_that("abuse", {
-  expect_error(DAISIE:::DAISIE_format_GW("nonsense"))
+  expect_error(DAISIE_format_GW("nonsense"))
 })
diff --git a/tests/testthat/test-DAISIE_format_IW.R b/tests/testthat/test-DAISIE_format_IW.R
index 246d0622..17d43c1d 100644
--- a/tests/testthat/test-DAISIE_format_IW.R
+++ b/tests/testthat/test-DAISIE_format_IW.R
@@ -4,7 +4,7 @@ test_that("silent with empty island with correct output", {
   mainland_n <- 10
   verbose <- FALSE
   sample_freq <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -17,7 +17,7 @@ test_that("silent with empty island with correct output", {
 
   set.seed(1)
   island_replicates <- list()
-  island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  island_replicates[[1]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
@@ -26,7 +26,7 @@ test_that("silent with empty island with correct output", {
     nonoceanic_pars = nonoceanic_pars
   )
   expect_silent(
-    formatted_IW_sim <- DAISIE:::DAISIE_format_IW(
+    formatted_IW_sim <- DAISIE_format_IW(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -56,7 +56,7 @@ test_that("silent with non-empty island with correct output", {
   mainland_n <- 10
   verbose <- FALSE
   sample_freq <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -68,7 +68,7 @@ test_that("silent with non-empty island with correct output", {
   nonoceanic_pars <- c(0, 0)
   set.seed(1)
   island_replicates <- list()
-  island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  island_replicates[[1]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
@@ -77,7 +77,7 @@ test_that("silent with non-empty island with correct output", {
     nonoceanic_pars = nonoceanic_pars
   )
   expect_silent(
-    formatted_IW_sim <- DAISIE:::DAISIE_format_IW(
+    formatted_IW_sim <- DAISIE_format_IW(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -126,7 +126,7 @@ test_that("DAISIE_format_IW prints when verbose = TRUE", {
   mainland_n <- 1000
   verbose <- TRUE
   sample_freq <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -138,7 +138,7 @@ test_that("DAISIE_format_IW prints when verbose = TRUE", {
   nonoceanic_pars <- c(0, 0)
   set.seed(1)
   island_replicates <- list()
-  island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  island_replicates[[1]] <- DAISIE_sim_core_cr(
     time = time,
     pars = pars,
     mainland_n = mainland_n,
@@ -147,7 +147,7 @@ test_that("DAISIE_format_IW prints when verbose = TRUE", {
     nonoceanic_pars = nonoceanic_pars
   )
   expect_message(
-    formatted_IW_sim <- DAISIE:::DAISIE_format_IW(
+    formatted_IW_sim <- DAISIE_format_IW(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -165,7 +165,7 @@ test_that("silent with empty nonoceanic island with correct output", {
   nonoceanic_pars <- c(0.2, 0.5)
   verbose <- FALSE
   sample_freq <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -176,7 +176,7 @@ test_that("silent with empty nonoceanic island with correct output", {
   hyper_pars <- create_hyper_pars(d = 0, x = 0)
   set.seed(1)
   island_replicates <- list()
-  island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+  island_replicates[[1]] <- DAISIE_sim_core_cr(
     time = time,
     mainland_n = mainland_n,
     pars = pars,
@@ -185,7 +185,7 @@ test_that("silent with empty nonoceanic island with correct output", {
     nonoceanic_pars = nonoceanic_pars
   )
   expect_silent(
-    formatted_IW_sim <- DAISIE:::DAISIE_format_IW(
+    formatted_IW_sim <- DAISIE_format_IW(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -217,7 +217,7 @@ test_that("silent with non-empty nonoceanic island with
             nonoceanic_pars <- c(0.2, 0.5)
             verbose <- FALSE
             sample_freq <- 1
-            area_pars <- DAISIE::create_area_pars(
+            area_pars <- create_area_pars(
               max_area = 1,
               current_area = 1,
               proportional_peak_t = 0,
@@ -229,7 +229,7 @@ test_that("silent with non-empty nonoceanic island with
 
             set.seed(1)
             island_replicates <- list()
-            island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+            island_replicates[[1]] <- DAISIE_sim_core_cr(
               time = time,
               mainland_n = mainland_n,
               pars = pars,
@@ -238,7 +238,7 @@ test_that("silent with non-empty nonoceanic island with
               hyper_pars = hyper_pars
             )
             expect_silent(
-              formatted_IW_sim <- DAISIE:::DAISIE_format_IW(
+              formatted_IW_sim <- DAISIE_format_IW(
                 island_replicates = island_replicates,
                 time = time,
                 M = mainland_n,
@@ -278,7 +278,7 @@ test_that("silent with non-empty nonoceanic island with
             nonoceanic_pars <- c(0.2, 0.5)
             verbose <- FALSE
             sample_freq <- 1
-            area_pars <- DAISIE::create_area_pars(
+            area_pars <- create_area_pars(
               max_area = 1,
               current_area = 1,
               proportional_peak_t = 0,
@@ -290,7 +290,7 @@ test_that("silent with non-empty nonoceanic island with
 
             set.seed(1)
             island_replicates <- list()
-            island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_cr(
+            island_replicates[[1]] <- DAISIE_sim_core_cr(
               time = time,
               mainland_n = mainland_n,
               pars = pars,
@@ -299,7 +299,7 @@ test_that("silent with non-empty nonoceanic island with
               hyper_pars = hyper_pars
             )
             expect_silent(
-              formatted_IW_sim <- DAISIE:::DAISIE_format_IW(
+              formatted_IW_sim <- DAISIE_format_IW(
                 island_replicates = island_replicates,
                 time = time,
                 M = mainland_n,
@@ -342,7 +342,7 @@ test_that("add_brt_table output is correct when length(island) == 1", {
                       stt_all = stt_all,
                       init_nonend_spec = 0,
                       init_end_spec = 0)
-  formatted_brt <- DAISIE:::add_brt_table(island)
+  formatted_brt <- add_brt_table(island)
   brt_table <- matrix(ncol = 5, nrow = 1)
   colnames(brt_table) <- c("brt", "clade", "event", "endemic", "col")
   brt_table[1, ] <- c(1, 0, 0, NA, NA)
@@ -381,7 +381,7 @@ test_that("add_brt_table output is correct when length(island) != 1", {
                                          0.5288428),
                       stac = 4,
                       missing_species = 0)
-  formatted_brt <- DAISIE:::add_brt_table(island)
+  formatted_brt <- add_brt_table(island)
   brt_table <- matrix(ncol = 5, nrow = 5)
   colnames(brt_table) <- c("brt", "clade", "event", "endemic", "col")
   brt_table[1, ] <- c(1, 0, 0, NA, NA)
@@ -413,11 +413,11 @@ test_that("add_brt_table output is correct when length(island) != 1", {
 #test_that("add_brt_table output is correct when length(island_no_stac1or5) != 0")
 
 test_that("abuse", {
-  expect_error(DAISIE:::DAISIE_format_IW("nonsense"))
+  expect_error(DAISIE_format_IW("nonsense"))
 })
 
 test_that("abuse", {
-  expect_error(DAISIE:::add_brt_table("nonsense"))
+  expect_error(add_brt_table("nonsense"))
 })
 
 
@@ -440,11 +440,11 @@ test_that("silent with empty island with correct output", {
   start_midway <- FALSE
   set.seed(1)
   island_replicates <- list()
-  island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_trait_dep(
+  island_replicates[[1]] <- DAISIE_sim_core_trait_dep(
     time = time,
     pars = pars,
     hyper_pars = create_hyper_pars(d = 0, x = 0),
-    area_pars = DAISIE::create_area_pars(
+    area_pars = create_area_pars(
       max_area = 1,
       current_area = 1,
       proportional_peak_t = 0,
@@ -456,7 +456,7 @@ test_that("silent with empty island with correct output", {
     mainland_n = mainland_n
   )
   expect_silent(
-    formatted_IW_sim <- DAISIE:::DAISIE_format_IW(
+    formatted_IW_sim <- DAISIE_format_IW(
       island_replicates = island_replicates,
       time = time,
       M = mainland_n,
@@ -503,7 +503,7 @@ test_that("silent when species with two trait states with
             island_replicates <- list()
             verbose <- FALSE
             set.seed(1)
-            island_replicates[[1]] <- DAISIE:::DAISIE_sim_core_trait_dep(
+            island_replicates[[1]] <- DAISIE_sim_core_trait_dep(
               time = time,
               mainland_n = mainland_n,
               pars = pars,
@@ -511,7 +511,7 @@ test_that("silent when species with two trait states with
               island_ontogeny = island_ontogeny,
               sea_level = sea_level,
               hyper_pars = create_hyper_pars(d = 0, x = 0),
-              area_pars = DAISIE::create_area_pars(
+              area_pars = create_area_pars(
                 max_area = 1,
                 current_area = 1,
                 proportional_peak_t = 0,
@@ -522,7 +522,7 @@ test_that("silent when species with two trait states with
               extcutoff = extcutoff
             )
             expect_silent(
-              formatted_IW_sim <- DAISIE:::DAISIE_format_IW(
+              formatted_IW_sim <- DAISIE_format_IW(
                 island_replicates = island_replicates,
                 time = time,
                 M = mainland_n,
diff --git a/tests/testthat/test-DAISIE_loglik_CS.R b/tests/testthat/test-DAISIE_loglik_CS.R
index bb55aba9..034fe078 100644
--- a/tests/testthat/test-DAISIE_loglik_CS.R
+++ b/tests/testthat/test-DAISIE_loglik_CS.R
@@ -82,7 +82,7 @@ test_that("DAISIE_loglik_all produces correct output for relaxed-rate model", {
   skip_on_cran()
   utils::data(Galapagos_datalist)
   invisible(capture.output(suppressWarnings(
-    loglik <- DAISIE::DAISIE_loglik_all(
+    loglik <- DAISIE_loglik_all(
       pars1 = c(2.55068735, 2.68345455, 10.00000000, 0.00933207, 1.01007312),
       pars2 = c(100, 0, 0, 0, NA),
       datalist = Galapagos_datalist,
@@ -126,8 +126,8 @@ test_that("DAISIE_loglik_all produces same output for CS_version 0 and 1 with
     Galapagos_datalist2[[i]]$branching_times <- c(4, 4 - 2*i*0.1,4 -2*i*0.1-0.1)
     Galapagos_datalist2[[i]]$stac <- 2
   }
-  Galapagos_datalist2 <- DAISIE:::add_brt_table(Galapagos_datalist2)
-  loglik_CS00 <- DAISIE::DAISIE_loglik_all(
+  Galapagos_datalist2 <- add_brt_table(Galapagos_datalist2)
+  loglik_CS00 <- DAISIE_loglik_all(
     pars1 = c(2.55068735, 2.68345455, 10.00000000, 0.00933207, 1.01007312),
     pars2 = c(100, 11, 0, 0, NA),
     datalist = Galapagos_datalist2,
@@ -135,7 +135,7 @@ test_that("DAISIE_loglik_all produces same output for CS_version 0 and 1 with
     CS_version = 0,
     abstolint = 1e-16,
     reltolint = 1e-10)
-  loglik_CS10 <- DAISIE::DAISIE_loglik_all(
+  loglik_CS10 <- DAISIE_loglik_all(
     pars1 = c(2.55068735, 2.68345455, 10.00000000, 0.00933207, 1.01007312),
     pars2 = c(100, 11, 0, 0, NA),
     datalist = Galapagos_datalist2,
@@ -144,7 +144,7 @@ test_that("DAISIE_loglik_all produces same output for CS_version 0 and 1 with
     abstolint = 1e-16,
     reltolint = 1e-10)
   testthat::expect_equal(loglik_CS00, loglik_CS10, tol = 5E-6)
-  loglik_CS01 <- DAISIE::DAISIE_loglik_all(
+  loglik_CS01 <- DAISIE_loglik_all(
     pars1 = c(2.55068735, 2.68345455, 10.00000000, 0.00933207, 1.01007312),
     pars2 = c(100, 11, 1, 0, NA),
     datalist = Galapagos_datalist2,
@@ -152,7 +152,7 @@ test_that("DAISIE_loglik_all produces same output for CS_version 0 and 1 with
     CS_version = 0,
     abstolint = 1e-16,
     reltolint = 1e-10)
-  loglik_CS11 <- DAISIE::DAISIE_loglik_all(
+  loglik_CS11 <- DAISIE_loglik_all(
     pars1 = c(2.55068735, 2.68345455, 10.00000000, 0.00933207, 1.01007312),
     pars2 = c(100, 11, 1, 0, NA),
     datalist = Galapagos_datalist2,
@@ -174,14 +174,14 @@ test_that("DAISIE_loglik_CS_choice produces equivalent output for ODEINT RKCK54
             0.0527, 0.0327, 0.0221, 0.1180, 0.0756, 0.0525, 0.0322, 0.0118)
   stac <- 2
   missnumspec <- 0
-  loglik1 <- DAISIE:::DAISIE_loglik_CS_choice(
+  loglik1 <- DAISIE_loglik_CS_choice(
     pars1 = pars1,
     pars2 = pars2,
     brts = brts,
     stac = stac,
     missnumspec = missnumspec
   )
-  loglik2 <- DAISIE:::DAISIE_loglik_CS_choice(
+  loglik2 <- DAISIE_loglik_CS_choice(
     pars1 = pars1,
     pars2 = pars2,
     brts = brts,
diff --git a/tests/testthat/test-DAISIE_loglik_IW_solver.R b/tests/testthat/test-DAISIE_loglik_IW_solver.R
index c7013f37..4add87b2 100644
--- a/tests/testthat/test-DAISIE_loglik_IW_solver.R
+++ b/tests/testthat/test-DAISIE_loglik_IW_solver.R
@@ -24,7 +24,7 @@ test_that("IW and CS loglik is same when K = Inf", {
   #Galapagos_datalist_IW[[8]]$branching_times <- c(4, 2, 1.41)
   #Galapagos_datalist_IW[[8]]$stac <- 2
 
-  Galapagos_datalist_IW <- DAISIE:::add_brt_table(Galapagos_datalist_IW)
+  Galapagos_datalist_IW <- add_brt_table(Galapagos_datalist_IW)
   invisible(capture.output(
     loglik_IW <- DAISIE_loglik_IW(
       pars1 = pars1,
@@ -56,7 +56,7 @@ test_that("loglik IW various solver options give similar results", {
   pars1 <- c(0.2, 0.1, 1000.1, 0.001, 0.3)
   pars2 <- c(40, 11, 0, 0)
 
-  IW0 <- DAISIE::DAISIE_loglik_IW(
+  IW0 <- DAISIE_loglik_IW(
     pars1 = pars1,
     pars2 = pars2,
     datalist = frogs_datalist,
@@ -64,7 +64,7 @@ test_that("loglik IW various solver options give similar results", {
     abstolint = 1E-12,
     reltolint = 1E-10,
   )
-  IW1 <- DAISIE::DAISIE_loglik_IW(
+  IW1 <- DAISIE_loglik_IW(
     pars1 = pars1,
     pars2 = pars2,
     datalist = frogs_datalist,
@@ -72,7 +72,7 @@ test_that("loglik IW various solver options give similar results", {
     abstolint = 1E-12,
     reltolint = 1E-10,
   )
-  IW2 <- DAISIE::DAISIE_loglik_IW(
+  IW2 <- DAISIE_loglik_IW(
     pars1 = pars1,
     pars2 = pars2,
     datalist = frogs_datalist,
@@ -80,7 +80,7 @@ test_that("loglik IW various solver options give similar results", {
     abstolint = 1E-12,
     reltolint = 1E-10,
   )
-  IW3 <- DAISIE::DAISIE_loglik_IW(
+  IW3 <- DAISIE_loglik_IW(
     pars1 = pars1,
     pars2 = pars2,
     datalist = frogs_datalist,
@@ -88,7 +88,7 @@ test_that("loglik IW various solver options give similar results", {
     abstolint = 1E-12,
     reltolint = 1E-10,
   )
-  IW4 <- DAISIE::DAISIE_loglik_IW(
+  IW4 <- DAISIE_loglik_IW(
     pars1 = pars1,
     pars2 = pars2,
     datalist = frogs_datalist,
diff --git a/tests/testthat/test-DAISIE_max_rates.R b/tests/testthat/test-DAISIE_max_rates.R
index 22413493..1971c399 100644
--- a/tests/testthat/test-DAISIE_max_rates.R
+++ b/tests/testthat/test-DAISIE_max_rates.R
@@ -1,7 +1,7 @@
 test_that("use ontogeny", {
 
   total_time <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 5000,
     current_area = 2500,
     proportional_peak_t = 0.5,
@@ -12,9 +12,9 @@ test_that("use ontogeny", {
   )
   island_ontogeny <- 1
   sea_level <- 0
-  peak <- DAISIE:::calc_peak(total_time = total_time, area_pars = area_pars)
+  peak <- calc_peak(total_time = total_time, area_pars = area_pars)
   testthat::expect_silent(
-    global_max_area <- DAISIE:::get_global_max_area(
+    global_max_area <- get_global_max_area(
       total_time = total_time,
       area_pars = area_pars,
       peak = peak,
@@ -25,7 +25,7 @@ test_that("use ontogeny", {
   total_time <- 15
   # Gets actual peak for entire curve
   testthat::expect_equal(
-    global_max_area <- DAISIE:::get_global_max_area(
+    global_max_area <- get_global_max_area(
       total_time = total_time,
       area_pars = area_pars,
       peak = peak,
@@ -39,7 +39,7 @@ test_that("use ontogeny", {
 test_that("use sea level", {
 
   total_time <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1000,
     current_area = 1,
     proportional_peak_t = 0,
@@ -52,7 +52,7 @@ test_that("use sea level", {
   island_ontogeny <- 0
   sea_level <- 1
   testthat::expect_silent(
-    global_max_area <- DAISIE:::get_global_max_area(
+    global_max_area <- get_global_max_area(
       total_time = total_time,
       area_pars = area_pars,
       peak = peak,
diff --git a/tests/testthat/test-DAISIE_min_rates.R b/tests/testthat/test-DAISIE_min_rates.R
index 1122c1cf..9128a43b 100644
--- a/tests/testthat/test-DAISIE_min_rates.R
+++ b/tests/testthat/test-DAISIE_min_rates.R
@@ -1,7 +1,7 @@
 test_that("use ontogeny", {
 
   total_time <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 5000,
     current_area = 2500,
     proportional_peak_t = 0.5,
@@ -12,9 +12,9 @@ test_that("use ontogeny", {
   )
   island_ontogeny <- 1
   sea_level <- 0
-  peak <- DAISIE:::calc_peak(total_time = total_time, area_pars = area_pars)
+  peak <- calc_peak(total_time = total_time, area_pars = area_pars)
   testthat::expect_silent(
-    global_min_area <- DAISIE:::get_global_min_area(
+    global_min_area <- get_global_min_area(
       total_time = total_time,
       area_pars = area_pars,
       peak = peak,
@@ -26,7 +26,7 @@ test_that("use ontogeny", {
 
 test_that("use sea level", {
   total_time <- 1
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1000,
     current_area = 1000,
     proportional_peak_t = 0,
@@ -38,7 +38,7 @@ test_that("use sea level", {
   island_ontogeny <- 0
   sea_level <- 1
   testthat::expect_silent(
-    global_min_area <- DAISIE:::get_global_min_area(
+    global_min_area <- get_global_min_area(
       total_time = total_time,
       area_pars = area_pars,
       island_ontogeny = island_ontogeny,
diff --git a/tests/testthat/test-DAISIE_plot_stt.R b/tests/testthat/test-DAISIE_plot_stt.R
index 45a9faea..303f663d 100644
--- a/tests/testthat/test-DAISIE_plot_stt.R
+++ b/tests/testthat/test-DAISIE_plot_stt.R
@@ -1,12 +1,12 @@
 test_that("use", {
   skip("Plots: Run and manually inspect output")
   utils::data(islands_1type_1000reps, package = "DAISIE")
-  plot_lists <- DAISIE:::DAISIE_convert_to_classic_plot(
+  plot_lists <- DAISIE_convert_to_classic_plot(
     simulation_outputs = islands_1type_1000reps
   )
   type <- names(plot_lists)[1]
   expect_silent(
-    DAISIE:::DAISIE_plot_stt(
+    DAISIE_plot_stt(
       plot_plus_one = FALSE,
       time = 4,
       plot_lists = plot_lists,
diff --git a/tests/testthat/test-DAISIE_sim_core.R b/tests/testthat/test-DAISIE_sim_core.R
index 886c05db..5c977aa0 100644
--- a/tests/testthat/test-DAISIE_sim_core.R
+++ b/tests/testthat/test-DAISIE_sim_core.R
@@ -10,7 +10,7 @@ test_that("Clean run should be silent", {
   ana_rate <- 1.0
 
   testthat::expect_silent(
-    DAISIE:::DAISIE_sim_core_cr(
+    DAISIE_sim_core_cr(
       time = sim_time,
       mainland_n = n_mainland_species,
       pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate),
@@ -32,7 +32,7 @@ test_that("Clean run should be silent", {
 
 test_that("Ontogeny simulation should run silent", {
   set.seed(234567890)
-  testthat::expect_silent(DAISIE:::DAISIE_sim_core_time_dep(
+  testthat::expect_silent(DAISIE_sim_core_time_dep(
     time = 10,
     mainland_n = 1000,
     pars = c(0.0001, 2.2, 0.005, 0.001, 1),
diff --git a/tests/testthat/test-DAISIE_sim_core_cr.R b/tests/testthat/test-DAISIE_sim_core_cr.R
index 1a50caec..51527dcc 100644
--- a/tests/testthat/test-DAISIE_sim_core_cr.R
+++ b/tests/testthat/test-DAISIE_sim_core_cr.R
@@ -7,7 +7,7 @@ test_that("Clean run should be silent", {
   carr_cap <- 4
   imm_rate <- 1.0
   ana_rate <- 1.0
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -18,7 +18,7 @@ test_that("Clean run should be silent", {
   hyper_pars <- create_hyper_pars(d = 0, x = 0)
   nonoceanic_pars <- c(0, 0)
   expect_silent(
-    DAISIE:::DAISIE_sim_core_cr(
+    DAISIE_sim_core_cr(
       time = sim_time,
       mainland_n = n_mainland_species,
       pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate),
@@ -31,7 +31,7 @@ test_that("Clean run should be silent", {
 
 test_that("A non-oceanic run with non-zero sampling should have native
           species on the island", {
-            area_pars <- DAISIE::create_area_pars(
+            area_pars <- create_area_pars(
               max_area = 1,
               current_area = 1,
               proportional_peak_t = 0,
@@ -40,7 +40,7 @@ test_that("A non-oceanic run with non-zero sampling should have native
               sea_level_frequency = 0,
               island_gradient_angle = 0)
             hyper_pars <- create_hyper_pars(d = 0, x = 0)
-            nonoceanic_sim <- DAISIE:::DAISIE_sim_core_cr(
+            nonoceanic_sim <- DAISIE_sim_core_cr(
               time = 0.4,
               mainland_n = 1000,
               pars = c(
@@ -62,7 +62,7 @@ test_that("DAISIE_sim_core output is correct", {
   time <- 1
   mainland_n <- 100
   set.seed(5)
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -72,7 +72,7 @@ test_that("DAISIE_sim_core output is correct", {
     island_gradient_angle = 0)
   nonoceanic_pars <- c(0, 0)
   hyper_pars <- create_hyper_pars(d = 0, x = 0)
-  sim_core <- DAISIE:::DAISIE_sim_core_cr(
+  sim_core <- DAISIE_sim_core_cr(
     time = time,
     mainland_n = mainland_n,
     pars = c(2, 2, 20, 0.1, 1),
@@ -94,7 +94,7 @@ test_that("DAISIE_sim_core output is correct", {
 
 test_that("DAISIE_sim_core with land-bridge starting at time = 0 for CS uses
           the second parameter set at time = 0", {
-            area_pars <- DAISIE::create_area_pars(
+            area_pars <- create_area_pars(
               max_area = 1,
               current_area = 1,
               proportional_peak_t = 0,
@@ -104,7 +104,7 @@ test_that("DAISIE_sim_core with land-bridge starting at time = 0 for CS uses
               island_gradient_angle = 0)
             hyper_pars <- create_hyper_pars(d = 0, x = 0)
             expect_silent(
-              DAISIE:::DAISIE_sim_core_cr_shift(
+              DAISIE_sim_core_cr_shift(
                 time = 10,
                 mainland_n = 1,
                 pars = c(1, 1, 10, 0.1, 1, 2, 2, 20, 0.2, 1),
@@ -117,7 +117,7 @@ test_that("DAISIE_sim_core with land-bridge starting at time = 0 for CS uses
 
 test_that("DAISIE_sim_core fails when pars[4] == 0 &&
           nonoceanic_pars[1] == 0", {
-            area_pars <- DAISIE::create_area_pars(
+            area_pars <- create_area_pars(
               max_area = 1,
               current_area = 1,
               proportional_peak_t = 0,
@@ -128,7 +128,7 @@ test_that("DAISIE_sim_core fails when pars[4] == 0 &&
             nonoceanic_pars <- c(0, 0)
             hyper_pars <- create_hyper_pars(d = 0, x = 0)
             expect_error(
-              DAISIE:::DAISIE_sim_core_cr(
+              DAISIE_sim_core_cr(
                 time = 1,
                 mainland_n = 100,
                 pars = c(2, 2, 20, 0, 1),
diff --git a/tests/testthat/test-DAISIE_sim_core_cr_shift.R b/tests/testthat/test-DAISIE_sim_core_cr_shift.R
index ec7a6aea..200f496b 100644
--- a/tests/testthat/test-DAISIE_sim_core_cr_shift.R
+++ b/tests/testthat/test-DAISIE_sim_core_cr_shift.R
@@ -1,7 +1,7 @@
 test_that("split-rate model runs silent and
           gives correct output", {
             set.seed(1)
-            area_pars <- DAISIE::create_area_pars(
+            area_pars <- create_area_pars(
               max_area = 1,
               current_area = 1,
               proportional_peak_t = 0,
@@ -12,7 +12,7 @@ test_that("split-rate model runs silent and
             nonoceanic_pars <- c(0, 0)
             hyper_pars <- create_hyper_pars(d = 0, x = 0)
             expect_silent(
-              DAISIE:::DAISIE_sim_core_cr_shift(
+              DAISIE_sim_core_cr_shift(
                 time = 10,
                 mainland_n = 1,
                 pars = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
@@ -25,7 +25,7 @@ test_that("split-rate model runs silent and
 })
 
 test_that("abuse split-rate model with time smaller than shift_times", {
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -35,7 +35,7 @@ test_that("abuse split-rate model with time smaller than shift_times", {
     island_gradient_angle = 0)
   nonoceanic_pars <- c(0, 0)
   hyper_pars <- create_hyper_pars(d = 0, x = 0)
-  expect_error(DAISIE:::DAISIE_sim_core_cr_shift(
+  expect_error(DAISIE_sim_core_cr_shift(
     time = 1,
     mainland_n = 1,
     pars = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
@@ -45,7 +45,7 @@ test_that("abuse split-rate model with time smaller than shift_times", {
 })
 
 test_that("abuse split-rate model with gamma = 0", {
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -55,7 +55,7 @@ test_that("abuse split-rate model with gamma = 0", {
     island_gradient_angle = 0)
   nonoceanic_pars <- c(0, 0)
   hyper_pars <- create_hyper_pars(d = 0, x = 0)
-  expect_error(DAISIE:::DAISIE_sim_core_cr_shift(
+  expect_error(DAISIE_sim_core_cr_shift(
     time = 1,
     mainland_n = 1,
     pars = c(1, 1, 1, 0, 1, 1, 1, 1, 1, 1),
diff --git a/tests/testthat/test-DAISIE_sim_core_time_dep.R b/tests/testthat/test-DAISIE_sim_core_time_dep.R
index 17bc5b89..c2002d18 100644
--- a/tests/testthat/test-DAISIE_sim_core_time_dep.R
+++ b/tests/testthat/test-DAISIE_sim_core_time_dep.R
@@ -12,23 +12,23 @@ test_that("Ontogeny oceanic should run silent IW", {
     island_gradient_angle = 0)
   nonoceanic_pars <- c(0, 0)
   hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
-  island_ontogeny <- DAISIE:::translate_island_ontogeny("beta")
-  sea_level <- DAISIE:::translate_sea_level("const")
-  peak <- DAISIE:::calc_peak(total_time = total_time,
+  island_ontogeny <- translate_island_ontogeny("beta")
+  sea_level <- translate_sea_level("const")
+  peak <- calc_peak(total_time = total_time,
                              area_pars = area_pars)
-  Amax <- DAISIE:::get_global_max_area(total_time = total_time,
+  Amax <- get_global_max_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
-  Amin <- DAISIE:::get_global_min_area(total_time = total_time,
+  Amin <- get_global_min_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
   set.seed(234567890)
   expect_silent(
-    DAISIE:::DAISIE_sim_core_time_dep(
+    DAISIE_sim_core_time_dep(
       time = total_time,
       mainland_n = mainland_n,
       pars = pars,
@@ -49,8 +49,8 @@ test_that("Ontogeny oceanic should run silent CS", {
   total_time <- 10
   mainland_n <- 1
   pars <- c(0.0001, 2.2, 0.005, 0.001, 1)
-  island_ontogeny <- DAISIE:::translate_island_ontogeny("beta")
-  sea_level <- DAISIE:::translate_sea_level("const")
+  island_ontogeny <- translate_island_ontogeny("beta")
+  sea_level <- translate_sea_level("const")
   area_pars <- create_area_pars(
     max_area = 5000,
     current_area = 2500,
@@ -61,21 +61,21 @@ test_that("Ontogeny oceanic should run silent CS", {
     island_gradient_angle = 0)
   nonoceanic_pars <- c(0, 0)
   hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
-  peak <- DAISIE:::calc_peak(total_time = total_time,
+  peak <- calc_peak(total_time = total_time,
                              area_pars = area_pars)
-  Amax <- DAISIE:::get_global_max_area(total_time = total_time,
+  Amax <- get_global_max_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
-  Amin <- DAISIE:::get_global_min_area(total_time = total_time,
+  Amin <- get_global_min_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
   set.seed(420)
   expect_silent(
-    DAISIE:::DAISIE_sim_core_time_dep(
+    DAISIE_sim_core_time_dep(
       time = total_time,
       mainland_n = mainland_n,
       pars = pars,
@@ -105,23 +105,23 @@ test_that("Ontogeny oceanic with sea level should run silent CS", {
     island_gradient_angle = 30)
   nonoceanic_pars <- c(0, 0)
   hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
-  island_ontogeny <- DAISIE:::translate_island_ontogeny("beta")
+  island_ontogeny <- translate_island_ontogeny("beta")
   sea_level <- translate_sea_level("const")
-  peak <- DAISIE:::calc_peak(total_time = total_time,
+  peak <- calc_peak(total_time = total_time,
                              area_pars = area_pars)
-  Amax <- DAISIE:::get_global_max_area(total_time = total_time,
+  Amax <- get_global_max_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
-  Amin <- DAISIE:::get_global_min_area(total_time = total_time,
+  Amin <- get_global_min_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
   set.seed(439)
   expect_silent(
-    out <- DAISIE:::DAISIE_sim_core_time_dep(
+    out <- DAISIE_sim_core_time_dep(
       time = total_time,
       mainland_n = mainland_n,
       pars = pars,
@@ -152,22 +152,22 @@ test_that("all species extinct if island dead", {
     sea_level_frequency = 0,
     island_gradient_angle = 0)
   nonoceanic_pars <- c(0, 0)
-  island_ontogeny <- DAISIE:::translate_island_ontogeny("beta")
-  sea_level <- DAISIE:::translate_sea_level("const")
-  peak <- DAISIE:::calc_peak(total_time = total_time,
+  island_ontogeny <- translate_island_ontogeny("beta")
+  sea_level <- translate_sea_level("const")
+  peak <- calc_peak(total_time = total_time,
                              area_pars = area_pars)
-  Amax <- DAISIE:::get_global_max_area(total_time = total_time,
+  Amax <- get_global_max_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
-  Amin <- DAISIE:::get_global_min_area(total_time = total_time,
+  Amin <- get_global_min_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
   set.seed(1)
-  ontogeny_sim <- DAISIE:::DAISIE_sim_core_time_dep(
+  ontogeny_sim <- DAISIE_sim_core_time_dep(
     time = total_time,
     mainland_n = mainland_n,
     pars = pars,
@@ -209,7 +209,7 @@ test_that("!is.null(area_pars) && island_ontogeny == 'const'", {
   Amax <- 1
   Amin <- 1
   expect_error(
-    DAISIE:::DAISIE_sim_core_time_dep(
+    DAISIE_sim_core_time_dep(
       time = total_time,
       mainland_n = mainland_n,
       pars = pars,
@@ -237,7 +237,7 @@ test_that("(is.null(ext_pars) || is.null(area_pars)) &&
             sea_level <- 1
 
             expect_error(
-              DAISIE:::DAISIE_sim_core_time_dep(
+              DAISIE_sim_core_time_dep(
                 time = time,
                 mainland_n = mainland_n,
                 pars = pars,
@@ -254,7 +254,7 @@ test_that("(is.null(ext_pars) || is.null(area_pars)) &&
 
 test_that("abuse time dependent model with gamma = 0", {
 
-  expect_error(DAISIE:::DAISIE_sim_core_time_dep(
+  expect_error(DAISIE_sim_core_time_dep(
     time = 1,
     mainland_n = 1,
     pars = c(1, 1, 1, 0, 1),
diff --git a/tests/testthat/test-DAISIE_sim_core_trait_dep.R b/tests/testthat/test-DAISIE_sim_core_trait_dep.R
index a7ec0b84..1687ef8f 100644
--- a/tests/testthat/test-DAISIE_sim_core_trait_dep.R
+++ b/tests/testthat/test-DAISIE_sim_core_trait_dep.R
@@ -1,11 +1,11 @@
 test_that("nonontogeny oceanic trait_dependnet island should run silent IW", {
   set.seed(234567890)
   expect_silent(
-    DAISIE:::DAISIE_sim_core_trait_dep(
+    DAISIE_sim_core_trait_dep(
       time = 10,
       mainland_n = 100,
       hyper_pars = create_hyper_pars(d = 0, x = 0),
-      area_pars = DAISIE::create_area_pars(
+      area_pars = create_area_pars(
         max_area = 1,
         current_area = 1,
         proportional_peak_t = 0,
@@ -29,11 +29,11 @@ test_that("nonontogeny oceanic trait_dependnet island should run silent IW", {
 test_that("nonontogeny oceanic trait_dependnet island should run silent CS", {
   set.seed(420)
   expect_silent(
-    DAISIE:::DAISIE_sim_core_trait_dep(
+    DAISIE_sim_core_trait_dep(
       time = 10,
       mainland_n = 0,
       hyper_pars = create_hyper_pars(d = 0, x = 0),
-      area_pars = DAISIE::create_area_pars(
+      area_pars = create_area_pars(
         max_area = 1,
         current_area = 1,
         proportional_peak_t = 0,
@@ -57,11 +57,11 @@ test_that("nonontogeny oceanic trait_dependnet island should run silent CS", {
 test_that("abuse NULL trait pars", {
   set.seed(234567890)
   expect_error(
-    DAISIE:::DAISIE_sim_core_trait_dep(
+    DAISIE_sim_core_trait_dep(
       time = 10,
       mainland_n = 100,
       hyper_pars = create_hyper_pars(d = 0, x = 0),
-      area_pars = DAISIE::create_area_pars(
+      area_pars = create_area_pars(
         max_area = 1,
         current_area = 1,
         proportional_peak_t = 0,
@@ -79,11 +79,11 @@ test_that("abuse NULL trait pars", {
 test_that("abuse NULL trait pars", {
   set.seed(234567890)
   expect_error(
-    DAISIE:::DAISIE_sim_core_trait_dep(
+    DAISIE_sim_core_trait_dep(
       time = 10,
       mainland_n = 100,
       hyper_pars = create_hyper_pars(d = 0, x = 0),
-      area_pars = DAISIE::create_area_pars(
+      area_pars = create_area_pars(
         max_area = 1,
         current_area = 1,
         proportional_peak_t = 0,
diff --git a/tests/testthat/test-DAISIE_sim_cr.R b/tests/testthat/test-DAISIE_sim_cr.R
index c5053986..19c1eb7c 100644
--- a/tests/testthat/test-DAISIE_sim_cr.R
+++ b/tests/testthat/test-DAISIE_sim_cr.R
@@ -567,8 +567,8 @@ test_that("constant rate oceanic CS prints correct output when
             replicates <- 1
             verbose <- TRUE
             set.seed(1)
-            expect_output(
-              sim <- DAISIE::DAISIE_sim_cr(time = total_time,
+            expect_message(
+              sim <- DAISIE_sim_cr(time = total_time,
                                            M = mainland_n,
                                            pars = pars,
                                            replicates = replicates,
@@ -586,8 +586,8 @@ test_that("constant rate oceanic IW prints correct output when
             replicates <- 1
             verbose <- TRUE
             set.seed(1)
-            expect_output(
-              sim <- DAISIE::DAISIE_sim_cr(time = total_time,
+            expect_message(
+              sim <- DAISIE_sim_cr(time = total_time,
                                            M = mainland_n,
                                            pars = pars,
                                            replicates = replicates,
@@ -615,7 +615,7 @@ test_that("2 type simulation with divdepmodel = 'CS' verbose run should
             ana_rate_type_2 <- 1.0
             prop_type2_pool <- 0.1
             replicates_apply_type2 <- FALSE
-            expect_output(
+            expect_message(
               sim <- DAISIE_sim_cr(
                 time = island_age,
                 M = n_mainland_species,
@@ -648,7 +648,7 @@ test_that("A divdepmodel = 'GW' run with verbose should print", {
   imm_rate <- 0.01
   ana_rate <- 1.0
   num_guilds <- 5
-  expect_output(
+  expect_message(
     DAISIE_sim_cr(
       time = island_age,
       M = n_mainland_species,
@@ -672,7 +672,7 @@ test_that("2 type, no geodynamics, nonoceanic should give error", {
   set.seed(1)
   prop_type2_pool <- 0.4
   nonoceanic_pars <- c(0.5, 0.5)
-  expect_error(DAISIE::DAISIE_sim_cr(
+  expect_error(DAISIE_sim_cr(
     time = total_time,
     M = M,
     pars = pars,
diff --git a/tests/testthat/test-DAISIE_sim_cr_shift.R b/tests/testthat/test-DAISIE_sim_cr_shift.R
index 9abbc4c1..a33f7ee2 100644
--- a/tests/testthat/test-DAISIE_sim_cr_shift.R
+++ b/tests/testthat/test-DAISIE_sim_cr_shift.R
@@ -129,7 +129,7 @@ test_that("abuse split-rates model", {
 })
 
 test_that("split-rates model prints when verbose = TRUE", {
-  expect_output(
+  expect_message(
     DAISIE_sim_cr_shift(
       time = 10,
       M = 10,
diff --git a/tests/testthat/test-DAISIE_sim_time_dep.R b/tests/testthat/test-DAISIE_sim_time_dep.R
index 4382d0be..d1dd8dee 100644
--- a/tests/testthat/test-DAISIE_sim_time_dep.R
+++ b/tests/testthat/test-DAISIE_sim_time_dep.R
@@ -341,7 +341,7 @@ test_that("A clean CS ontogeny run with verbose should print to console", {
   sea_level <- "const"
   extcutoff <- 1000
   hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
-  expect_output(
+  expect_message(
     DAISIE_sim_time_dep(
       time = island_age,
       M = n_mainland_species,
@@ -387,7 +387,7 @@ test_that("A clean IW ontogeny run should produce no output", {
   extcutoff <- 1000
   hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
   nonoceanic_pars <- c(0, 0)
-  expect_output(
+  expect_message(
     DAISIE_sim_time_dep(
       time = island_age,
       M = n_mainland_species,
@@ -436,7 +436,7 @@ test_that("A clean GW ontogeny run should produce no output", {
   extcutoff <- 1000
   hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
   nonoceanic_pars <- c(0, 0)
-  expect_output(
+  expect_message(
     DAISIE_sim_time_dep(
       time = island_age,
       M = n_mainland_species,
diff --git a/tests/testthat/test-are_max_rates_gt_rates.R b/tests/testthat/test-are_max_rates_gt_rates.R
index 72586a40..130217f3 100644
--- a/tests/testthat/test-are_max_rates_gt_rates.R
+++ b/tests/testthat/test-are_max_rates_gt_rates.R
@@ -1,6 +1,6 @@
 test_that("basic use", {
   expect_true(
-    DAISIE:::are_max_rates_gt_rates(
+    are_max_rates_gt_rates(
       rates = list(
         immig_rate = 0.1,
         ext_rate = 0.2,
@@ -16,7 +16,7 @@ test_that("basic use", {
     )
   )
   expect_true(
-    DAISIE:::are_max_rates_gt_rates(
+    are_max_rates_gt_rates(
       rates = list(
         immig_rate = 0.1,
         ext_rate = 0.2,
@@ -36,7 +36,7 @@ test_that("basic use", {
 test_that("check returns FALSE when wrong", {
 
   expect_false(
-    DAISIE:::are_max_rates_gt_rates(
+    are_max_rates_gt_rates(
       rates = list(
         immig_rate = 0.1,
         ext_rate = 0.2,
@@ -53,7 +53,7 @@ test_that("check returns FALSE when wrong", {
   )
 
   expect_false(
-    DAISIE:::are_max_rates_gt_rates(
+    are_max_rates_gt_rates(
       rates = list(
         immig_rate = 0.1,
         ext_rate = 0.2,
@@ -69,7 +69,7 @@ test_that("check returns FALSE when wrong", {
     )
   )
   expect_false(
-    DAISIE:::are_max_rates_gt_rates(
+    are_max_rates_gt_rates(
       rates = list(
         immig_rate = 0.1,
         ext_rate = 0.2,
@@ -86,7 +86,7 @@ test_that("check returns FALSE when wrong", {
   )
 
   expect_false(
-    DAISIE:::are_max_rates_gt_rates(
+    are_max_rates_gt_rates(
       rates = list(
         immig_rate = 0.1,
         ext_rate = 0.2,
@@ -102,7 +102,7 @@ test_that("check returns FALSE when wrong", {
     )
   )
   expect_false(
-    DAISIE:::are_max_rates_gt_rates(
+    are_max_rates_gt_rates(
       rates = list(
         immig_rate = "nonsense",
         ext_rate = 0.2,
@@ -118,7 +118,7 @@ test_that("check returns FALSE when wrong", {
     )
   )
   expect_false(
-    DAISIE:::are_max_rates_gt_rates(
+    are_max_rates_gt_rates(
       rates = list(
         immig_rate = 0.1,
         ext_rate = 0.2,
diff --git a/tests/testthat/test-get_ana_rate.R b/tests/testthat/test-get_ana_rate.R
index 8055238c..23dd32d8 100644
--- a/tests/testthat/test-get_ana_rate.R
+++ b/tests/testthat/test-get_ana_rate.R
@@ -1,10 +1,10 @@
 test_that("use", {
   ps_ana_rate <- 1
   n_immigrants <- 5
-  ana_rate <- DAISIE:::get_ana_rate(
+  ana_rate <- get_ana_rate(
     laa = ps_ana_rate,
     num_immigrants = n_immigrants)
-  created <- DAISIE:::get_ana_rate(
+  created <- get_ana_rate(
     laa = 1,
     num_immigrants = 5)
   expected <- ps_ana_rate * n_immigrants
diff --git a/tests/testthat/test-get_clado_rate.R b/tests/testthat/test-get_clado_rate.R
index c2d8399b..c356f1e0 100644
--- a/tests/testthat/test-get_clado_rate.R
+++ b/tests/testthat/test-get_clado_rate.R
@@ -2,9 +2,9 @@ test_that("use area constant diversity-independent", {
   ps_clado_rate <- 0.2
   carr_cap <- Inf
   n_species <- 4
-  hyper_pars <- DAISIE:::create_hyper_pars(d = 0, x = 0)
+  hyper_pars <- create_hyper_pars(d = 0, x = 0)
   area <- 1
-  created <- DAISIE:::get_clado_rate(
+  created <- get_clado_rate(
     lac = ps_clado_rate,
     hyper_pars = hyper_pars,
     num_spec = n_species,
@@ -19,9 +19,9 @@ test_that("use area constant diversity-dependent", {
   ps_clado_rate <- 0.2
   carr_cap <- 9
   n_species <- 4
-  hyper_pars <- DAISIE:::create_hyper_pars(d = 0, x = 0)
+  hyper_pars <- create_hyper_pars(d = 0, x = 0)
   area <- 1
-  created <- DAISIE:::get_clado_rate(
+  created <- get_clado_rate(
     lac = ps_clado_rate,
     hyper_pars = hyper_pars,
     num_spec = n_species,
@@ -36,9 +36,9 @@ test_that("use area variable diversity-independent", {
   ps_clado_rate <- 0.2
   carr_cap <- Inf
   n_species <- 4
-  hyper_pars <- DAISIE:::create_hyper_pars(d = 0.2, x = 0.1)
+  hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
   area <- 10
-  created <- DAISIE:::get_clado_rate(
+  created <- get_clado_rate(
     lac = ps_clado_rate,
     hyper_pars = hyper_pars,
     num_spec = n_species,
@@ -53,9 +53,9 @@ test_that("use area variable diversity-dependent", {
   ps_clado_rate <- 0.2
   carr_cap <- 9
   n_species <- 4
-  hyper_pars <- DAISIE:::create_hyper_pars(d = 0.2, x = 0.1)
+  hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
   area <- 10
-  created <- DAISIE:::get_clado_rate(
+  created <- get_clado_rate(
     lac = ps_clado_rate,
     hyper_pars = hyper_pars,
     num_spec = n_species,
diff --git a/tests/testthat/test-get_ext_rate.R b/tests/testthat/test-get_ext_rate.R
index 78acb145..66ed0042 100644
--- a/tests/testthat/test-get_ext_rate.R
+++ b/tests/testthat/test-get_ext_rate.R
@@ -1,9 +1,9 @@
 test_that("use area constant", {
   ps_ext_rate <- 2
   n_species <- 4
-  hyper_pars = DAISIE:::create_hyper_pars(d = 0, x = 0)
+  hyper_pars = create_hyper_pars(d = 0, x = 0)
   area <- 1
-  created <- DAISIE:::get_ext_rate(
+  created <- get_ext_rate(
     mu = ps_ext_rate,
     hyper_pars = hyper_pars,
     extcutoff = 1000,
@@ -17,9 +17,9 @@ test_that("use area constant", {
 test_that("use area variable", {
   ps_ext_rate <- 2
   n_species <- 4
-  hyper_pars = DAISIE:::create_hyper_pars(d = 0.2, x = 0.1)
+  hyper_pars = create_hyper_pars(d = 0.2, x = 0.1)
   area <- 10
-  created <- DAISIE:::get_ext_rate(
+  created <- get_ext_rate(
     mu = ps_ext_rate,
     hyper_pars = hyper_pars,
     extcutoff = 1000,
diff --git a/tests/testthat/test-get_immig_rate.R b/tests/testthat/test-get_immig_rate.R
index e3fac823..51fbeda3 100644
--- a/tests/testthat/test-get_immig_rate.R
+++ b/tests/testthat/test-get_immig_rate.R
@@ -3,9 +3,9 @@ test_that("use area constant diversity-independent", {
   ps_imm_rate <- 0.1
   n_island_species <- 5
   n_mainland_species <- 1
-  hyper_pars <- DAISIE:::create_hyper_pars(0, 0)
+  hyper_pars <- create_hyper_pars(0, 0)
   area <- 1
-  created <- DAISIE:::get_immig_rate(
+  created <- get_immig_rate(
     gam = ps_imm_rate,
     A = area,
     num_spec = n_island_species,
@@ -22,9 +22,9 @@ test_that("use area constant diversity-dependent", {
   ps_imm_rate <- 0.1
   n_island_species <- 5
   n_mainland_species <- 1
-  hyper_pars <- DAISIE:::create_hyper_pars(0, 0)
+  hyper_pars <- create_hyper_pars(0, 0)
   area <- 1
-  created <- DAISIE:::get_immig_rate(
+  created <- get_immig_rate(
     gam = ps_imm_rate,
     A = area,
     num_spec = n_island_species,
@@ -41,9 +41,9 @@ test_that("use area variable (ontogeny) diversity-dependent", {
   ps_imm_rate <- 0.1
   n_island_species <- 5
   n_mainland_species <- 1
-  hyper_pars <- DAISIE:::create_hyper_pars(0, 0)
+  hyper_pars <- create_hyper_pars(0, 0)
   area <- 10
-  created <- DAISIE:::get_immig_rate(
+  created <- get_immig_rate(
     gam = ps_imm_rate,
     A = area,
     num_spec = n_island_species,
diff --git a/tests/testthat/test-integration_DAISIE.R b/tests/testthat/test-integration_DAISIE.R
index c6923be8..70eac94b 100644
--- a/tests/testthat/test-integration_DAISIE.R
+++ b/tests/testthat/test-integration_DAISIE.R
@@ -73,7 +73,7 @@ test_that("IW and CS loglik is same when K = Inf", {
     Galapagos_datalist_IW[[i]]$stac <- 2
   }
 
-  Galapagos_datalist_IW <- DAISIE:::add_brt_table(Galapagos_datalist_IW)
+  Galapagos_datalist_IW <- add_brt_table(Galapagos_datalist_IW)
   loglik_IW <- DAISIE_loglik_IW(
     pars1 = pars1,
     pars2 = pars2,
diff --git a/tests/testthat/test-is_simulation_outputs.R b/tests/testthat/test-is_simulation_outputs.R
index 35d780af..79177c02 100644
--- a/tests/testthat/test-is_simulation_outputs.R
+++ b/tests/testthat/test-is_simulation_outputs.R
@@ -8,7 +8,7 @@ test_that("use", {
     plot_sims = FALSE,
     verbose = FALSE)))
 
-  expect_true(is_simulation_outputs(DAISIE::DAISIE_sim_time_dep(
+  expect_true(is_simulation_outputs(DAISIE_sim_time_dep(
     time = 2,
     M = 500,
     pars = c(0.00001, 1, 0.05, 0.001, 1),
diff --git a/tests/testthat/test-island_area.R b/tests/testthat/test-island_area.R
index c5d287c6..9d02ee77 100644
--- a/tests/testthat/test-island_area.R
+++ b/tests/testthat/test-island_area.R
@@ -25,7 +25,7 @@ test_that("is valid island area with ontogeny", {
     sea_level_frequency = 0,
     island_gradient_angle = 0
   )
-  peak <- DAISIE:::calc_peak(total_time = 4, area_pars = area_pars)
+  peak <- calc_peak(total_time = 4, area_pars = area_pars)
 
   area <- island_area(timeval = 2,
                       total_time = 4,
@@ -64,7 +64,7 @@ test_that("is valid island area with ontogeny and sea level", {
     sea_level_frequency = 10,
     island_gradient_angle = 85
   )
-  peak <- DAISIE:::calc_peak(total_time = 4, area_pars = area_pars)
+  peak <- calc_peak(total_time = 4, area_pars = area_pars)
   area <- island_area(timeval = 2,
                       total_time = 4,
                       area_pars = area_pars,
diff --git a/tests/testthat/test-printing.R b/tests/testthat/test-printing.R
new file mode 100644
index 00000000..30fac8de
--- /dev/null
+++ b/tests/testthat/test-printing.R
@@ -0,0 +1,89 @@
+test_that("print_parameters_and_loglik works", {
+  expect_message(
+    print_parameters_and_loglik(
+      pars = c(1, 2:6),
+      loglik = -3,
+      verbose = 3,
+      type = 'clade_loglik'
+    ),
+    regexp = "Status of colonist: 1, Parameters: 2.000000, 3.000000, 4.000000, 5.000000, 6.000000, Loglikelihood: -3.000000")
+  expect_message(print_parameters_and_loglik(pars = c(2:6), loglik = -3, verbose = 3, type = 'island_loglik'))
+
+  expect_message(print_parameters_and_loglik(pars = c(2:6), loglik = -3, verbose = 3, type = 'island_ML'))
+  expect_message(print_parameters_and_loglik(pars = c(1:11), loglik = -3, verbose = 3, type = 'global_ML', distance_dep = 'power'))
+  expect_message(print_parameters_and_loglik(pars = c(1:11), loglik = -3, verbose = 3, type = 'global_ML', distance_dep = 'sigmoidal_col'))
+  expect_message(print_parameters_and_loglik(pars = data.frame(rbind(c(2:6),c(12:16))), loglik = -3, verbose = 3, type = 'multiple_island_ML'))
+
+  expect_silent(print_parameters_and_loglik(pars = data.frame(rbind(c(2:6),c(12:16))), loglik = -3, verbose = 1, type = 'multiple_island_ML'))
+  expect_silent(print_parameters_and_loglik(pars = data.frame(rbind(c(2:6),c(12:16))), loglik = -3, verbose = 0, type = 'multiple_island_ML'))
+})
+
+test_that("print_ml_par_settings works", {
+
+  expect_message(
+    print_ml_par_settings(
+      namepars = letters[1:5],
+      idparsopt = 1:5,
+      idparsfix = NULL,
+      idparsnoshift = 1:5,
+      all_no_shift = 1:5,
+      verbose = 1
+    ),
+    regexp = "You are optimizing: a b c d e
+You are fixing: nothing")
+
+  expect_message(
+    print_ml_par_settings(
+      namepars = letters[1:5],
+      idparsopt = 1:4,
+      idparsfix = 5,
+      idparsnoshift = 1:5,
+      all_no_shift = 1:5,
+      verbose = 1
+    ),
+    regexp = "You are optimizing: a b c d
+You are fixing: e")
+
+  expect_message(
+    print_ml_par_settings(
+      namepars = letters[1:5],
+      idparsopt = 1:5,
+      idparsfix = NULL,
+      idparsnoshift = 1:4,
+      all_no_shift = 1:4,
+      verbose = 1
+    ),
+    regexp = "You are optimizing: a b c d e
+You are fixing: nothing
+You are not shifting: a b c d")
+
+  expect_silent(
+    print_ml_par_settings(
+      namepars = letters[1:5],
+      idparsopt = 1:5,
+      idparsfix = NULL,
+      idparsnoshift = 1:4,
+      all_no_shift = 1:4,
+      verbose = 0
+    )
+  )
+
+})
+
+test_that("print_init_ll works", {
+  expect_message(
+    print_init_ll(
+      initloglik = 10,
+      verbose = 1
+    ),
+    regexp = "Calculating the likelihood for the initial parameters.
+The loglikelihood for the initial parameter values is 10
+Optimizing the likelihood - this may take a while.")
+
+  expect_silent(
+    print_init_ll(
+      initloglik = 10,
+      verbose = 0
+    )
+  )
+})
diff --git a/tests/testthat/test-time_dep_vs_cr.R b/tests/testthat/test-time_dep_vs_cr.R
index adc6f213..8751739f 100644
--- a/tests/testthat/test-time_dep_vs_cr.R
+++ b/tests/testthat/test-time_dep_vs_cr.R
@@ -16,7 +16,7 @@ test_that("constant rate output matches time dependent code", {
   imm_rate <- 1.0
   ana_rate <- 1.0
   pars <- c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate)
-  area_pars <- DAISIE::create_area_pars(
+  area_pars <- create_area_pars(
     max_area = 1,
     current_area = 1,
     proportional_peak_t = 0,
@@ -25,11 +25,11 @@ test_that("constant rate output matches time dependent code", {
     sea_level_frequency = 0,
     island_gradient_angle = 0
   )
-  hyper_pars <- DAISIE::create_hyper_pars(d = 0, x = 0)
+  hyper_pars <- create_hyper_pars(d = 0, x = 0)
   nonoceanic_pars <- c(0, 0)
   rng_seed <- 42
   set.seed(rng_seed)
-  cr_out <- DAISIE:::DAISIE_sim_cr(
+  cr_out <- DAISIE_sim_cr(
     time = sim_time,
     M = n_mainland_species,
     pars = pars,
@@ -43,9 +43,9 @@ test_that("constant rate output matches time dependent code", {
   #   Ontogeny code running constant case -----------------------------------
   # We must use the core function to avoid calling calc_peak with a constant
   # area.
-  hyper_pars <- DAISIE::create_hyper_pars(d = 0, x = 0)
+  hyper_pars <- create_hyper_pars(d = 0, x = 0)
   set.seed(rng_seed)
-  time_dep_out <- DAISIE:::DAISIE_sim_core_time_dep(
+  time_dep_out <- DAISIE_sim_core_time_dep(
     time = sim_time,
     mainland_n = n_mainland_species,
     pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate),
diff --git a/tests/testthat/test-update_max_rates.R b/tests/testthat/test-update_max_rates.R
index d319131c..6f33bb53 100644
--- a/tests/testthat/test-update_max_rates.R
+++ b/tests/testthat/test-update_max_rates.R
@@ -23,12 +23,12 @@ test_that("update_max_rates constant rates is silent and gives correct output",
   num_immigrants <- 0
   mainland_n <- 1
   peak <- 1
-  Amin <- DAISIE:::get_global_min_area(total_time = total_time,
+  Amin <- get_global_min_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
                                        sea_level = sea_level)
-  Amax <- DAISIE:::get_global_max_area(total_time = total_time,
+  Amax <- get_global_max_area(total_time = total_time,
                                        area_pars = area_pars,
                                        peak = peak,
                                        island_ontogeny = island_ontogeny,
@@ -70,7 +70,7 @@ test_that("update area-dependent max rates is silent and gives correct output",
     island_gradient_angle = 0
   )
   hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
-  peak <- DAISIE:::calc_peak(total_time = 0.7, area_pars = area_pars)
+  peak <- calc_peak(total_time = 0.7, area_pars = area_pars)
   Amin <- get_global_min_area(total_time = 0.7,
                               area_pars = area_pars,
                               peak = peak,
@@ -82,7 +82,7 @@ test_that("update area-dependent max rates is silent and gives correct output",
                               island_ontogeny = 1,
                               sea_level = 0)
 
-  expect_silent(rates <- DAISIE:::update_max_rates(
+  expect_silent(rates <- update_max_rates(
     gam = 0.009,
     laa = 1.0,
     lac = 2.5,
diff --git a/tests/testthat/test-update_rates.R b/tests/testthat/test-update_rates.R
index 502c243a..4a0479b4 100644
--- a/tests/testthat/test-update_rates.R
+++ b/tests/testthat/test-update_rates.R
@@ -63,7 +63,7 @@ test_that("update area-dependent rates is silent and gives correct output", {
     island_gradient_angle = 0)
   hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
   peak <- calc_peak(total_time = 1, area_pars = area_pars)
-  expect_silent(rates <- DAISIE:::update_rates(
+  expect_silent(rates <- update_rates(
     timeval = 0,
     total_time = 1,
     gam = gam,
diff --git a/tests/testthat/test_printing.R b/tests/testthat/test_printing.R
deleted file mode 100644
index 4d331126..00000000
--- a/tests/testthat/test_printing.R
+++ /dev/null
@@ -1,8 +0,0 @@
-test_that("printing is done", {
-  print_parameters_and_loglik(pars = c(1,2:6), loglik = -3, verbose = T, type = 'clade_loglik')
-  print_parameters_and_loglik(pars = c(2:6), loglik = -3, verbose = T, type = 'island_loglik')
-  print_parameters_and_loglik(pars = c(2:6), loglik = -3, verbose = T, type = 'island_ML')
-  print_parameters_and_loglik(pars = c(1:11), loglik = -3, verbose = T, type = 'global_ML', distance_dep = 'power')
-  print_parameters_and_loglik(pars = c(1:11), loglik = -3, verbose = T, type = 'global_ML', distance_dep = 'sigmoidal_col')
-  print_parameters_and_loglik(pars = data.frame(rbind(c(2:6),c(12:16))), loglik = -3, verbose = T, type = 'multiple_island_ML')
-})