Merge branch 'develop' into new-ddmodels

.Rbuildignore

@@ -2,3 +2,6 @@
 ^\.Rproj\.user$
 ^README\.md
 ^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/R-CMD-check.yaml

@@ -1,5 +1,5 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches:
@@ -25,85 +25,37 @@ jobs:
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
+    if: "contains(github.event.head_commit.message, '[run ci]') || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') || github.event.pull_request"
+
     strategy:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-
-      - name: Install libcurl4-openssl-dev
-        if: matrix.config.r == 'devel'
-        run: sudo apt install -qq libcurl4-openssl-dev
-
-      - uses: r-lib/actions/setup-pandoc@v1
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("crayon")
-          if (.Platform$OS.type == "unix") remotes::install_cran("doMC")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Install covr and test coverage
-        if: matrix.config.r == 'devel'
-        run: |
-          remotes::install_cran("covr", dependencies = TRUE, upgrade = "always")
-          covr::codecov()
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck, doMC=?ignore
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+  pull_request:
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    if: "contains(github.event.head_commit.message, '[run ci]') || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop')"
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -8,3 +8,4 @@ src/*.so
 src/*.dll
 src-i386
 src-x64
+docs

DESCRIPTION

@@ -1,10 +1,9 @@
 Package: DDD
 Type: Package
 Title: Diversity-Dependent Diversification
-Version: 5.2.0
-Date: 2023-02-06
+Version: 5.2.3
+Date: 2024-11-26
 Depends: R (>= 3.5.0)
-SystemRequirements: C++14
 Imports:
   deSolve,
   ape,
@@ -16,12 +15,13 @@ Imports:
   SparseM,
   Rcpp (>= 1.0.10)
 LinkingTo: 
-  Rcpp,
+  Rcpp (>= 1.0.10),
   RcppEigen,
   BH (>= 1.81.0-1)
 Suggests:
-  testthat,
-  testit
+    testthat (>= 3.0.0),
+    testit,
+    igraph
 Authors@R: c(
     person(given = "Rampal S.",
            family = "Etienne",
@@ -61,4 +61,6 @@ Description:
  <DOI:10.1093/sysbio/syaa048>.
  Also contains functions to simulate the diversity-dependent
  process.
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
+Config/testthat/edition: 3
+URL: https://rsetienne.github.io/DDD/

NAMESPACE

@@ -31,4 +31,5 @@ export(td_sim)
 export(transform_pars)
 export(untransform_pars)
 export(what_is_this_ddmodel)
+import(Rcpp)
 useDynLib(DDD)

R/DDD-package.R

@@ -0,0 +1,7 @@
+#' @keywords internal
+#' @import Rcpp
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL

R/dd_KI_sim.R

@@ -304,8 +304,10 @@ tes = L2phylo(L[,1:4],dropextinct = T)
 tas = L2phylo(L[,1:4],dropextinct = F)
 tesS = NULL
 tes2 = NULL
+tasS = NULL
+tas2 = NULL
 graphics::par(mfrow = c(1,2))
-graphics::par(mai=c(0,0.5,0.5,0))
+graphics::par(mai = c(0,0.5,0.5,0))
 graphics::plot(tes)
 graphics::title('Reconstructed tree', cex.main = 0.7)
 graphics::plot(tas)
@@ -332,8 +334,6 @@ if(length(linlistS) > 0)
    phytools::plotSimmap(tes2,cols,lwd = 3,pts = F, mar = c(0.1,0.1,1,0.1))
    graphics::title('Reconstructed tree', cex.main = 0.7)
 }
-tasS = NULL
-tas2 = NULL
 allS = which(L[,5] == 1)
 if(length(allS) > 0)
 {

R/dd_loglik.R

@@ -607,11 +607,11 @@ dd_integrate <- function(initprobs,tvec,rhs_func,pars,rtol,atol,method)
     rhs_func_name <- 'no_name'
     if (is.character(rhs_func)) {
       rhs_func_name <- rhs_func
-      if(rhs_func_name != 'dd_loglik_rhs' & rhs_func_name != 'dd_loglik_bw_rhs')
-      {
+      #if(rhs_func_name != 'dd_loglik_rhs' & rhs_func_name != 'dd_loglik_bw_rhs')
+      #{
         rhs_func = match.fun(rhs_func)
-      }
-    }
+      #}
+    #}
     if(rhs_func_name == 'dd_loglik_rhs' || rhs_func_name == 'dd_loglik_bw_rhs')
     {
       parsvec = c(dd_loglik_rhs_precomp(pars,initprobs),pars[length(pars) - 1])

R/dd_utils.R

@@ -698,7 +698,7 @@ simplex = function(fun,trparsopt,optimpars,...)
 #' 'subplex'
 #' @param optimpars Parameters of the optimization: relative tolerance in
 #' function arguments, relative tolerance in function value, absolute tolerance
-#' in function arguments, and maximum number of iterations
+#' in function arguments as well as the function value, and maximum number of iterations
 #' @param num_cycles Number of cycles of the optimization. When set to Inf, the
 #' optimization will be repeated until the result is, within the tolerance,
 #' equal to the starting values, with a maximum of 10 cycles.
@@ -760,7 +760,9 @@ optimizer <- function(
       trparsopt[trparsopt == 0.5] <- 0.5 - jitter
       outnew <- suppressWarnings(subplex::subplex(par = trparsopt,
                                                   fn = minfun1,
-                                                  control = list(abstol = optimpars[3],reltol = optimpars[1],maxit = optimpars[4]),
+                                                  control = list(abstol = optimpars[3],
+                                                                 reltol = optimpars[1],
+                                                                 maxit = optimpars[4]),
                                                   fun = fun,
                                                   ...))
       outnew <- list(par = outnew$par, fvalues = -outnew$value, conv = outnew$convergence)
@@ -773,7 +775,7 @@ optimizer <- function(
       outnew <- suppressWarnings(DEoptim::DEoptim(fn = minfun2,
                                                   lower = rep(0, length(trparsopt)),
                                                   upper = rep(1, length(trparsopt)),
-                                                  control = list(reltol = optimpars[1],
+                                                  control = list(reltol = optimpars[2],
                                                                  strategy = 2,
                                                                  steptol = 100,
                                                                  trace = FALSE,
@@ -783,6 +785,21 @@ optimizer <- function(
 
                                                   ...))$optim
       outnew <- list(par = outnew$bestmem, fvalues = -outnew$bestval, conv = 0)
+    } else if(substr(optimmethod,1,7) == 'optim::')
+    {
+      minfun3 <- function(trparsopt, fun, ...)
+      {           
+        return(-fun(trparsopt = trparsopt, ...))
+      }
+      outnew <- suppressWarnings(optim(par = trparsopt,
+                                       fn = minfun3,
+                                       method = substr(optimmethod,8,nchar(optimmethod)),
+                                       control = list(reltol = optimpars[2],
+                                                      abstol = optimpars[3],
+                                                      maxit = optimpars[4]),
+                                       fun = fun,
+                                       ...))
+      outnew <- list(par = outnew$par, fvalues = -outnew$value, conv = outnew$convergence)
     }
     if(cy > 1 & (any(is.na(outnew$par)) | any(is.nan(outnew$par)) | is.na(outnew$fvalues) | is.nan(outnew$fvalues) | outnew$conv != 0))
     {