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Merge pull request #116 from rsetienne/develop
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Tidyr install fix
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@rsetienne
rsetienne authored Aug 11, 2020
2 parents cf8cedd + 3916fe4 commit 25d0285
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1 change: 1 addition & 0 deletions .travis.yml
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Expand Up @@ -25,6 +25,7 @@ before_install:
- sudo apt-get update
- sudo add-apt-repository -y ppa:opencpu/imagemagick
- sudo apt-get install -y libmagick++-dev
- sudo apt install r-cran-rcpp

script:
- travis_wait 30 R CMD build .
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data-raw/frog_M1_ML.R:5:1: style: Variable and function name style should be snake_case.

​frog_M1_ML <- DAISIE_ML(
^~~~~~~~~~

data-raw/frog_M1_ML.R:7:24: style: Commas should always have a space after.

​  initparsopt = c(0.18,0.03,0.0006,2),
                       ^

data-raw/frog_M1_ML.R:7:29: style: Commas should always have a space after.

​  initparsopt = c(0.18,0.03,0.0006,2),
                            ^

data-raw/frog_M1_ML.R:7:36: style: Commas should always have a space after.

​  initparsopt = c(0.18,0.03,0.0006,2),
                                   ^

data-raw/frog_M1_ML.R:8:19: style: Commas should always have a space after.

​  idparsopt = c(1,2,4,5),
                  ^

data-raw/frog_M1_ML.R:8:21: style: Commas should always have a space after.

​  idparsopt = c(1,2,4,5),
                    ^

data-raw/frog_M1_ML.R:8:23: style: Commas should always have a space after.

​  idparsopt = c(1,2,4,5),
                      ^

R/create_pars.R:21:1: style: functions should have cyclomatic complexity of less than 15, this has 35.

​are_area_pars <- function(area_pars) {
^

R/create_pars.R:151:1: style: functions should have cyclomatic complexity of less than 15, this has 33.

​are_trait_pars <- function(trait_pars) {
^

R/create_pars.R:174:1: style: Lines should not be more than 80 characters.

​#' @param immig_rate2  A numeric with the per capita immigration rate with state2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/create_pars.R:177:1: style: Lines should not be more than 80 characters.

​#' @param clado_rate2  A numeric with the per capita cladogenesis rate with state2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/create_pars.R:179:1: style: Lines should not be more than 80 characters.

​#' @param M2           A numeric with the number of species with trait state 2 on mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/create_pars.R:200:31: style: Variable and function name style should be snake_case.

​                              M2) {
                              ^~

R/create_pars.R:213:30: style: Put spaces around all infix operators.

​  testit::assert(trans_rate2 >=0.0)
                             ^~~

R/create_pars.R:214:21: style: Put spaces around all infix operators.

​  testit::assert(M2 >=0)
                    ^~~

R/DAISIE_check_format.R:7:1: style: functions should have cyclomatic complexity of less than 15, this has 44.

​are_rates <- function(rates) {
^

R/DAISIE_check_format.R:18:5: style: Place a space before left parenthesis, except in a function call.

​  if(length(rates) > 4) {
    ^

R/DAISIE_check_format.R:43:1: style: functions should have cyclomatic complexity of less than 15, this has 19.

​are_max_rates <- function(max_rates) {
^

R/DAISIE_check_format.R:155:7: style: Commented code should be removed.

​    # if (!"branching_times" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_check_format.R:156:7: style: Commented code should be removed.

​    # if (!"stac" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_check_format.R:157:7: style: Commented code should be removed.

​    # if (!"missing_species" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:8:1: style: Variable and function name style should be snake_case.

​DAISIE_create_island <- function(stt_table,
^~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:76:1: style: Variable and function name style should be snake_case.

​DAISIE_create_island_trait <- function(stt_table,
^~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:80:50: style: There should be a space between right parenthesis and an opening curly brace.

​                                       trait_pars){
                                                 ^~

R/DAISIE_create_island.R:82:1: style: Lines should not be more than 80 characters.

​  ### if there are no species on the island branching_times = island_age, stac = 0, missing_species = 0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:83:27: style: Commas should always have a space after.

​  if (length(island_spec[,1]) == 0) {
                          ^

R/DAISIE_create_island.R:102:1: style: Lines should not be more than 80 characters.

​    island_spec[, "branching time (BP)"] <- totaltime - as.numeric(island_spec[, "branching time (BP)"])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:103:1: style: Lines should not be more than 80 characters.

​    island_spec[, "Colonisation time (BP)"] <- totaltime - as.numeric(island_spec[, "Colonisation time (BP)"])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:105:21: style: Use <-, not =, for assignment.

​    mainland_ntotal = mainland_n + trait_pars$M2
                    ^

R/DAISIE_create_island.R:116:1: style: Lines should not be more than 80 characters.

​      colonists_present <- sort(as.numeric(unique(island_spec[, 'Mainland Ancestor'])))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:116:65: style: Only use double-quotes.

​      colonists_present <- sort(as.numeric(unique(island_spec[, 'Mainland Ancestor'])))
                                                                ^~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:139:1: style: Trailing blank lines are superfluous.

​
^

R/DAISIE_data.R:2:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 8 terrestrial avifaunal clades in list
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:7:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:23:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:24:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:25:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:47:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 8 terrestrial avifaunal clades in list
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:52:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:68:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:69:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close relatives
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:92:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:96:1: style: Lines should not be more than 80 characters.

​#' @description A table containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:103:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic: for non-endemic island species when an approximate time of colonisation is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:104:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic_MaxAge: for non-endemic island species when colonisation time is unknown \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:105:1: style: Lines should not be more than 80 characters.

​#' * Endemic: for endemic species when an approximate colonisation time is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:106:1: style: Lines should not be more than 80 characters.

​#' * "Endemic_MaxAge": applies to endemic species or endemic clades for cases where the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:109:1: style: Lines should not be more than 80 characters.

​#' This could for example apply to endemic species that have recently gone extinct because
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:113:1: style: Lines should not be more than 80 characters.

​#' time of the first cladogenetic event is known, but the precise time of colonisation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:120:1: style: Lines should not be more than 80 characters.

​#' \code{$Branching_times} - Stem age of the population/species in the case of "Non_endemic",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:121:1: style: Lines should not be more than 80 characters.

​#'  "Non_endemic_MaxAge" and "Endemic" species with no extant close relatives on the island.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:124:1: style: Lines should not be more than 80 characters.

​#' radiation, including the stem age of the radiation (colonisation time estimate).\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:134:1: style: Lines should not be more than 80 characters.

​#' @title 1000 islands in RAW format simulated with the ML parameters of the CR model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:137:1: style: Lines should not be more than 80 characters.

​#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:159:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_sim_constant_rate}()}, \code{\link{DAISIE_plot_sims}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:168:1: style: Lines should not be more than 80 characters.

​#' @title 1000 islands in DAISIE format simulated with the ML parameters of the CR
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:171:1: style: Lines should not be more than 80 characters.

​#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:195:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_sim_constant_rate}()}, \code{\link{DAISIE_plot_sims}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:207:1: style: Lines should not be more than 80 characters.

​#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:242:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_sim_constant_rate}()}, \code{\link{DAISIE_plot_sims}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:257:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:266:1: style: Lines should not be more than 80 characters.

​#' The following elements of the list each contains information on a single colonist lineage
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:270:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:271:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:272:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:274:1: style: Lines should not be more than 80 characters.

​#' branching times of the island clade including the stem age of the clade. \cr \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:288:1: style: Lines should not be more than 80 characters.

​#' R. Equilibrium bird species diversity in Atlantic islands. 2017 Current Biology, 27, 1660-1666.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:298:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the birds of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:300:1: style: Lines should not be more than 80 characters.

​#' Valente, Etienne, Garcia-R (2019) Current Biology. Island age 52 Myr and mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:312:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:313:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:314:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:328:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:329:1: style: Lines should not be more than 80 characters.

​#' @source Valente L, Etienne RS, Garcia-R JC (2019) Deep Macroevolutionary Impact of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:338:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of Noctilionoid bats from the Greater Antilles.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:341:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the noctilionoid
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:343:1: style: Lines should not be more than 80 characters.

​#' Valente, Etienne and Dávalos (2017) Nature Ecology and Evolution. Island age 20 Myr and
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:355:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:356:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:357:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:371:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:372:1: style: Lines should not be more than 80 characters.

​#' @source Valente L, Etienne RS, Dávalos (2017) Recent extinctions disturb path to
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:373:1: style: Lines should not be more than 80 characters.

​#' equilibrium diversity in Caribbean bats. Nature Ecology and Evolution, 1, 26.\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:385:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the fishes of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:386:1: style: Lines should not be more than 80 characters.

​#' Lake Biwa (Japan). Main dataset used in Hauffe et al (2020). This list can be generated
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:401:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:402:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:403:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:417:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:419:1: style: Lines should not be more than 80 characters.

​#' elevates equilibrium diversity via increasing colonisation. (2020) Journal of Biogeography \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:426:1: style: Lines should not be more than 80 characters.

​#' @format A dataframe containing information on archipelago name, area, age and distance from the mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:427:1: style: Lines should not be more than 80 characters.

​#' @description A dataframe with in subsequent columns the name of the archipelago (Archipelago)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:428:1: style: Lines should not be more than 80 characters.

​#' the area of the archipelago (Area), the age (Age) and the distance from the mainland (Distance)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:430:1: style: Lines should not be more than 80 characters.

​#'  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. A simple dynamic model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:440:1: style: Lines should not be more than 80 characters.

​#' @format A datalist containing data on the 41 archipelagos studied in Valente et
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:441:1: style: Lines should not be more than 80 characters.

​#' al 2020 (Main Dataset D1). Contains colonisation and branching times for bird species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:442:1: style: Lines should not be more than 80 characters.

​#' in each of the archipelagos. It also contains information on archipelago name, area,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:445:1: style: Lines should not be more than 80 characters.

​#' Each archipelago can be called separately using archipelagos41[[x]] with x being a
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:447:1: style: Lines should not be more than 80 characters.

​#' top part of the archipelago item where the archipelago name and physical features
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:448:1: style: Lines should not be more than 80 characters.

​#' are displayed. The structure of each of the archipelagos is the same as regular DAISIE
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:451:1: style: Lines should not be more than 80 characters.

​#'  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. A simple dynamic model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:460:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:464:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the Eleutherodactylus frogs of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:466:1: style: Lines should not be more than 80 characters.

​#' using the DAISIE_dataprep function, which converts a user-specified data table into a data object,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:480:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:481:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:482:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:496:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:497:1: style: Lines should not be more than 80 characters.

​#' @source Etienne RS, Haegeman B, Dugo-Cota A, Vila C, Gonzalez-Voyer A & Valente L. The
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:504:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 5 Eleutherodactylus (frogs) clades from
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:508:1: style: Lines should not be more than 80 characters.

​#' @description A table containing the colonization and branching times of the Eleutherodacytlus
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:509:1: style: Lines should not be more than 80 characters.

​#'frogs of the island of Hispaniola (Greater Antilles). Each row on the table represents and independent
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:515:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic: for non-endemic island species when an approximate time of colonisation is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:516:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic_MaxAge: for non-endemic island species when colonisation time is unknown \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:517:1: style: Lines should not be more than 80 characters.

​#' * Endemic: for endemic species when an approximate colonisation time is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:518:1: style: Lines should not be more than 80 characters.

​#' * "Endemic_MaxAge": applies to endemic species or endemic clades for cases where the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:521:1: style: Lines should not be more than 80 characters.

​#' This could for example apply to endemic species that have recently gone extinct because
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:525:1: style: Lines should not be more than 80 characters.

​#' time of the first cladogenetic event is known, but the precise time of colonisation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:529:1: style: Lines should not be more than 80 characters.

​#' @source Etienne RS, Haegeman B, Dugo-Cota A, Vila C, Gonzalez-Voyer A & Valente L. The
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:16:1: style: Lines should not be more than 80 characters.

​#' "Non_endemic": applies to non-endemic species when an approximate colonisation time is known \cr *
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:18:1: style: Lines should not be more than 80 characters.

​#' colonisation time is unknown \cr * "Endemic": applies to endemic species or endemic
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:19:1: style: Lines should not be more than 80 characters.

​#' clades when an approximate colonisation time is known \cr * "Endemic_MaxAge": applies to endemic
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:20:1: style: Lines should not be more than 80 characters.

​#' species or endemic clades for cases where the colonisation time is unknown, or when
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:22:1: style: Lines should not be more than 80 characters.

​#' This could for example apply to endemic species that have recently gone extinct because
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:26:1: style: Lines should not be more than 80 characters.

​#' time of the first cladogenetic event is known, but the precise time of colonisation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:27:1: style: Lines should not be more than 80 characters.

​#' is not. \cr * "Endemic&Non_Endemic": when endemic clade is present and its mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:31:1: style: Lines should not be more than 80 characters.

​#'  be equal to the number of species in the clade minus 1 \cr \code{$Branching_times}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:32:1: style: Lines should not be more than 80 characters.

​#'  - Stem age of the population/species in the case of "Non_endemic", "Non_endemic_MaxAge"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:33:1: style: Lines should not be more than 80 characters.

​#'  and "Endemic" species with no extant close relatives on the island. Set "NA" if
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:36:1: style: Lines should not be more than 80 characters.

​#' radiation, including the stem age of the radiation (colonisation time estimate).\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:82:1: style: Lines should not be more than 80 characters.

​#' \cr * Endemic_MaxAge: 6 (if colonisation time and cladogenesis times were given)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:84:1: style: Lines should not be more than 80 characters.

​#' for particular clade (only applicable for endemic clades) \cr \code{$type_1or2}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:96:1: style: Lines should not be more than 80 characters.

​#' ### Create Galapagos data object where all taxa have the same macroevolutionary process
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:106:1: style: Lines should not be more than 80 characters.

​#' # for the Darwin's finches. One process applies to type 1 species (all species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:121:1: style: Lines should not be more than 80 characters.

​#' # for the Darwin's finches. One process applies to type 1 species (all species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:123:1: style: Lines should not be more than 80 characters.

​#' # (Darwin's finches). Set fraction of potential colonists of type 2 to be 0.163.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:136:1: style: functions should have cyclomatic complexity of less than 15, this has 29.

​DAISIE_dataprep = function(datatable,
^

R/DAISIE_dataprep.R:136:1: style: Variable and function name style should be snake_case.

​DAISIE_dataprep = function(datatable,
^~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:136:17: style: Use <-, not =, for assignment.

​DAISIE_dataprep = function(datatable,
                ^

R/DAISIE_dataprep.R:138:28: style: Variable and function name style should be snake_case.

​                           M,
                           ^

R/DAISIE_dataprep.R:144:1: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​{
^

R/DAISIE_dataprep.R:147:13: style: Variable and function name style should be snake_case.

​  datatable$Missing_species <- as.numeric(as.character
            ^~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:158:40: style: Do not place spaces around code in parentheses or square brackets.

​      not_present_type1 <- DDD::roundn( (M / number_colonisations) *
                                       ^

R/DAISIE_dataprep.R:161:40: style: Do not place spaces around code in parentheses or square brackets.

​      not_present_type2 <- DDD::roundn( (M / number_colonisations) *
                                       ^

R/DAISIE_dataprep.R:174:13: warning: Avoid 1:nrow(...) expressions, use seq_len.

​  for (i in 1:nrow(datatable)) {
            ^

R/DAISIE_dataprep.R:184:7: style: Place a space before left parenthesis, except in a function call.

​    if(is.na(the_brts[1])){
      ^

R/DAISIE_dataprep.R:184:26: style: There should be a space between right parenthesis and an opening curly brace.

​    if(is.na(the_brts[1])){
                         ^~

R/DAISIE_dataprep.R:185:15: style: Put spaces around all infix operators.

​      the_brts<-island_age
             ~^~~

R/DAISIE_dataprep.R:186:1: style: Lines should not be more than 80 characters.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:186:9: style: Place a space before left parenthesis, except in a function call.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
        ^

R/DAISIE_dataprep.R:186:22: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                     ^

R/DAISIE_dataprep.R:186:59: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                          ^

R/DAISIE_dataprep.R:186:81: style: Do not place spaces around code in parentheses or square brackets.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                ^

R/DAISIE_dataprep.R:186:82: style: There should be a space between right parenthesis and an opening curly brace.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                 ^~

R/DAISIE_dataprep.R:187:1: style: Lines should not be more than 80 characters.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:187:34: style: Use <-, not =, for assignment.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                 ^

R/DAISIE_dataprep.R:187:68: style: Commas should always have a space after.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                                                   ^

R/DAISIE_dataprep.R:188:21: style: Commas should always have a space after.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                    ^

R/DAISIE_dataprep.R:188:31: style: Put spaces around all infix operators.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                              ^~~

R/DAISIE_dataprep.R:188:49: style: Closing curly-braces should always be on their own line, unless it's followed by an else.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                                                ^

R/DAISIE_dataprep.R:189:1: style: Lines should not be more than 80 characters.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:189:9: style: Place a space before left parenthesis, except in a function call.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
        ^

R/DAISIE_dataprep.R:189:22: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
                     ^

R/DAISIE_dataprep.R:189:63: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
                                                              ^

R/DAISIE_dataprep.R:189:89: style: There should be a space between right parenthesis and an opening curly brace.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
                                                                                        ^~

R/DAISIE_dataprep.R:190:1: style: Lines should not be more than 80 characters.

​        levels(datatable$Status) = append(levels(datatable$Status),"Non_endemic_MaxAge")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:190:34: style: Use <-, not =, for assignment.

​        levels(datatable$Status) = append(levels(datatable$Status),"Non_endemic_MaxAge")
                                 ^

R/DAISIE_dataprep.R:190:68: style: Commas should always have a space after.

​        levels(datatable$Status) = append(levels(datatable$Status),"Non_endemic_MaxAge")
                                                                   ^

R/DAISIE_dataprep.R:191:21: style: Commas should always have a space after.

​        datatable[i,"Status"] <-"Non_endemic_MaxAge"}
                    ^

R/DAISIE_dataprep.R:191:31: style: Put spaces around all infix operators.

​        datatable[i,"Status"] <-"Non_endemic_MaxAge"}
                              ^~~

R/DAISIE_dataprep.R:191:53: style: Closing curly-braces should always be on their own line, unless it's followed by an else.

​        datatable[i,"Status"] <-"Non_endemic_MaxAge"}
                                                    ^

R/DAISIE_dataprep.R:194:7: style: Place a space before left parenthesis, except in a function call.

​    if(max(the_brts)>island_age){
      ^

R/DAISIE_dataprep.R:194:21: style: Put spaces around all infix operators.

​    if(max(the_brts)>island_age){
                   ~^~

R/DAISIE_dataprep.R:194:32: style: There should be a space between right parenthesis and an opening curly brace.

​    if(max(the_brts)>island_age){
                               ^~

R/DAISIE_dataprep.R:202:1: style: Lines should not be more than 80 characters.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:202:9: style: Place a space before left parenthesis, except in a function call.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
        ^

R/DAISIE_dataprep.R:202:22: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                     ^

R/DAISIE_dataprep.R:202:59: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                          ^

R/DAISIE_dataprep.R:202:81: style: Do not place spaces around code in parentheses or square brackets.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                ^

R/DAISIE_dataprep.R:202:82: style: There should be a space between right parenthesis and an opening curly brace.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                 ^~

R/DAISIE_dataprep.R:203:1: style: Lines should not be more than 80 characters.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:203:34: style: Use <-, not =, for assignment.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                 ^

R/DAISIE_dataprep.R:203:68: style: Commas should always have a space after.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                                                   ^

R/DAISIE_dataprep.R:204:21: style: Commas should always have a space after.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                    ^

R/DAISIE_dataprep.R:204:31: style: Put spaces around all infix operators.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                              ^~~

R/DAISIE_dataprep.R:204:49: style: Closing curly-braces should always be on their own line, unless it's followed by an else.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                                                ^

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data-raw/frog_M1_ML.R:5:1: style: Variable and function name style should be snake_case.

​frog_M1_ML <- DAISIE_ML(
^~~~~~~~~~

data-raw/frog_M1_ML.R:7:24: style: Commas should always have a space after.

​  initparsopt = c(0.18,0.03,0.0006,2),
                       ^

data-raw/frog_M1_ML.R:7:29: style: Commas should always have a space after.

​  initparsopt = c(0.18,0.03,0.0006,2),
                            ^

data-raw/frog_M1_ML.R:7:36: style: Commas should always have a space after.

​  initparsopt = c(0.18,0.03,0.0006,2),
                                   ^

data-raw/frog_M1_ML.R:8:19: style: Commas should always have a space after.

​  idparsopt = c(1,2,4,5),
                  ^

data-raw/frog_M1_ML.R:8:21: style: Commas should always have a space after.

​  idparsopt = c(1,2,4,5),
                    ^

data-raw/frog_M1_ML.R:8:23: style: Commas should always have a space after.

​  idparsopt = c(1,2,4,5),
                      ^

R/create_pars.R:21:1: style: functions should have cyclomatic complexity of less than 15, this has 35.

​are_area_pars <- function(area_pars) {
^

R/create_pars.R:151:1: style: functions should have cyclomatic complexity of less than 15, this has 33.

​are_trait_pars <- function(trait_pars) {
^

R/create_pars.R:174:1: style: Lines should not be more than 80 characters.

​#' @param immig_rate2  A numeric with the per capita immigration rate with state2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/create_pars.R:177:1: style: Lines should not be more than 80 characters.

​#' @param clado_rate2  A numeric with the per capita cladogenesis rate with state2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/create_pars.R:179:1: style: Lines should not be more than 80 characters.

​#' @param M2           A numeric with the number of species with trait state 2 on mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/create_pars.R:200:31: style: Variable and function name style should be snake_case.

​                              M2) {
                              ^~

R/create_pars.R:213:30: style: Put spaces around all infix operators.

​  testit::assert(trans_rate2 >=0.0)
                             ^~~

R/create_pars.R:214:21: style: Put spaces around all infix operators.

​  testit::assert(M2 >=0)
                    ^~~

R/DAISIE_check_format.R:7:1: style: functions should have cyclomatic complexity of less than 15, this has 44.

​are_rates <- function(rates) {
^

R/DAISIE_check_format.R:18:5: style: Place a space before left parenthesis, except in a function call.

​  if(length(rates) > 4) {
    ^

R/DAISIE_check_format.R:43:1: style: functions should have cyclomatic complexity of less than 15, this has 19.

​are_max_rates <- function(max_rates) {
^

R/DAISIE_check_format.R:155:7: style: Commented code should be removed.

​    # if (!"branching_times" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_check_format.R:156:7: style: Commented code should be removed.

​    # if (!"stac" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_check_format.R:157:7: style: Commented code should be removed.

​    # if (!"missing_species" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:8:1: style: Variable and function name style should be snake_case.

​DAISIE_create_island <- function(stt_table,
^~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:76:1: style: Variable and function name style should be snake_case.

​DAISIE_create_island_trait <- function(stt_table,
^~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:80:50: style: There should be a space between right parenthesis and an opening curly brace.

​                                       trait_pars){
                                                 ^~

R/DAISIE_create_island.R:82:1: style: Lines should not be more than 80 characters.

​  ### if there are no species on the island branching_times = island_age, stac = 0, missing_species = 0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:83:27: style: Commas should always have a space after.

​  if (length(island_spec[,1]) == 0) {
                          ^

R/DAISIE_create_island.R:102:1: style: Lines should not be more than 80 characters.

​    island_spec[, "branching time (BP)"] <- totaltime - as.numeric(island_spec[, "branching time (BP)"])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:103:1: style: Lines should not be more than 80 characters.

​    island_spec[, "Colonisation time (BP)"] <- totaltime - as.numeric(island_spec[, "Colonisation time (BP)"])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:105:21: style: Use <-, not =, for assignment.

​    mainland_ntotal = mainland_n + trait_pars$M2
                    ^

R/DAISIE_create_island.R:116:1: style: Lines should not be more than 80 characters.

​      colonists_present <- sort(as.numeric(unique(island_spec[, 'Mainland Ancestor'])))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:116:65: style: Only use double-quotes.

​      colonists_present <- sort(as.numeric(unique(island_spec[, 'Mainland Ancestor'])))
                                                                ^~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:139:1: style: Trailing blank lines are superfluous.

​
^

R/DAISIE_data.R:2:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 8 terrestrial avifaunal clades in list
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:7:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:23:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:24:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:25:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:47:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 8 terrestrial avifaunal clades in list
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:52:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:68:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:69:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close relatives
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:92:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:96:1: style: Lines should not be more than 80 characters.

​#' @description A table containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:103:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic: for non-endemic island species when an approximate time of colonisation is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:104:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic_MaxAge: for non-endemic island species when colonisation time is unknown \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:105:1: style: Lines should not be more than 80 characters.

​#' * Endemic: for endemic species when an approximate colonisation time is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:106:1: style: Lines should not be more than 80 characters.

​#' * "Endemic_MaxAge": applies to endemic species or endemic clades for cases where the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:109:1: style: Lines should not be more than 80 characters.

​#' This could for example apply to endemic species that have recently gone extinct because
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:113:1: style: Lines should not be more than 80 characters.

​#' time of the first cladogenetic event is known, but the precise time of colonisation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:120:1: style: Lines should not be more than 80 characters.

​#' \code{$Branching_times} - Stem age of the population/species in the case of "Non_endemic",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:121:1: style: Lines should not be more than 80 characters.

​#'  "Non_endemic_MaxAge" and "Endemic" species with no extant close relatives on the island.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:124:1: style: Lines should not be more than 80 characters.

​#' radiation, including the stem age of the radiation (colonisation time estimate).\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:134:1: style: Lines should not be more than 80 characters.

​#' @title 1000 islands in RAW format simulated with the ML parameters of the CR model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:137:1: style: Lines should not be more than 80 characters.

​#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:159:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_sim_constant_rate}()}, \code{\link{DAISIE_plot_sims}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:168:1: style: Lines should not be more than 80 characters.

​#' @title 1000 islands in DAISIE format simulated with the ML parameters of the CR
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:171:1: style: Lines should not be more than 80 characters.

​#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:195:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_sim_constant_rate}()}, \code{\link{DAISIE_plot_sims}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:207:1: style: Lines should not be more than 80 characters.

​#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:242:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_sim_constant_rate}()}, \code{\link{DAISIE_plot_sims}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:257:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:266:1: style: Lines should not be more than 80 characters.

​#' The following elements of the list each contains information on a single colonist lineage
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:270:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:271:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:272:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:274:1: style: Lines should not be more than 80 characters.

​#' branching times of the island clade including the stem age of the clade. \cr \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:288:1: style: Lines should not be more than 80 characters.

​#' R. Equilibrium bird species diversity in Atlantic islands. 2017 Current Biology, 27, 1660-1666.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:298:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the birds of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:300:1: style: Lines should not be more than 80 characters.

​#' Valente, Etienne, Garcia-R (2019) Current Biology. Island age 52 Myr and mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:312:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:313:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:314:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:328:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:329:1: style: Lines should not be more than 80 characters.

​#' @source Valente L, Etienne RS, Garcia-R JC (2019) Deep Macroevolutionary Impact of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:338:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of Noctilionoid bats from the Greater Antilles.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:341:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the noctilionoid
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:343:1: style: Lines should not be more than 80 characters.

​#' Valente, Etienne and Dávalos (2017) Nature Ecology and Evolution. Island age 20 Myr and
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:355:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:356:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:357:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:371:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:372:1: style: Lines should not be more than 80 characters.

​#' @source Valente L, Etienne RS, Dávalos (2017) Recent extinctions disturb path to
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:373:1: style: Lines should not be more than 80 characters.

​#' equilibrium diversity in Caribbean bats. Nature Ecology and Evolution, 1, 26.\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:385:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the fishes of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:386:1: style: Lines should not be more than 80 characters.

​#' Lake Biwa (Japan). Main dataset used in Hauffe et al (2020). This list can be generated
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:401:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:402:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:403:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:417:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:419:1: style: Lines should not be more than 80 characters.

​#' elevates equilibrium diversity via increasing colonisation. (2020) Journal of Biogeography \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:426:1: style: Lines should not be more than 80 characters.

​#' @format A dataframe containing information on archipelago name, area, age and distance from the mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:427:1: style: Lines should not be more than 80 characters.

​#' @description A dataframe with in subsequent columns the name of the archipelago (Archipelago)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:428:1: style: Lines should not be more than 80 characters.

​#' the area of the archipelago (Area), the age (Age) and the distance from the mainland (Distance)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:430:1: style: Lines should not be more than 80 characters.

​#'  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. A simple dynamic model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:440:1: style: Lines should not be more than 80 characters.

​#' @format A datalist containing data on the 41 archipelagos studied in Valente et
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:441:1: style: Lines should not be more than 80 characters.

​#' al 2020 (Main Dataset D1). Contains colonisation and branching times for bird species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:442:1: style: Lines should not be more than 80 characters.

​#' in each of the archipelagos. It also contains information on archipelago name, area,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:445:1: style: Lines should not be more than 80 characters.

​#' Each archipelago can be called separately using archipelagos41[[x]] with x being a
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:447:1: style: Lines should not be more than 80 characters.

​#' top part of the archipelago item where the archipelago name and physical features
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:448:1: style: Lines should not be more than 80 characters.

​#' are displayed. The structure of each of the archipelagos is the same as regular DAISIE
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:451:1: style: Lines should not be more than 80 characters.

​#'  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. A simple dynamic model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:460:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:464:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the Eleutherodactylus frogs of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:466:1: style: Lines should not be more than 80 characters.

​#' using the DAISIE_dataprep function, which converts a user-specified data table into a data object,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:480:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:481:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:482:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:496:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:497:1: style: Lines should not be more than 80 characters.

​#' @source Etienne RS, Haegeman B, Dugo-Cota A, Vila C, Gonzalez-Voyer A & Valente L. The
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:504:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 5 Eleutherodactylus (frogs) clades from
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:508:1: style: Lines should not be more than 80 characters.

​#' @description A table containing the colonization and branching times of the Eleutherodacytlus
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:509:1: style: Lines should not be more than 80 characters.

​#'frogs of the island of Hispaniola (Greater Antilles). Each row on the table represents and independent
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:515:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic: for non-endemic island species when an approximate time of colonisation is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:516:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic_MaxAge: for non-endemic island species when colonisation time is unknown \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:517:1: style: Lines should not be more than 80 characters.

​#' * Endemic: for endemic species when an approximate colonisation time is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:518:1: style: Lines should not be more than 80 characters.

​#' * "Endemic_MaxAge": applies to endemic species or endemic clades for cases where the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:521:1: style: Lines should not be more than 80 characters.

​#' This could for example apply to endemic species that have recently gone extinct because
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:525:1: style: Lines should not be more than 80 characters.

​#' time of the first cladogenetic event is known, but the precise time of colonisation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:529:1: style: Lines should not be more than 80 characters.

​#' @source Etienne RS, Haegeman B, Dugo-Cota A, Vila C, Gonzalez-Voyer A & Valente L. The
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:16:1: style: Lines should not be more than 80 characters.

​#' "Non_endemic": applies to non-endemic species when an approximate colonisation time is known \cr *
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:18:1: style: Lines should not be more than 80 characters.

​#' colonisation time is unknown \cr * "Endemic": applies to endemic species or endemic
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:19:1: style: Lines should not be more than 80 characters.

​#' clades when an approximate colonisation time is known \cr * "Endemic_MaxAge": applies to endemic
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:20:1: style: Lines should not be more than 80 characters.

​#' species or endemic clades for cases where the colonisation time is unknown, or when
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:22:1: style: Lines should not be more than 80 characters.

​#' This could for example apply to endemic species that have recently gone extinct because
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:26:1: style: Lines should not be more than 80 characters.

​#' time of the first cladogenetic event is known, but the precise time of colonisation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:27:1: style: Lines should not be more than 80 characters.

​#' is not. \cr * "Endemic&Non_Endemic": when endemic clade is present and its mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:31:1: style: Lines should not be more than 80 characters.

​#'  be equal to the number of species in the clade minus 1 \cr \code{$Branching_times}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:32:1: style: Lines should not be more than 80 characters.

​#'  - Stem age of the population/species in the case of "Non_endemic", "Non_endemic_MaxAge"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:33:1: style: Lines should not be more than 80 characters.

​#'  and "Endemic" species with no extant close relatives on the island. Set "NA" if
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:36:1: style: Lines should not be more than 80 characters.

​#' radiation, including the stem age of the radiation (colonisation time estimate).\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:82:1: style: Lines should not be more than 80 characters.

​#' \cr * Endemic_MaxAge: 6 (if colonisation time and cladogenesis times were given)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:84:1: style: Lines should not be more than 80 characters.

​#' for particular clade (only applicable for endemic clades) \cr \code{$type_1or2}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:96:1: style: Lines should not be more than 80 characters.

​#' ### Create Galapagos data object where all taxa have the same macroevolutionary process
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:106:1: style: Lines should not be more than 80 characters.

​#' # for the Darwin's finches. One process applies to type 1 species (all species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:121:1: style: Lines should not be more than 80 characters.

​#' # for the Darwin's finches. One process applies to type 1 species (all species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:123:1: style: Lines should not be more than 80 characters.

​#' # (Darwin's finches). Set fraction of potential colonists of type 2 to be 0.163.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:136:1: style: functions should have cyclomatic complexity of less than 15, this has 29.

​DAISIE_dataprep = function(datatable,
^

R/DAISIE_dataprep.R:136:1: style: Variable and function name style should be snake_case.

​DAISIE_dataprep = function(datatable,
^~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:136:17: style: Use <-, not =, for assignment.

​DAISIE_dataprep = function(datatable,
                ^

R/DAISIE_dataprep.R:138:28: style: Variable and function name style should be snake_case.

​                           M,
                           ^

R/DAISIE_dataprep.R:144:1: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​{
^

R/DAISIE_dataprep.R:147:13: style: Variable and function name style should be snake_case.

​  datatable$Missing_species <- as.numeric(as.character
            ^~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:158:40: style: Do not place spaces around code in parentheses or square brackets.

​      not_present_type1 <- DDD::roundn( (M / number_colonisations) *
                                       ^

R/DAISIE_dataprep.R:161:40: style: Do not place spaces around code in parentheses or square brackets.

​      not_present_type2 <- DDD::roundn( (M / number_colonisations) *
                                       ^

R/DAISIE_dataprep.R:174:13: warning: Avoid 1:nrow(...) expressions, use seq_len.

​  for (i in 1:nrow(datatable)) {
            ^

R/DAISIE_dataprep.R:184:7: style: Place a space before left parenthesis, except in a function call.

​    if(is.na(the_brts[1])){
      ^

R/DAISIE_dataprep.R:184:26: style: There should be a space between right parenthesis and an opening curly brace.

​    if(is.na(the_brts[1])){
                         ^~

R/DAISIE_dataprep.R:185:15: style: Put spaces around all infix operators.

​      the_brts<-island_age
             ~^~~

R/DAISIE_dataprep.R:186:1: style: Lines should not be more than 80 characters.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:186:9: style: Place a space before left parenthesis, except in a function call.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
        ^

R/DAISIE_dataprep.R:186:22: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                     ^

R/DAISIE_dataprep.R:186:59: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                          ^

R/DAISIE_dataprep.R:186:81: style: Do not place spaces around code in parentheses or square brackets.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                ^

R/DAISIE_dataprep.R:186:82: style: There should be a space between right parenthesis and an opening curly brace.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                 ^~

R/DAISIE_dataprep.R:187:1: style: Lines should not be more than 80 characters.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:187:34: style: Use <-, not =, for assignment.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                 ^

R/DAISIE_dataprep.R:187:68: style: Commas should always have a space after.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                                                   ^

R/DAISIE_dataprep.R:188:21: style: Commas should always have a space after.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                    ^

R/DAISIE_dataprep.R:188:31: style: Put spaces around all infix operators.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                              ^~~

R/DAISIE_dataprep.R:188:49: style: Closing curly-braces should always be on their own line, unless it's followed by an else.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                                                ^

R/DAISIE_dataprep.R:189:1: style: Lines should not be more than 80 characters.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:189:9: style: Place a space before left parenthesis, except in a function call.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
        ^

R/DAISIE_dataprep.R:189:22: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
                     ^

R/DAISIE_dataprep.R:189:63: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
                                                              ^

R/DAISIE_dataprep.R:189:89: style: There should be a space between right parenthesis and an opening curly brace.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
                                                                                        ^~

R/DAISIE_dataprep.R:190:1: style: Lines should not be more than 80 characters.

​        levels(datatable$Status) = append(levels(datatable$Status),"Non_endemic_MaxAge")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:190:34: style: Use <-, not =, for assignment.

​        levels(datatable$Status) = append(levels(datatable$Status),"Non_endemic_MaxAge")
                                 ^

R/DAISIE_dataprep.R:190:68: style: Commas should always have a space after.

​        levels(datatable$Status) = append(levels(datatable$Status),"Non_endemic_MaxAge")
                                                                   ^

R/DAISIE_dataprep.R:191:21: style: Commas should always have a space after.

​        datatable[i,"Status"] <-"Non_endemic_MaxAge"}
                    ^

R/DAISIE_dataprep.R:191:31: style: Put spaces around all infix operators.

​        datatable[i,"Status"] <-"Non_endemic_MaxAge"}
                              ^~~

R/DAISIE_dataprep.R:191:53: style: Closing curly-braces should always be on their own line, unless it's followed by an else.

​        datatable[i,"Status"] <-"Non_endemic_MaxAge"}
                                                    ^

R/DAISIE_dataprep.R:194:7: style: Place a space before left parenthesis, except in a function call.

​    if(max(the_brts)>island_age){
      ^

R/DAISIE_dataprep.R:194:21: style: Put spaces around all infix operators.

​    if(max(the_brts)>island_age){
                   ~^~

R/DAISIE_dataprep.R:194:32: style: There should be a space between right parenthesis and an opening curly brace.

​    if(max(the_brts)>island_age){
                               ^~

R/DAISIE_dataprep.R:202:1: style: Lines should not be more than 80 characters.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:202:9: style: Place a space before left parenthesis, except in a function call.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
        ^

R/DAISIE_dataprep.R:202:22: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                     ^

R/DAISIE_dataprep.R:202:59: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                          ^

R/DAISIE_dataprep.R:202:81: style: Do not place spaces around code in parentheses or square brackets.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                ^

R/DAISIE_dataprep.R:202:82: style: There should be a space between right parenthesis and an opening curly brace.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                 ^~

R/DAISIE_dataprep.R:203:1: style: Lines should not be more than 80 characters.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:203:34: style: Use <-, not =, for assignment.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                 ^

R/DAISIE_dataprep.R:203:68: style: Commas should always have a space after.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                                                   ^

R/DAISIE_dataprep.R:204:21: style: Commas should always have a space after.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                    ^

R/DAISIE_dataprep.R:204:31: style: Put spaces around all infix operators.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                              ^~~

R/DAISIE_dataprep.R:204:49: style: Closing curly-braces should always be on their own line, unless it's followed by an else.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                                                ^

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data-raw/frog_M1_ML.R:5:1: style: Variable and function name style should be snake_case.

​frog_M1_ML <- DAISIE_ML(
^~~~~~~~~~

data-raw/frog_M1_ML.R:7:24: style: Commas should always have a space after.

​  initparsopt = c(0.18,0.03,0.0006,2),
                       ^

data-raw/frog_M1_ML.R:7:29: style: Commas should always have a space after.

​  initparsopt = c(0.18,0.03,0.0006,2),
                            ^

data-raw/frog_M1_ML.R:7:36: style: Commas should always have a space after.

​  initparsopt = c(0.18,0.03,0.0006,2),
                                   ^

data-raw/frog_M1_ML.R:8:19: style: Commas should always have a space after.

​  idparsopt = c(1,2,4,5),
                  ^

data-raw/frog_M1_ML.R:8:21: style: Commas should always have a space after.

​  idparsopt = c(1,2,4,5),
                    ^

data-raw/frog_M1_ML.R:8:23: style: Commas should always have a space after.

​  idparsopt = c(1,2,4,5),
                      ^

R/create_pars.R:21:1: style: functions should have cyclomatic complexity of less than 15, this has 35.

​are_area_pars <- function(area_pars) {
^

R/create_pars.R:151:1: style: functions should have cyclomatic complexity of less than 15, this has 33.

​are_trait_pars <- function(trait_pars) {
^

R/create_pars.R:174:1: style: Lines should not be more than 80 characters.

​#' @param immig_rate2  A numeric with the per capita immigration rate with state2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/create_pars.R:177:1: style: Lines should not be more than 80 characters.

​#' @param clado_rate2  A numeric with the per capita cladogenesis rate with state2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/create_pars.R:179:1: style: Lines should not be more than 80 characters.

​#' @param M2           A numeric with the number of species with trait state 2 on mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/create_pars.R:200:31: style: Variable and function name style should be snake_case.

​                              M2) {
                              ^~

R/create_pars.R:213:30: style: Put spaces around all infix operators.

​  testit::assert(trans_rate2 >=0.0)
                             ^~~

R/create_pars.R:214:21: style: Put spaces around all infix operators.

​  testit::assert(M2 >=0)
                    ^~~

R/DAISIE_check_format.R:7:1: style: functions should have cyclomatic complexity of less than 15, this has 44.

​are_rates <- function(rates) {
^

R/DAISIE_check_format.R:18:5: style: Place a space before left parenthesis, except in a function call.

​  if(length(rates) > 4) {
    ^

R/DAISIE_check_format.R:43:1: style: functions should have cyclomatic complexity of less than 15, this has 19.

​are_max_rates <- function(max_rates) {
^

R/DAISIE_check_format.R:155:7: style: Commented code should be removed.

​    # if (!"branching_times" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_check_format.R:156:7: style: Commented code should be removed.

​    # if (!"stac" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_check_format.R:157:7: style: Commented code should be removed.

​    # if (!"missing_species" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:8:1: style: Variable and function name style should be snake_case.

​DAISIE_create_island <- function(stt_table,
^~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:76:1: style: Variable and function name style should be snake_case.

​DAISIE_create_island_trait <- function(stt_table,
^~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:80:50: style: There should be a space between right parenthesis and an opening curly brace.

​                                       trait_pars){
                                                 ^~

R/DAISIE_create_island.R:82:1: style: Lines should not be more than 80 characters.

​  ### if there are no species on the island branching_times = island_age, stac = 0, missing_species = 0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:83:27: style: Commas should always have a space after.

​  if (length(island_spec[,1]) == 0) {
                          ^

R/DAISIE_create_island.R:102:1: style: Lines should not be more than 80 characters.

​    island_spec[, "branching time (BP)"] <- totaltime - as.numeric(island_spec[, "branching time (BP)"])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:103:1: style: Lines should not be more than 80 characters.

​    island_spec[, "Colonisation time (BP)"] <- totaltime - as.numeric(island_spec[, "Colonisation time (BP)"])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:105:21: style: Use <-, not =, for assignment.

​    mainland_ntotal = mainland_n + trait_pars$M2
                    ^

R/DAISIE_create_island.R:116:1: style: Lines should not be more than 80 characters.

​      colonists_present <- sort(as.numeric(unique(island_spec[, 'Mainland Ancestor'])))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:116:65: style: Only use double-quotes.

​      colonists_present <- sort(as.numeric(unique(island_spec[, 'Mainland Ancestor'])))
                                                                ^~~~~~~~~~~~~~~~~~~

R/DAISIE_create_island.R:139:1: style: Trailing blank lines are superfluous.

​
^

R/DAISIE_data.R:2:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 8 terrestrial avifaunal clades in list
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:7:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:23:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:24:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:25:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:47:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 8 terrestrial avifaunal clades in list
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:52:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:68:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:69:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close relatives
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:92:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:96:1: style: Lines should not be more than 80 characters.

​#' @description A table containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:103:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic: for non-endemic island species when an approximate time of colonisation is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:104:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic_MaxAge: for non-endemic island species when colonisation time is unknown \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:105:1: style: Lines should not be more than 80 characters.

​#' * Endemic: for endemic species when an approximate colonisation time is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:106:1: style: Lines should not be more than 80 characters.

​#' * "Endemic_MaxAge": applies to endemic species or endemic clades for cases where the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:109:1: style: Lines should not be more than 80 characters.

​#' This could for example apply to endemic species that have recently gone extinct because
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:113:1: style: Lines should not be more than 80 characters.

​#' time of the first cladogenetic event is known, but the precise time of colonisation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:120:1: style: Lines should not be more than 80 characters.

​#' \code{$Branching_times} - Stem age of the population/species in the case of "Non_endemic",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:121:1: style: Lines should not be more than 80 characters.

​#'  "Non_endemic_MaxAge" and "Endemic" species with no extant close relatives on the island.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:124:1: style: Lines should not be more than 80 characters.

​#' radiation, including the stem age of the radiation (colonisation time estimate).\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:134:1: style: Lines should not be more than 80 characters.

​#' @title 1000 islands in RAW format simulated with the ML parameters of the CR model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:137:1: style: Lines should not be more than 80 characters.

​#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:159:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_sim_constant_rate}()}, \code{\link{DAISIE_plot_sims}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:168:1: style: Lines should not be more than 80 characters.

​#' @title 1000 islands in DAISIE format simulated with the ML parameters of the CR
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:171:1: style: Lines should not be more than 80 characters.

​#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:195:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_sim_constant_rate}()}, \code{\link{DAISIE_plot_sims}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:207:1: style: Lines should not be more than 80 characters.

​#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:242:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_sim_constant_rate}()}, \code{\link{DAISIE_plot_sims}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:257:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:266:1: style: Lines should not be more than 80 characters.

​#' The following elements of the list each contains information on a single colonist lineage
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:270:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:271:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:272:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:274:1: style: Lines should not be more than 80 characters.

​#' branching times of the island clade including the stem age of the clade. \cr \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:288:1: style: Lines should not be more than 80 characters.

​#' R. Equilibrium bird species diversity in Atlantic islands. 2017 Current Biology, 27, 1660-1666.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:298:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the birds of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:300:1: style: Lines should not be more than 80 characters.

​#' Valente, Etienne, Garcia-R (2019) Current Biology. Island age 52 Myr and mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:312:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:313:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:314:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:328:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:329:1: style: Lines should not be more than 80 characters.

​#' @source Valente L, Etienne RS, Garcia-R JC (2019) Deep Macroevolutionary Impact of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:338:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of Noctilionoid bats from the Greater Antilles.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:341:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the noctilionoid
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:343:1: style: Lines should not be more than 80 characters.

​#' Valente, Etienne and Dávalos (2017) Nature Ecology and Evolution. Island age 20 Myr and
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:355:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:356:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:357:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:371:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:372:1: style: Lines should not be more than 80 characters.

​#' @source Valente L, Etienne RS, Dávalos (2017) Recent extinctions disturb path to
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:373:1: style: Lines should not be more than 80 characters.

​#' equilibrium diversity in Caribbean bats. Nature Ecology and Evolution, 1, 26.\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:385:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the fishes of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:386:1: style: Lines should not be more than 80 characters.

​#' Lake Biwa (Japan). Main dataset used in Hauffe et al (2020). This list can be generated
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:401:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:402:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:403:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:417:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:419:1: style: Lines should not be more than 80 characters.

​#' elevates equilibrium diversity via increasing colonisation. (2020) Journal of Biogeography \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:426:1: style: Lines should not be more than 80 characters.

​#' @format A dataframe containing information on archipelago name, area, age and distance from the mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:427:1: style: Lines should not be more than 80 characters.

​#' @description A dataframe with in subsequent columns the name of the archipelago (Archipelago)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:428:1: style: Lines should not be more than 80 characters.

​#' the area of the archipelago (Area), the age (Age) and the distance from the mainland (Distance)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:430:1: style: Lines should not be more than 80 characters.

​#'  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. A simple dynamic model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:440:1: style: Lines should not be more than 80 characters.

​#' @format A datalist containing data on the 41 archipelagos studied in Valente et
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:441:1: style: Lines should not be more than 80 characters.

​#' al 2020 (Main Dataset D1). Contains colonisation and branching times for bird species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:442:1: style: Lines should not be more than 80 characters.

​#' in each of the archipelagos. It also contains information on archipelago name, area,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:445:1: style: Lines should not be more than 80 characters.

​#' Each archipelago can be called separately using archipelagos41[[x]] with x being a
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:447:1: style: Lines should not be more than 80 characters.

​#' top part of the archipelago item where the archipelago name and physical features
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:448:1: style: Lines should not be more than 80 characters.

​#' are displayed. The structure of each of the archipelagos is the same as regular DAISIE
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:451:1: style: Lines should not be more than 80 characters.

​#'  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. A simple dynamic model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:460:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:464:1: style: Lines should not be more than 80 characters.

​#' @description A list containing the colonization and branching times of the Eleutherodactylus frogs of
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:466:1: style: Lines should not be more than 80 characters.

​#' using the DAISIE_dataprep function, which converts a user-specified data table into a data object,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:480:1: style: Lines should not be more than 80 characters.

​#' \code{$branching_times} - island age followed by stem age of the population/species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:481:1: style: Lines should not be more than 80 characters.

​#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:482:1: style: Lines should not be more than 80 characters.

​#' relatives on the island. For endemic clades with more than one species on the island
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:496:1: style: Lines should not be more than 80 characters.

​#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:497:1: style: Lines should not be more than 80 characters.

​#' @source Etienne RS, Haegeman B, Dugo-Cota A, Vila C, Gonzalez-Voyer A & Valente L. The
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:504:1: style: Lines should not be more than 80 characters.

​#' @title Colonization and branching times of 5 Eleutherodactylus (frogs) clades from
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:508:1: style: Lines should not be more than 80 characters.

​#' @description A table containing the colonization and branching times of the Eleutherodacytlus
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:509:1: style: Lines should not be more than 80 characters.

​#'frogs of the island of Hispaniola (Greater Antilles). Each row on the table represents and independent
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:515:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic: for non-endemic island species when an approximate time of colonisation is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:516:1: style: Lines should not be more than 80 characters.

​#' * Non_endemic_MaxAge: for non-endemic island species when colonisation time is unknown \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:517:1: style: Lines should not be more than 80 characters.

​#' * Endemic: for endemic species when an approximate colonisation time is known \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:518:1: style: Lines should not be more than 80 characters.

​#' * "Endemic_MaxAge": applies to endemic species or endemic clades for cases where the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:521:1: style: Lines should not be more than 80 characters.

​#' This could for example apply to endemic species that have recently gone extinct because
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:525:1: style: Lines should not be more than 80 characters.

​#' time of the first cladogenetic event is known, but the precise time of colonisation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_data.R:529:1: style: Lines should not be more than 80 characters.

​#' @source Etienne RS, Haegeman B, Dugo-Cota A, Vila C, Gonzalez-Voyer A & Valente L. The
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:16:1: style: Lines should not be more than 80 characters.

​#' "Non_endemic": applies to non-endemic species when an approximate colonisation time is known \cr *
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:18:1: style: Lines should not be more than 80 characters.

​#' colonisation time is unknown \cr * "Endemic": applies to endemic species or endemic
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:19:1: style: Lines should not be more than 80 characters.

​#' clades when an approximate colonisation time is known \cr * "Endemic_MaxAge": applies to endemic
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:20:1: style: Lines should not be more than 80 characters.

​#' species or endemic clades for cases where the colonisation time is unknown, or when
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:22:1: style: Lines should not be more than 80 characters.

​#' This could for example apply to endemic species that have recently gone extinct because
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:26:1: style: Lines should not be more than 80 characters.

​#' time of the first cladogenetic event is known, but the precise time of colonisation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:27:1: style: Lines should not be more than 80 characters.

​#' is not. \cr * "Endemic&Non_Endemic": when endemic clade is present and its mainland
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:31:1: style: Lines should not be more than 80 characters.

​#'  be equal to the number of species in the clade minus 1 \cr \code{$Branching_times}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:32:1: style: Lines should not be more than 80 characters.

​#'  - Stem age of the population/species in the case of "Non_endemic", "Non_endemic_MaxAge"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:33:1: style: Lines should not be more than 80 characters.

​#'  and "Endemic" species with no extant close relatives on the island. Set "NA" if
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:36:1: style: Lines should not be more than 80 characters.

​#' radiation, including the stem age of the radiation (colonisation time estimate).\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:82:1: style: Lines should not be more than 80 characters.

​#' \cr * Endemic_MaxAge: 6 (if colonisation time and cladogenesis times were given)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:84:1: style: Lines should not be more than 80 characters.

​#' for particular clade (only applicable for endemic clades) \cr \code{$type_1or2}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:96:1: style: Lines should not be more than 80 characters.

​#' ### Create Galapagos data object where all taxa have the same macroevolutionary process
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:106:1: style: Lines should not be more than 80 characters.

​#' # for the Darwin's finches. One process applies to type 1 species (all species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:121:1: style: Lines should not be more than 80 characters.

​#' # for the Darwin's finches. One process applies to type 1 species (all species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:123:1: style: Lines should not be more than 80 characters.

​#' # (Darwin's finches). Set fraction of potential colonists of type 2 to be 0.163.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:136:1: style: functions should have cyclomatic complexity of less than 15, this has 29.

​DAISIE_dataprep = function(datatable,
^

R/DAISIE_dataprep.R:136:1: style: Variable and function name style should be snake_case.

​DAISIE_dataprep = function(datatable,
^~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:136:17: style: Use <-, not =, for assignment.

​DAISIE_dataprep = function(datatable,
                ^

R/DAISIE_dataprep.R:138:28: style: Variable and function name style should be snake_case.

​                           M,
                           ^

R/DAISIE_dataprep.R:144:1: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​{
^

R/DAISIE_dataprep.R:147:13: style: Variable and function name style should be snake_case.

​  datatable$Missing_species <- as.numeric(as.character
            ^~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:158:40: style: Do not place spaces around code in parentheses or square brackets.

​      not_present_type1 <- DDD::roundn( (M / number_colonisations) *
                                       ^

R/DAISIE_dataprep.R:161:40: style: Do not place spaces around code in parentheses or square brackets.

​      not_present_type2 <- DDD::roundn( (M / number_colonisations) *
                                       ^

R/DAISIE_dataprep.R:174:13: warning: Avoid 1:nrow(...) expressions, use seq_len.

​  for (i in 1:nrow(datatable)) {
            ^

R/DAISIE_dataprep.R:184:7: style: Place a space before left parenthesis, except in a function call.

​    if(is.na(the_brts[1])){
      ^

R/DAISIE_dataprep.R:184:26: style: There should be a space between right parenthesis and an opening curly brace.

​    if(is.na(the_brts[1])){
                         ^~

R/DAISIE_dataprep.R:185:15: style: Put spaces around all infix operators.

​      the_brts<-island_age
             ~^~~

R/DAISIE_dataprep.R:186:1: style: Lines should not be more than 80 characters.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:186:9: style: Place a space before left parenthesis, except in a function call.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
        ^

R/DAISIE_dataprep.R:186:22: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                     ^

R/DAISIE_dataprep.R:186:59: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                          ^

R/DAISIE_dataprep.R:186:81: style: Do not place spaces around code in parentheses or square brackets.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                ^

R/DAISIE_dataprep.R:186:82: style: There should be a space between right parenthesis and an opening curly brace.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                 ^~

R/DAISIE_dataprep.R:187:1: style: Lines should not be more than 80 characters.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:187:34: style: Use <-, not =, for assignment.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                 ^

R/DAISIE_dataprep.R:187:68: style: Commas should always have a space after.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                                                   ^

R/DAISIE_dataprep.R:188:21: style: Commas should always have a space after.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                    ^

R/DAISIE_dataprep.R:188:31: style: Put spaces around all infix operators.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                              ^~~

R/DAISIE_dataprep.R:188:49: style: Closing curly-braces should always be on their own line, unless it's followed by an else.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                                                ^

R/DAISIE_dataprep.R:189:1: style: Lines should not be more than 80 characters.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:189:9: style: Place a space before left parenthesis, except in a function call.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
        ^

R/DAISIE_dataprep.R:189:22: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
                     ^

R/DAISIE_dataprep.R:189:63: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
                                                              ^

R/DAISIE_dataprep.R:189:89: style: There should be a space between right parenthesis and an opening curly brace.

​      if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"){
                                                                                        ^~

R/DAISIE_dataprep.R:190:1: style: Lines should not be more than 80 characters.

​        levels(datatable$Status) = append(levels(datatable$Status),"Non_endemic_MaxAge")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:190:34: style: Use <-, not =, for assignment.

​        levels(datatable$Status) = append(levels(datatable$Status),"Non_endemic_MaxAge")
                                 ^

R/DAISIE_dataprep.R:190:68: style: Commas should always have a space after.

​        levels(datatable$Status) = append(levels(datatable$Status),"Non_endemic_MaxAge")
                                                                   ^

R/DAISIE_dataprep.R:191:21: style: Commas should always have a space after.

​        datatable[i,"Status"] <-"Non_endemic_MaxAge"}
                    ^

R/DAISIE_dataprep.R:191:31: style: Put spaces around all infix operators.

​        datatable[i,"Status"] <-"Non_endemic_MaxAge"}
                              ^~~

R/DAISIE_dataprep.R:191:53: style: Closing curly-braces should always be on their own line, unless it's followed by an else.

​        datatable[i,"Status"] <-"Non_endemic_MaxAge"}
                                                    ^

R/DAISIE_dataprep.R:194:7: style: Place a space before left parenthesis, except in a function call.

​    if(max(the_brts)>island_age){
      ^

R/DAISIE_dataprep.R:194:21: style: Put spaces around all infix operators.

​    if(max(the_brts)>island_age){
                   ~^~

R/DAISIE_dataprep.R:194:32: style: There should be a space between right parenthesis and an opening curly brace.

​    if(max(the_brts)>island_age){
                               ^~

R/DAISIE_dataprep.R:202:1: style: Lines should not be more than 80 characters.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:202:9: style: Place a space before left parenthesis, except in a function call.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
        ^

R/DAISIE_dataprep.R:202:22: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                     ^

R/DAISIE_dataprep.R:202:59: style: Commas should always have a space after.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                          ^

R/DAISIE_dataprep.R:202:81: style: Do not place spaces around code in parentheses or square brackets.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                ^

R/DAISIE_dataprep.R:202:82: style: There should be a space between right parenthesis and an opening curly brace.

​      if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
                                                                                 ^~

R/DAISIE_dataprep.R:203:1: style: Lines should not be more than 80 characters.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DAISIE_dataprep.R:203:34: style: Use <-, not =, for assignment.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                 ^

R/DAISIE_dataprep.R:203:68: style: Commas should always have a space after.

​        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
                                                                   ^

R/DAISIE_dataprep.R:204:21: style: Commas should always have a space after.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                    ^

R/DAISIE_dataprep.R:204:31: style: Put spaces around all infix operators.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                              ^~~

R/DAISIE_dataprep.R:204:49: style: Closing curly-braces should always be on their own line, unless it's followed by an else.

​        datatable[i,"Status"] <-"Endemic_MaxAge"}
                                                ^

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