Package: DAISIE 4.4.1

Rampal S. Etienne

DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.

Authors:Rampal S. Etienne [aut, cre], Luis Valente [aut], Albert B. Phillimore [aut], Bart Haegeman [aut], Joshua W. Lambert [aut], Pedro Santos Neves [aut], Shu Xie [aut], Richèl J.C. Bilderbeek [aut], Hanno Hildenbrandt [aut], Torsten Hauffe [ctb], Giovanni Laudanno [ctb], Nadiah Kristensen [ctb], Raphael Scherrer [ctb]

DAISIE_4.4.1.tar.gz
DAISIE_4.4.1.tar.gz(r-4.5-noble)DAISIE_4.4.1.tar.gz(r-4.4-noble)
DAISIE_4.4.1.tgz(r-4.4-emscripten)DAISIE_4.4.1.tgz(r-4.3-emscripten)
DAISIE.pdf |DAISIE.html✨
DAISIE/json (API)
NEWS

# Install 'DAISIE' in R:
install.packages('DAISIE', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rsetienne/daisie/issues

Pkgdown site:https://rsetienne.github.io

Uses libs:
  • fortran– Runtime library for GNU Fortran applications
  • c++– GNU Standard C++ Library v3
Datasets:
  • Bats_GreaterAntilles - Colonization and branching times of Noctilionoid bats from the Greater Antilles.
  • Biwa_datalist - Colonization and branching times of 68 fish clades.
  • Galapagos_datalist - Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all
  • Galapagos_datalist_2types - Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all
  • Galapagos_datatable - Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format.
  • Macaronesia_datalist - Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all
  • NewZealand_birds_datalist - Colonization and branching times of New Zealand birds.
  • archipelago_data - Physical data on 41 archipelagos
  • archipelagos41 - DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos
  • frogs_datalist - Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island.
  • frogs_datatable - Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola.
  • islands_10reps_RAW - 1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data.
  • islands_1type_1000reps - 1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data
  • islands_2types_1000reps - 1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data
  • stac_table - Explanatory table on meaning and use of 'stac' settings

fortrancpp

3.78 score 1 packages 55 scripts 262 downloads 5 mentions 42 exports 44 dependencies

Last updated 1 years agofrom:737aa984de. Checks:OK: 1 NOTE: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 15 2024
R-4.5-linux-x86_64NOTEDec 15 2024

Exports:create_area_parscreate_CS_versioncreate_hyper_parscreate_parscreate_trait_parscreate_trait_pars_2KDAISIE_abm_factorDAISIE_convertprobdistDAISIE_count_speciesDAISIE_CS_max_stepsDAISIE_dataprepDAISIE_ExpEINDAISIE_ICDAISIE_IW_num_threadsDAISIE_loglik_allDAISIE_loglik_CSDAISIE_loglik_IWDAISIE_margprobdistDAISIE_MLDAISIE_ML_CSDAISIE_ML_IWDAISIE_MW_MLDAISIE_numcoldaisie_odeint_csdaisie_odeint_iwDAISIE_plot_age_diversityDAISIE_plot_inputDAISIE_plot_islandDAISIE_plot_simsDAISIE_probdistDAISIE_simDAISIE_sim_crDAISIE_sim_cr_shiftDAISIE_sim_MWDAISIE_sim_relaxed_rateDAISIE_sim_time_depDAISIE_sim_trait_depDAISIE_sim_trait_dep_2KDAISIE_SR_loglik_allDAISIE_SR_loglik_CSDAISIE_SR_MLDAISIE_SR_ML_CS

Dependencies:apeBHcliclusterGenerationcodacodetoolscombinatcpp11DDDDEoptimdeSolvedigestdoParallelexpmfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtnlmenumDerivoptimParallelphangornphytoolspkgconfigpracmaquadprogRcppRcppEigenrlangscatterplot3dSparseMsubplextensortestitvctrs

DAISIE stac values

Rendered fromstac_key.Rmdusingknitr::rmarkdownon Dec 15 2024.

Last update: 2022-06-02
Started: 2022-06-02

Demo optimizing parameters

Luis M. Valente, Albert B. Phillimore, Rampal S. Etienne

Rendered fromdemo_optimize.Rmdusingknitr::rmarkdownon Dec 15 2024.

Last update: 2022-06-02
Started: 2020-08-14

Demo simulating islands

Luis M. Valente, Albert B. Phillimore, Rampal S. Etienne

Rendered fromdemo_sim.Rmdusingknitr::rmarkdownon Dec 15 2024.

Last update: 2022-06-02
Started: 2020-08-14

Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE

Rendered fromdemo_CSvsIW.Rmdusingknitr::rmarkdownon Dec 15 2024.

Last update: 2022-06-02
Started: 2020-08-14

Readme and manuals

Help Manual

Help pageTopics
Add a column to a data frameadd_column_to_dataframe
Physical data on 41 archipelagosarchipelago_data
DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagosarchipelagos41
Colonization and branching times of Noctilionoid bats from the Greater Antilles.Bats_GreaterAntilles
Colonization and branching times of 68 fish clades.Biwa_datalist
Create named list of area parameterscreate_area_pars
Creates the list object for CS_version argument in DAISIE_ML_CScreate_CS_version
Create list of hyperparameterscreate_hyper_pars
Create vector of model parameterscreate_pars
Create named list of trait state parameterscreate_trait_pars
Create named list of trait state parameterscreate_trait_pars_2K
Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers.DAISIE_abm_factor
Converts the joint distribution of endemics and non-endemics under the DAISIE model to list formatDAISIE_convertprobdist
Count number of species in DAISIE datalist or simulated data.DAISIE_count_species
CS iteration controlDAISIE_CS_max_steps
Prepare colonisation and branching time data to run in DAISIE.DAISIE_dataprep
The expected number of endemics and non-endemics under the DAISIE modelDAISIE_ExpEIN
Formats clade-specific simulation output into standard DAISIE list output with complete STT tableDAISIE_format_CS_full_stt
Formats clade-specific simulation output into standard DAISIE list output with complete STT tableDAISIE_format_IW_full_stt
Calculates information criterion from DAISIE ML estimates?DAISIE_IC
IW concurrency controlDAISIE_IW_num_threads
Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parametersDAISIE_loglik_IW
The marginal distribution of endemics and non-endemics under the DAISIE modelDAISIE_margprobdist
Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependenceDAISIE_ML DAISIE_ML_CS
Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependenceDAISIE_ML_IW
Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur & WilsonDAISIE_MW_ML
The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE modelDAISIE_numcol
Driver for the boost::odeint solver for the CS modeldaisie_odeint_cs
Driver for the boost::odeint solver for the IW modeldaisie_odeint_iw
Plot clade age against clade diversity.DAISIE_plot_age_diversity
DAISIE tree plotDAISIE_plot_input
Plot colonisation and branching time of species found on an island dataset.DAISIE_plot_island
Plot island species-through-time (STT) plotsDAISIE_plot_sims
The joint distribution of endemics and non-endemics under the DAISIE modelDAISIE_probdist
Simulate (non-)oceanic islands with given parameters under time-constant ratesDAISIE_sim DAISIE_sim_cr
Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate processDAISIE_sim_cr_cs
Simulates island replicates with an guild-wide (GW) diversity-dependent processDAISIE_sim_cr_gw
Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate processDAISIE_sim_cr_iw
Simulate (non-)oceanic islands with given parameters under a rate-shift regimeDAISIE_sim_cr_shift
Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parametersDAISIE_sim_MW
Simulate (non-)oceanic islands with given parameters under a relaxed-rate modelDAISIE_sim_relaxed_rate
Simulate (non-)oceanic islands with given parameters under a time-dependent regimeDAISIE_sim_time_dep
Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent processDAISIE_sim_time_dep_cs
Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent processDAISIE_sim_time_dep_gw
Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent processDAISIE_sim_time_dep_iw
Simulate islands with given trait-dependent parameters.DAISIE_sim_trait_dep
Simulate islands with given trait-dependent parameters.DAISIE_sim_trait_dep_2K
Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some timeDAISIE_SR_loglik_all DAISIE_SR_loglik_CS
Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependenceDAISIE_SR_ML DAISIE_SR_ML_CS
Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island.frogs_datalist
Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola.frogs_datatable
Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_allGalapagos_datalist
Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_allGalapagos_datalist_2types
Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format.Galapagos_datatable
1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data.islands_10reps_RAW
1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos dataislands_1type_1000reps
1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species)islands_2types_1000reps
Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_allMacaronesia_datalist
Colonization and branching times of New Zealand birds.NewZealand_birds_datalist
Explanatory table on meaning and use of 'stac' settingsstac_table