Package: DAISIE 4.4.1
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:
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')) |
Bug tracker:https://github.com/rsetienne/daisie/issues
Pkgdown:https://rsetienne.github.io
- 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
Last updated 1 years agofrom:737aa984de. Checks:OK: 1 NOTE: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 15 2024 |
R-4.5-linux-x86_64 | NOTE | Nov 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.Rmd
usingknitr::rmarkdown
on Nov 15 2024.Last update: 2022-06-02
Started: 2022-06-02
Demo optimizing parameters
Rendered fromdemo_optimize.Rmd
usingknitr::rmarkdown
on Nov 15 2024.Last update: 2022-06-02
Started: 2020-08-14
Demo simulating islands
Rendered fromdemo_sim.Rmd
usingknitr::rmarkdown
on Nov 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.Rmd
usingknitr::rmarkdown
on Nov 15 2024.Last update: 2022-06-02
Started: 2020-08-14