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DAISIE  

Dynamical Assembly of Islands by Speciation, Immigration and Extinction
View on CRAN: Click here


Download and install DAISIE package within the R console
Install from CRAN:
install.packages("DAISIE")

Install from Github:
library("remotes")
install_github("cran/DAISIE")

Install by package version:
library("remotes")
install_version("DAISIE", "4.4.1")



Attach the package and use:
library("DAISIE")
Maintained by
Rampal S. Etienne
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-05-21
Latest Update: 2023-04-02
Description:
Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) .
How to cite:
Rampal S. Etienne (2015). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. R package version 4.4.1, https://cran.r-project.org/web/packages/DAISIE. Accessed 22 Dec. 2024.
Previous versions and publish date:
1.0.1 (2015-06-03 08:11), 1.0.2 (2015-09-29 17:46), 1.0 (2015-05-21 09:40), 1.2 (2016-11-14 11:32), 1.4 (2017-04-13 19:50), 3.0.0 (2020-08-14 12:12), 3.0.1 (2020-08-26 12:00), 4.2.0 (2022-06-02 13:30), 4.3.1 (2023-02-13 10:40), 4.4.0 (2023-04-03 00:10)
Other packages that cited DAISIE R package
View DAISIE citation profile
Other R packages that DAISIE depends, imports, suggests or enhances
Complete documentation for DAISIE
Functions, R codes and Examples using the DAISIE R package
Some associated functions: Bats_GreaterAntilles . Biwa_datalist . DAISIE-package . DAISIE_CS_max_steps . DAISIE_ExpEIN . DAISIE_IC . DAISIE_IW_num_threads . DAISIE_ML . DAISIE_ML1 . DAISIE_ML2 . DAISIE_ML4 . DAISIE_ML_IW . DAISIE_MW_ML . DAISIE_ONEcolonist . DAISIE_SR_ML . DAISIE_SR_loglik_CS . DAISIE_SR_sim . DAISIE_SR_sim_core . DAISIE_abm_factor . DAISIE_calc_sumstats_pcrates . DAISIE_convert_to_classic_plot . DAISIE_convertprobdist . DAISIE_create_island . DAISIE_dataprep . DAISIE_extract_stt_median . DAISIE_format_CS . DAISIE_format_CS_full_stt . DAISIE_format_CS_sampled_stt . DAISIE_format_GW . DAISIE_format_IW . DAISIE_format_IW_full_stt . DAISIE_format_IW_sampled_stt . DAISIE_loglik_CS . DAISIE_loglik_IW . DAISIE_loglik_integrand . DAISIE_loglik_integrate . DAISIE_make_archipelago . DAISIE_make_global . DAISIE_margprobdist . DAISIE_nonoceanic_spec . DAISIE_numcol . DAISIE_plot_age_diversity . DAISIE_plot_area . DAISIE_plot_cladogenesis . DAISIE_plot_comparison_stts . DAISIE_plot_extinction . DAISIE_plot_immigration . DAISIE_plot_input . DAISIE_plot_island . DAISIE_plot_pc_rates . DAISIE_plot_sims . DAISIE_plot_stt . DAISIE_probdist . DAISIE_sample_event_cr . DAISIE_sample_event_time_dep . DAISIE_sample_event_trait_dep . DAISIE_sim . DAISIE_sim_MW . DAISIE_sim_core_cr . DAISIE_sim_core_cr_shift . DAISIE_sim_core_time_dep . DAISIE_sim_core_trait_dep . DAISIE_sim_cr_cs . DAISIE_sim_cr_gw . DAISIE_sim_cr_iw . DAISIE_sim_cr_shift . DAISIE_sim_min_type2 . DAISIE_sim_relaxed_rate . DAISIE_sim_time_dep . DAISIE_sim_time_dep_cs . DAISIE_sim_time_dep_gw . DAISIE_sim_time_dep_iw . DAISIE_sim_trait_dep . DAISIE_sim_update_state_cr . DAISIE_sim_update_state_time_dep . DAISIE_sim_update_state_trait_dep . Galapagos_datalist . Galapagos_datalist_2types . Galapagos_datatable . Macaronesia_datalist . NewZealand_birds_datalist . add_column_to_dataframe . archipelago_data . archipelagos41 . are_area_pars . are_hyper_pars . are_max_rates . are_max_rates_gt_rates . are_rates . are_trait_pars . calc_Abeta . calc_next_timeval . calc_next_timeval_shift . calc_peak . countspecies . create_CS_version . create_area_pars . create_full_CS_stt . create_hyper_pars . create_pars . create_trait_pars . daisie_odeint_cs . daisie_odeint_iw . default_params_doc . frogs_datalist . frogs_datatable . get_ana_rate . get_clado_rate . get_clado_rate_per_capita . get_ext_rate . get_ext_rate_per_capita . get_global_max_area . get_global_min_area . get_immig_rate . get_immig_rate_per_capita . get_trans_rate . integral_peak . is_island_ontogeny_input . is_sea_level_input . is_simulation_outputs . island_area . island_area_vector . islands_10reps_RAW . islands_1type_1000reps . islands_2types_1000reps . remove_empty_elements . rho . sample_relaxed_rate . stac_table . transform_gamma_pars . translate_island_ontogeny . translate_sea_level . update_max_rates . update_rates . 
Some associated R codes: DAISIE-package.R . DAISIE_ExpEIN.R . DAISIE_IC.R . DAISIE_ML1.R . DAISIE_ML2.R . DAISIE_ML4.R . DAISIE_ML_CS.R . DAISIE_ML_IW.R . DAISIE_MW_ML.R . DAISIE_ONEcolonist.R . DAISIE_PEI.R . DAISIE_SR_ML_CS.R . DAISIE_SR_loglik_CS.R . DAISIE_SR_sim.R . DAISIE_SR_sim_core.R . DAISIE_check_format.R . DAISIE_create_island.R . DAISIE_data.R . DAISIE_dataprep.R . DAISIE_extract_stt_median.R . DAISIE_format_CS.R . DAISIE_format_CS_full_stt.R . DAISIE_format_CS_sampled_stt.R . DAISIE_format_CS_trait.R . DAISIE_format_GW.R . DAISIE_format_IW.R . DAISIE_format_IW_full_stt.R . DAISIE_format_IW_sampled_stt.R . DAISIE_loglik_CS.R . DAISIE_loglik_CS_time.R . DAISIE_loglik_IW.R . DAISIE_loglik_IW0.R . DAISIE_loglik_high_lambda.R . DAISIE_loglik_integrate.R . DAISIE_make_archipelago.R . DAISIE_max_rates.R . DAISIE_plot_age_diversity.R . DAISIE_plot_comparison_stts.R . DAISIE_plot_input.R . DAISIE_plot_island.R . DAISIE_plot_params.R . DAISIE_plot_pc_rates.R . DAISIE_plot_sims.R . DAISIE_plot_stt.R . DAISIE_rates.R . DAISIE_sample_event_cr.R . DAISIE_sample_event_time_dep.R . DAISIE_sample_event_trait_dep.R . DAISIE_sim_MW.R . DAISIE_sim_core_cr.R . DAISIE_sim_core_cr_shift.R . DAISIE_sim_core_time_dep.R . DAISIE_sim_core_trait_dep.R . DAISIE_sim_cr.R . DAISIE_sim_cr_cs.R . DAISIE_sim_cr_gw.R . DAISIE_sim_cr_iw.R . DAISIE_sim_cr_shift.R . DAISIE_sim_min_type2.R . DAISIE_sim_relaxed_rate.R . DAISIE_sim_time_dep.R . DAISIE_sim_time_dep_cs.R . DAISIE_sim_time_dep_gw.R . DAISIE_sim_time_dep_iw.R . DAISIE_sim_trait_dep.R . DAISIE_sim_update_state_cr.R . DAISIE_sim_update_state_time_dep.R . DAISIE_sim_update_state_trait_dep.R . DAISIE_sumstats_rates.R . DAISIE_utils.R . RcppExports.R . create_pars.R . default_params_doc.R . remove_empty_elements.R .  Full DAISIE package functions and examples
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