Files in DAISIE
Dynamical Assembly of Islands by Speciation, Immigration and Extinction

MD5
NAMESPACE
DESCRIPTION
build/vignette.rds
src/R_init_DAISIE.c
src/Makevars
src/DAISIE_loglik_rhs_FORTRAN.f95
data/archipelago_data.RData
data/Galapagos_datatable.RData
data/frogs_datalist.RData
data/Galapagos_datalist_2types.RData
data/Galapagos_datalist.RData
data/islands_1type_1000reps.RData
data/islands_10reps_RAW.RData
data/NewZealand_birds_datalist.RData
data/islands_2types_1000reps.RData
data/archipelagos41.RData
data/frogs_datatable.RData
data/Macaronesia_datalist.RData
data/Bats_GreaterAntilles.RData
data/Biwa_datalist.RData
R/DAISIE_format_GW.R R/DAISIE_get_brts_mya.R R/DAISIE_SR_ML_CS.R R/DAISIE_plot_age_diversity.R R/DAISIE_loglik_high_lambda.R R/DAISIE_plot_island.R R/DAISIE-package.R R/DAISIE_format_CS_full_stt.R R/default_params_doc.R R/DAISIE_sample_event_constant_rate.R R/DAISIE_data.R R/DAISIE_sim_constant_rate_shift.R R/DAISIE_dataprep.R R/DAISIE_loglik_CS.R R/DAISIE_sim_MW.R R/DAISIE_create_island.R R/DAISIE_format_CS.R R/DAISIE_MW_ML.R R/DAISIE_sim_update_state_time_dependent.R R/DAISIE_format_IW.R R/DAISIE_single_branch.R R/DAISIE_ML_IW.R R/DAISIE_loglik_IW.R R/DAISIE_sample_event_trait_dependent.R R/DAISIE_sim_update_state_constant_rate.R R/DAISIE_sim_core_1_4a.R R/DAISIE_SR_loglik_CS.R R/DAISIE_format_IW_v1_5.R R/DAISIE_sim_core_trait_dependent.R R/DAISIE_plot_pc_rates.R R/DAISIE_sim_core_constant_rate_shift.R R/DAISIE_plot_comparison_stts.R R/DAISIE_sim_time_dependent.R R/DAISIE_rates.R R/DAISIE_make_archipelago.R R/DAISIE_utils.R R/DAISIE_sumstats_rates.R R/DAISIE_check_format.R R/DAISIE_ML2.R R/DAISIE_SR_sim.R R/DAISIE_sim_core_1_5.R R/DAISIE_sim_min_type2.R R/DAISIE_plot_sims.R R/DAISIE_format_CS_sampled_stt.R R/DAISIE_plot_input.R R/utils-pipe.R R/DAISIE_loglik_CS_time.R R/DAISIE_plot_params.R R/DAISIE_ExpEIN.R R/DAISIE_loglik_IW0.R R/DAISIE_sim_update_state_trait_dependent.R R/DAISIE_sim_relaxed_rate.R R/create_pars.R R/DAISIE_loglik_integrate.R R/remove_empty_elements.R R/DAISIE_IC.R R/DAISIE_sim_trait_dependent.R R/DAISIE_ML3.R R/DAISIE_SR_sim_core.R R/DAISIE_ONEcolonist.R R/DAISIE_sim_constant_rate.R R/DAISIE_plot_stt.R R/DAISIE_PEI.R R/DAISIE_sample_event_time_dependent.R R/DAISIE_ML1.R R/DAISIE_sim_core_constant_rate.R R/DAISIE_extract_stt_median.R R/DAISIE_max_rates.R R/DAISIE_ML4.R R/DAISIE_sim_core_1_4.R R/DAISIE_sim_core_time_dependent.R R/DAISIE_ML_CS.R vignettes/demo_CSvsIW.Rmd vignettes/demo_sim.Rmd vignettes/demo_optimize.Rmd man/DAISIE_sample_event_constant_rate.Rd man/Galapagos_datalist_2types.Rd man/translate_sea_level.Rd man/calc_next_timeval.Rd man/create_trait_pars.Rd man/is_simulation_outputs.Rd man/DAISIE_sim_core_constant_rate_shift.Rd man/update_max_rates.Rd man/rho.Rd man/archipelago_data.Rd man/DAISIE_sim_constant_rate_shift.Rd man/DAISIE_single_branch.Rd man/DAISIE_sim_MW.Rd man/island_area_vector.Rd man/DAISIE_sim_update_state_constant_rate.Rd man/DAISIE_calc_clade_clado_rate.Rd man/DAISIE_loglik_IW.Rd man/DAISIE_calc_clade_ext_rate.Rd man/get_global_min_area.Rd man/DAISIE_plot_pc_rates.Rd man/are_hyper_pars.Rd man/integral_peak.Rd man/DAISIE_sim_update_state_time_dependent.Rd man/DAISIE_probdist.Rd man/Macaronesia_datalist.Rd man/DAISIE_format_IW.Rd man/DAISIE_plot_immigration.Rd man/DAISIE_MW_ML.Rd man/is_island_ontogeny_input.Rd man/DAISIE_convertprobdist.Rd man/countspecies.Rd man/DAISIE_margprobdist.Rd man/DAISIE_sim_trait_dependent.Rd man/DAISIE_calc_sumstats_pcrates.Rd man/DAISIE_sample_event_trait_dependent.Rd man/DAISIE_sim_core_1_4a.Rd man/get_ana_rate.Rd man/Galapagos_datalist.Rd man/DAISIE_format_CS_full_stt.Rd man/DAISIE_sim_core_1_4.Rd man/DAISIE_calc_clade_ana_rate.Rd man/DAISIE_sim_update_state_trait_dependent.Rd man/DAISIE_IC.Rd man/DAISIE_SR_ML.Rd man/pipe.Rd man/get_clado_rate.Rd man/archipelagos41.Rd man/translate_island_ontogeny.Rd man/calc_peak.Rd man/DAISIE_extract_stt_median.Rd man/DAISIE_plot_extinction.Rd man/DAISIE_nonoceanic_spec.Rd man/DAISIE_format_GW.Rd man/are_trait_pars.Rd man/are_max_rates.Rd man/DAISIE_SR_loglik_CS.Rd man/islands_1type_1000reps.Rd man/DAISIE_create_island.Rd man/remove_empty_elements.Rd man/DAISIE_convert_to_classic_plot.Rd man/DAISIE_numcol.Rd man/DAISIE_loglik_integrand.Rd man/DAISIE_get_brts_mya.Rd man/DAISIE_plot_comparison_stts.Rd man/are_area_pars.Rd man/DAISIE_ExpEIN.Rd man/DAISIE_sim_core_trait_dependent.Rd man/DAISIE_make_global.Rd man/are_max_rates_gt_rates.Rd man/DAISIE_plot_age_diversity.Rd man/get_trans_rate.Rd man/create_CS_version.Rd man/DAISIE_format_CS.Rd man/frogs_datalist.Rd man/Biwa_datalist.Rd man/DAISIE_plot_area.Rd man/DAISIE_plot_sims.Rd man/get_ext_rate.Rd man/calc_next_timeval_shift.Rd man/Galapagos_datatable.Rd man/DAISIE_plot_input.Rd man/islands_2types_1000reps.Rd man/DAISIE_sim_min_type2.Rd man/create_full_CS_stt.Rd man/sample_relaxed_rate.Rd man/DAISIE_loglik_integrate.Rd man/create_area_pars.Rd man/island_area.Rd man/islands_10reps_RAW.Rd man/get_immig_rate.Rd man/DAISIE_sim.Rd man/calc_Abeta.Rd man/is_sea_level_input.Rd man/DAISIE_ML.Rd man/DAISIE_make_archipelago.Rd man/DAISIE_SR_sim.Rd man/DAISIE-package.Rd man/DAISIE_ML_IW.Rd man/DAISIE_ML4.Rd man/DAISIE_ML1.Rd man/DAISIE_ML2.Rd man/update_rates.Rd man/DAISIE_plot_stt.Rd man/get_global_max_area.Rd man/are_rates.Rd man/NewZealand_birds_datalist.Rd man/frogs_datatable.Rd man/DAISIE_sim_time_dependent.Rd man/DAISIE_sim_core_constant_rate.Rd man/DAISIE_plot_island.Rd man/DAISIE_dataprep.Rd man/DAISIE_SR_sim_core.Rd man/DAISIE_sample_event_time_dependent.Rd man/default_params_doc.Rd man/DAISIE_plot_cladogenesis.Rd man/DAISIE_sim_core_time_dependent.Rd man/DAISIE_ONEcolonist.Rd man/DAISIE_format_CS_sampled_stt.Rd man/Bats_GreaterAntilles.Rd man/DAISIE_ML3.Rd man/create_hyper_pars.Rd man/DAISIE_calc_clade_imm_rate.Rd man/DAISIE_sim_relaxed_rate.Rd man/DAISIE_loglik_CS.Rd tests/testthat.R tests/testthat/test-DAISIE_ML_CS.R tests/testthat/test-are_rates.R tests/testthat/test-DAISIE_convert_to_classic_plot.R tests/testthat/test-DAISIE_SR_loglik.R tests/testthat/test-are_max_rates.R tests/testthat/test-DAISIE_ONEcolonist.R tests/testthat/test-create_trait_pars.R tests/testthat/test-DAISIE_loglik_CS.R tests/testthat/test-DAISIE_format_IW.R tests/testthat/test-DAISIE_sim_core_trait_dependent.R tests/testthat/test-integration_DAISIE.R tests/testthat/test-is_sea_level_input.R tests/testthat/test-DAISIE_format_CS_full_stt.R tests/testthat/test-DAISIE_ExpEIN.R tests/testthat/test-DAISIE_sim_time_dependent.R tests/testthat/test-DAISIE_ML2.R tests/testthat/test-DAISIE_loglik_integrate.R tests/testthat/test-are_trait_pars.R tests/testthat/test-DAISIE_dataprep.R tests/testthat/test-DAISIE_sim_constant_rate_shift.R tests/testthat/test-DAISIE_format_CS_sampled_stt.R tests/testthat/test-DAISIE_plot_stt.R tests/testthat/test-DAISIE_sim_core_constant_rate.R tests/testthat/test-DAISIE_sim_constant_rate.R tests/testthat/test-DAISIE_sumstats_rates.R tests/testthat/test-DAISIE_min_rates.R tests/testthat/test-are_max_rates_gt_rates.R tests/testthat/test-are_area_pars.R tests/testthat/test-update_max_rates.R tests/testthat/test-DAISIE_ML4.R tests/testthat/test-DAISIE_plot_comparison_stts.R tests/testthat/test-DAISIE_plot_sims.R tests/testthat/test-DAISIE_sim_MW.R tests/testthat/test-DAISIE_sim_core_constant_rate_shift.R tests/testthat/test-DAISIE_ML1.R tests/testthat/test-DAISIE_extract_stt_median.R tests/testthat/test-DAISIE_sim_core_time_dependent.R tests/testthat/test-DAISIE_format_CS.R tests/testthat/test-DAISIE_format_GW.R tests/testthat/test-DAISIE_utils.R tests/testthat/test-is_simulation_outputs.R tests/testthat/test-is_island_ontogeny_input.R tests/testthat/test-update_rates.R tests/testthat/test-DAISIE_sim_relaxed_rate.R tests/testthat/test-DAISIE_MW_ML.R tests/testthat/test-island_area.R tests/testthat/test-create_area_pars.R tests/testthat/test-DAISIE_sim_trait_dependent.R tests/testthat/test-DAISIE_get_brts_mya.R tests/testthat/test-DAISIE_max_rates.R tests/testthat/test-DAISIE_sim_core.R inst/doc/demo_optimize.R
inst/doc/demo_sim.html
inst/doc/demo_CSvsIW.R inst/doc/demo_CSvsIW.Rmd
inst/doc/demo_optimize.html
inst/doc/demo_sim.R inst/doc/demo_sim.Rmd inst/doc/demo_optimize.Rmd
inst/doc/demo_CSvsIW.html
inst/extdata/frog_M1_ML.rds
DAISIE documentation built on Aug. 26, 2020, 5:12 p.m.