Files in xieshu95/DAISIE_new

Dynamical Assembly of Islands by Speciation, Immigration and Extinction

.Rbuildignore

.gitignore

DAISIE_new.Rproj

DESCRIPTION

NAMESPACE

R/.gitignore

R/DAISIE_ExpEIN.R R/DAISIE_IC.R R/DAISIE_ML1.R R/DAISIE_ML2.R R/DAISIE_ML3.R R/DAISIE_ML_CS.R R/DAISIE_ML_IW.R R/DAISIE_MW_ML.R R/DAISIE_ONEcolonist.R R/DAISIE_PEI.R R/DAISIE_SR_ML_CS.R R/DAISIE_SR_loglik_CS.R R/DAISIE_check_format.R R/DAISIE_create_island.R R/DAISIE_data.R R/DAISIE_dataprep.R R/DAISIE_extract_stt_median.R R/DAISIE_format_CS.R R/DAISIE_format_CS_full_stt.R R/DAISIE_format_CS_sampled_stt.R R/DAISIE_format_GW.R R/DAISIE_format_IW.R R/DAISIE_get_brts_mya.R R/DAISIE_loglik_CS.R R/DAISIE_loglik_CS_time.R R/DAISIE_loglik_IW.R R/DAISIE_loglik_IW0.R R/DAISIE_loglik_high_lambda.R R/DAISIE_make_archipelago.R R/DAISIE_max_rates.R R/DAISIE_plot_age_diversity.R R/DAISIE_plot_comparison_stts.R R/DAISIE_plot_island.R R/DAISIE_plot_params.R R/DAISIE_plot_pc_rates.R R/DAISIE_plot_sims.R R/DAISIE_plot_stt.R R/DAISIE_rates.R R/DAISIE_sample_event_constant_rate.R R/DAISIE_sample_event_time_dependent.R R/DAISIE_sample_event_trait_dependent.R R/DAISIE_sim_constant_rate.R R/DAISIE_sim_constant_rate_shift.R R/DAISIE_sim_core_constant_rate.R R/DAISIE_sim_core_constant_rate_shift.R R/DAISIE_sim_core_time_dependent.R R/DAISIE_sim_core_trait_dependent.R R/DAISIE_sim_min_type2.R R/DAISIE_sim_time_dependent.R R/DAISIE_sim_trait_dependent.R R/DAISIE_sim_update_state_constant_rate.R R/DAISIE_sim_update_state_time_dependent.R R/DAISIE_sim_update_state_trait_dependent.R R/DAISIE_sumstats_rates.R R/DAISIE_utils.R R/create_pars.R R/default_params_doc.R README.md

data/Biwa_datalist.RData

data/Galapagos_datalist.RData

data/Galapagos_datalist_2types.RData

data/Galapagos_datatable.RData

data/Macaronesia_datalist.RData

data/islands_10reps_RAW.RData

data/islands_1type_1000reps.RData

data/islands_2types_1000reps.RData

man/Biwa_datalist.Rd man/DAISIE_ExpEIN.Rd man/DAISIE_IC.Rd man/DAISIE_ML.Rd man/DAISIE_ML1.Rd man/DAISIE_ML2.Rd man/DAISIE_ML3.Rd man/DAISIE_ML_IW.Rd man/DAISIE_MW_ML.Rd man/DAISIE_ONEcolonist.Rd man/DAISIE_SR_ML.Rd man/DAISIE_SR_loglik_CS.Rd man/DAISIE_calc_sumstats_pcrates.Rd man/DAISIE_convert_to_classic_plot.Rd man/DAISIE_convertprobdist.Rd man/DAISIE_create_island.Rd man/DAISIE_dataprep.Rd man/DAISIE_extract_stt_median.Rd man/DAISIE_format_CS.Rd man/DAISIE_format_CS_full_stt.Rd man/DAISIE_format_CS_sampled_stt.Rd man/DAISIE_format_GW.Rd man/DAISIE_format_IW.Rd man/DAISIE_get_brts_mya.Rd man/DAISIE_loglik_CS.Rd man/DAISIE_loglik_IW.Rd man/DAISIE_make_archipelago.Rd man/DAISIE_make_global.Rd man/DAISIE_margprobdist.Rd man/DAISIE_nonoceanic_spec.Rd man/DAISIE_numcol.Rd man/DAISIE_plot_age_diversity.Rd man/DAISIE_plot_area.Rd man/DAISIE_plot_cladogenesis.Rd man/DAISIE_plot_comparison_stts.Rd man/DAISIE_plot_extinction.Rd man/DAISIE_plot_immigration.Rd man/DAISIE_plot_island.Rd man/DAISIE_plot_pc_rates.Rd man/DAISIE_plot_sims.Rd man/DAISIE_plot_stt.Rd man/DAISIE_probdist.Rd man/DAISIE_sample_event_constant_rate.Rd man/DAISIE_sample_event_time_dependent.Rd man/DAISIE_sample_event_trait_dependent.Rd man/DAISIE_sim_constant_rate.Rd man/DAISIE_sim_constant_rate_shift.Rd man/DAISIE_sim_core_constant_rate.Rd man/DAISIE_sim_core_constant_rate_shift.Rd man/DAISIE_sim_core_time_dependent.Rd man/DAISIE_sim_core_trait_dependent.Rd man/DAISIE_sim_min_type2.Rd man/DAISIE_sim_time_dependent.Rd man/DAISIE_sim_trait_dependent.Rd man/DAISIE_sim_update_state_constant_rate.Rd man/DAISIE_sim_update_state_time_dependent.Rd man/Galapagos_datalist.Rd man/Galapagos_datalist_2types.Rd man/Galapagos_datatable.Rd man/Macaronesia_datalist.Rd man/are_area_pars.Rd man/are_dist_pars.Rd man/are_hyper_pars.Rd man/are_max_rates.Rd man/are_max_rates_gt_rates.Rd man/are_rates.Rd man/are_trait_pars.Rd man/calc_next_timeval.Rd man/countimmi.Rd man/countspecies.Rd man/countspeciestype1.Rd man/countstac.Rd man/counttype1.Rd man/create_area_pars.Rd man/create_default_pars.Rd man/create_dist_pars.Rd man/create_full_CS_stt.Rd man/create_hyper_pars.Rd man/create_singleton_phylo.Rd man/create_trait_pars.Rd man/default_params_doc.Rd man/get_ana_rate.Rd man/get_clado_rate.Rd man/get_ext_rate.Rd man/get_global_max_area_time.Rd man/get_global_min_area_time.Rd man/get_immig_rate.Rd man/get_trans_rate.Rd man/is_island_ontogeny_input.Rd man/is_numeric_list.Rd man/is_sea_level_input.Rd man/is_simulation_outputs.Rd man/island_area.Rd man/island_area_vector.Rd man/islands_10reps_RAW.Rd man/islands_1type_1000reps.Rd man/islands_2types_1000reps.Rd man/translate_island_ontogeny.Rd man/translate_sea_level.Rd man/update_max_rates.Rd man/update_rates.Rd

src/DAISIE.dll

src/DAISIE_loglik_rhs_FORTRAN.f95

src/Makevars

src/R_init_DAISIE.c

tests/testthat.R

tests/testthat/.gitignore

tests/testthat/test-DAISIE_ExpEIN.R tests/testthat/test-DAISIE_ML1.R tests/testthat/test-DAISIE_ML2.R tests/testthat/test-DAISIE_ONEcolonist.R tests/testthat/test-DAISIE_SR_loglik.R tests/testthat/test-DAISIE_convert_to_classic_plot.R tests/testthat/test-DAISIE_dataprep.R tests/testthat/test-DAISIE_extract_stt_median.R tests/testthat/test-DAISIE_format_CS.R tests/testthat/test-DAISIE_format_CS_full_stt.R tests/testthat/test-DAISIE_format_CS_sampled_stt.R tests/testthat/test-DAISIE_format_GW.R tests/testthat/test-DAISIE_format_IW.R tests/testthat/test-DAISIE_get_brts_mya.R tests/testthat/test-DAISIE_max_rates.R tests/testthat/test-DAISIE_min_rates.R tests/testthat/test-DAISIE_plot_comparison_stts.R tests/testthat/test-DAISIE_plot_sims.R tests/testthat/test-DAISIE_plot_stt.R tests/testthat/test-DAISIE_sim_constant_rate.R tests/testthat/test-DAISIE_sim_constant_rate_shift.R tests/testthat/test-DAISIE_sim_core_constant_rate.R tests/testthat/test-DAISIE_sim_core_constant_rate_shift.R tests/testthat/test-DAISIE_sim_core_time_dependent.R tests/testthat/test-DAISIE_sim_core_trait_dependent.R tests/testthat/test-DAISIE_sim_time_dependent.R tests/testthat/test-DAISIE_sim_trait_dependent.R tests/testthat/test-DAISIE_sumstats_rates.R tests/testthat/test-DAISIE_utils.R tests/testthat/test-are_area_pars.R tests/testthat/test-are_max_rates.R tests/testthat/test-are_max_rates_gt_rates.R tests/testthat/test-are_rates.R tests/testthat/test-are_trait_pars.R tests/testthat/test-create_area_params.R tests/testthat/test-create_trait_pars.R tests/testthat/test-is_island_ontogeny_input.R tests/testthat/test-is_numeric_list.R tests/testthat/test-is_sea_level_input.R tests/testthat/test-is_simulation_outputs.R tests/testthat/test-island_area.R tests/testthat/test-update_max_rates.R tests/testthat/test-update_rates.R vignettes/demo_optimize.R vignettes/demo_optimize.Rmd vignettes/demo_sim.R vignettes/demo_sim.Rmd

xieshu95/DAISIE_new documentation built on March 20, 2020, 5:31 a.m.