Files in xieshu95/Trait_dependent_TraiSIE

Dynamical Assembly of Islands by Speciation, Immigration and Extinction

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

NAMESPACE

R/.gitignore

R/DAISIE_ExpEIN.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_PEI.R R/DAISIE_SR_ML_CS.R R/DAISIE_SR_loglik_CS.R R/DAISIE_SR_sim.R R/DAISIE_SR_sim_core.R R/DAISIE_area_params.R R/DAISIE_check_format.R R/DAISIE_compare.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_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_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.R R/DAISIE_sim.R R/DAISIE_sim_core.R R/DAISIE_sim_core_1_4.R R/DAISIE_sim_core_checked.R R/DAISIE_sim_min_type2.R R/DAISIE_sim_update_state.R R/DAISIE_sim_with_mainland.R R/DAISIE_sim_with_ontogeny.R R/DAISIE_sumstats_rates.R R/DAISIE_tutorial.R R/DAISIE_utils.R R/ML_CS_table.R R/are_rates.R R/create_rates.R R/create_test_simulation_output.R R/create_test_trait_state_params.R R/create_trait_state_params.R R/default_params_doc.R R/sim_with_estimated_pars.R

R/simulation_results_same.RData

README.md

Trait_dependent_TraiSIE.Rproj

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

inst/DAISIE_tutorial.pdf

man/.gitignore

man/Biwa_datalist.Rd man/DAISIE_ExpEIN.Rd man/DAISIE_ML.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_SR_sim.Rd man/DAISIE_calc_clade_ana_rate.Rd man/DAISIE_calc_clade_clado_rate.Rd man/DAISIE_calc_clade_ext_rate.Rd man/DAISIE_calc_clade_imm_rate.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_IW.Rd man/DAISIE_get_brts_mya.Rd man/DAISIE_loglik_CS.Rd man/DAISIE_loglik_IW.Rd man/DAISIE_margprobdist.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.Rd man/DAISIE_sim.Rd man/DAISIE_sim_core.Rd man/DAISIE_sim_core_1_4.Rd man/DAISIE_sim_core_checked.Rd man/DAISIE_sim_core_checked_1_4.Rd man/DAISIE_sim_update_state.Rd man/DAISIE_sim_with_mainland.Rd man/DAISIE_sim_with_ontogeny.Rd man/DAISIE_tutorial.Rd man/Galapagos_datalist.Rd man/Galapagos_datalist_2types.Rd man/Galapagos_datatable.Rd man/Macaronesia_datalist.Rd man/are_area_params.Rd man/are_rates.Rd man/are_trait_state_params.Rd man/calc_next_timeval.Rd man/compare_diff.Rd man/countspecies.Rd man/create_area_params.Rd man/create_daisie_params.Rd man/create_rates.Rd man/create_test_daisie_params.Rd man/create_test_simulation_outputs.Rd man/create_trait_state_params.Rd man/default_params_doc.Rd man/get_ana_rate.Rd man/get_clado_rate.Rd man/get_ext_rate.Rd man/get_immig_rate.Rd man/get_t_hor.Rd man/get_trans_rate.Rd man/is.odd.Rd man/is_island_ontogeny_input.Rd man/is_island_ontogeny_runtime.Rd man/is_numeric_list.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/update_rates.Rd

plot/DAISIE_sample2.png

plot/TRASIE_balance_sample2.png

plot/TRASIE_check1_sample2.png

plot/TRASIE_check2_sample2.png

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_ONEcolonist.R tests/testthat/test-DAISIE_SR_code.R tests/testthat/test-DAISIE_calc_clade_ana_rate.R tests/testthat/test-DAISIE_calc_clade_clado_rate.R tests/testthat/test-DAISIE_calc_clade_ext_rate.R tests/testthat/test-DAISIE_calc_clade_imm_rate.R tests/testthat/test-DAISIE_convert_to_classic_plot.R tests/testthat/test-DAISIE_ext_test.R tests/testthat/test-DAISIE_extract_stt_median.R tests/testthat/test-DAISIE_format_CS.R tests/testthat/test-DAISIE_format_IW.R tests/testthat/test-DAISIE_get_brts_mya.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.R tests/testthat/test-DAISIE_sim_core.R tests/testthat/test-DAISIE_sim_core_checked.R tests/testthat/test-DAISIE_sim_with_mainland.R tests/testthat/test-DAISIE_vs_TRASIE.R tests/testthat/test-IW_crash.R tests/testthat/test-are_area_params.R tests/testthat/test-are_rates.R tests/testthat/test-are_trait_state_params.R tests/testthat/test-create_area_params.R tests/testthat/test-create_daisie_params.R tests/testthat/test-create_rates.R tests/testthat/test-create_test_daisie_params.R tests/testthat/test-create_test_trait_state_params.R tests/testthat/test-create_trait_state_params.R tests/testthat/test-daisie_utils.R tests/testthat/test-get_clado_rate.R tests/testthat/test-get_ext_rate.R tests/testthat/test-get_immig_rate.R tests/testthat/test-get_thor.R tests/testthat/test-integration_DAISIE.R tests/testthat/test-is_numeric_list.R tests/testthat/test-is_odd.R tests/testthat/test-is_simulation_outputs.R tests/testthat/test-island_area.R tests/testthat/test-rng_respecting_sample.R tests/testthat/test-sample.R tests/testthat/test-update_rates.R

vignettes/.gitignore

vignettes/demo_optimize.Rmd vignettes/demo_sim.Rmd vignettes/demo_trasie.Rmd vignettes/demo_trasie_CS.Rmd

vignettes/demo_trasie_CS_files/figure-html/unnamed-chunk-10-1.png

vignettes/demo_trasie_CS_files/figure-html/unnamed-chunk-11-1.png

vignettes/demo_trasie_CS_files/figure-html/unnamed-chunk-12-1.png

vignettes/demo_trasie_CS_files/figure-html/unnamed-chunk-13-1.png

vignettes/demo_trasie_CS_files/figure-html/unnamed-chunk-13-2.png

vignettes/demo_trasie_CS_files/figure-html/unnamed-chunk-13-3.png

vignettes/demo_trasie_CS_files/figure-html/unnamed-chunk-4-1.png

vignettes/demo_trasie_CS_files/figure-html/unnamed-chunk-5-1.png

vignettes/demo_trasie_CS_files/figure-html/unnamed-chunk-6-1.png

vignettes/demo_trasie_CS_files/figure-html/unnamed-chunk-7-1.png

vignettes/demo_trasie_CS_files/figure-html/unnamed-chunk-9-1.png

vignettes/demo_trasie_immig_IW.Rmd

vignettes/results_Value_1.jpg

xieshu95/Trait_dependent_TraiSIE documentation built on Nov. 22, 2019, 7:51 a.m.