Files in deepSTRAPP
Test for Differences in Diversification Rates over Time

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R/plot_traits_vs_rates_on_phylogeny_for_focal_time.R R/datasets_doc_for_CRAN.R R/extract_diversification_data_melted_df_for_focal_time.R R/compute_STRAPP_test_for_focal_time.R R/extract_most_likely_trait_values_for_focal_time.R R/prepare_trait_data.R R/cut_phylo_for_focal_time.R R/plot_histogram_STRAPP_test_for_focal_time.R R/plot_densityMaps_overlay.R R/update_rates_and_regimes_for_focal_time.R R/cut_contMap_for_focal_time.R R/run_deepSTRAPP_for_focal_time.R R/cut_densityMaps_for_focal_time.R R/plot_STRAPP_pvalues_over_time.R R/plot_rates_through_time.R R/plot_traits_vs_rates_on_phylogeny_over_time.R R/update_maps_for_focal_time.R R/is_dev_version.R R/plot_rates_vs_trait_data_over_time.R R/run_deepSTRAPP_over_time.R R/plot_rates_vs_trait_data_for_focal_time.R R/plot_histograms_STRAPP_tests_over_time.R R/plot_BAMM_rates.R R/prepare_diversification_data.R R/plot_contMap.R

src/deepSTRAPP_init.c

src/treetraverse.c

inst/COPYRIGHTS

inst/CITATION

inst/BAMM_template_diversification.txt

inst/doc/plot_rates_through_time.Rmd inst/doc/deepSTRAPP_categorical_data.R inst/doc/cut_phylogenies.R

inst/doc/model_continuous_trait_evolution.html

inst/doc/model_diversification_dynamics.Rmd

inst/doc/explore_STRAPP_test_types.html

inst/doc/deepSTRAPP_continuous_data.html

inst/doc/model_categorical_trait_evolution.Rmd inst/doc/model_continuous_trait_evolution.Rmd inst/doc/deepSTRAPP_biogeographic_data.Rmd inst/doc/model_biogeographic_range_evolution.R inst/doc/cut_phylogenies.Rmd inst/doc/deepSTRAPP.R

inst/doc/model_biogeographic_range_evolution.html

inst/doc/deepSTRAPP_biogeographic_data.html

inst/doc/plot_rates_through_time.html

inst/doc/main_tutorial.html

inst/doc/cut_phylogenies.html

inst/doc/model_categorical_trait_evolution.R inst/doc/plot_rates_through_time.R inst/doc/model_biogeographic_range_evolution.Rmd

inst/doc/model_diversification_dynamics.html

inst/doc/main_tutorial.Rmd

inst/doc/model_categorical_trait_evolution.html

inst/doc/deepSTRAPP_continuous_data.R inst/doc/deepSTRAPP_biogeographic_data.R inst/doc/main_tutorial.R inst/doc/explore_STRAPP_test_types.Rmd

inst/doc/deepSTRAPP_categorical_data.html

inst/doc/deepSTRAPP.html

inst/doc/model_diversification_dynamics.R inst/doc/model_continuous_trait_evolution.R inst/doc/deepSTRAPP.Rmd inst/doc/deepSTRAPP_categorical_data.Rmd inst/doc/explore_STRAPP_test_types.R inst/doc/deepSTRAPP_continuous_data.Rmd

build/vignette.rds

build/partial.rdb

vignettes/plot_rates_through_time.Rmd vignettes/model_diversification_dynamics.Rmd vignettes/model_categorical_trait_evolution.Rmd vignettes/model_continuous_trait_evolution.Rmd vignettes/deepSTRAPP_biogeographic_data.Rmd vignettes/cut_phylogenies.Rmd vignettes/model_biogeographic_range_evolution.Rmd vignettes/main_tutorial.Rmd vignettes/explore_STRAPP_test_types.Rmd vignettes/deepSTRAPP.Rmd vignettes/deepSTRAPP_categorical_data.Rmd vignettes/deepSTRAPP_continuous_data.Rmd

vignettes/figures/4_Explore_STRAPP_hypotheses_1.2_Example_continuous_two_tailed_2.PNG

vignettes/figures/1.3_deepSTRAPP_biogeographic_data_4.5_plot_updated_densityMaps_2.PNG

vignettes/figures/1.3_deepSTRAPP_biogeographic_data_4.3_plot_rates_through_time.PNG

vignettes/figures/1.2_deepSTRAPP_categorical_3lvl_data_4.7_plot_traits_vs_rate_maps_2.PNG

vignettes/figures/0_deepSTRAPP_categorical_2lvl_data_4.5_plot_updated_densityMaps_2.PNG

vignettes/figures/1.2_deepSTRAPP_categorical_3lvl_data_4.3_plot_rates_through_time.PNG

vignettes/figures/1.3_deepSTRAPP_biogeographic_data_4.2_plot_STRAPP_tests.PNG

vignettes/figures/0_deepSTRAPP_categorical_2lvl_data_4.7_plot_traits_vs_rate_maps_1.PNG

vignettes/figures/4_Explore_STRAPP_hypotheses_2.2_Example_cat_2lvl_two_tailed_2.PNG

vignettes/figures/1.2_deepSTRAPP_categorical_3lvl_data_4.7_plot_traits_vs_rate_maps_1.PNG

vignettes/figures/1.3_deepSTRAPP_biogeographic_data_4.6_plot_BAMM_rates.PNG

vignettes/figures/0_deepSTRAPP_categorical_2lvl_data_4.3_plot_rates_through_time.PNG

vignettes/figures/1.1_deepSTRAPP_continuous_data_4.2_plot_STRAPP_tests.PNG

vignettes/figures/1.1_deepSTRAPP_continuous_data_4.5_plot_updated_contMap_1.PNG

vignettes/figures/0_deepSTRAPP_categorical_2lvl_data_4.4_plot_rates_vs_traits.PNG

vignettes/figures/0_deepSTRAPP_categorical_2lvl_data_4.2_plot_STRAPP_tests.PNG

vignettes/figures/1.1_deepSTRAPP_continuous_data_4.5_plot_updated_contMap_2.PNG

vignettes/figures/1.3_deepSTRAPP_biogeographic_data_4.7_plot_traits_vs_rate_maps_2.PNG

vignettes/figures/1.2_deepSTRAPP_categorical_3lvl_data_4.1_plot_pvalues_1.PNG

vignettes/figures/1.1_deepSTRAPP_continuous_data_4.7_plot_traits_vs_rate_maps_2.PNG

vignettes/figures/1.3_deepSTRAPP_biogeographic_data_4.1_plot_pvalues.PNG

vignettes/figures/1.3_deepSTRAPP_biogeographic_data_4.7_plot_traits_vs_rate_maps_1.PNG

vignettes/figures/whale_PP_nb_shifts_plot.png

vignettes/figures/4_Explore_STRAPP_hypotheses_2.2_Example_cat_2lvl_two_tailed.PNG

vignettes/figures/whale_MCMC_trace_logLik.png

vignettes/figures/4_Explore_STRAPP_hypotheses_3.2_Example_cat_3lvl_overall_2.PNG

vignettes/figures/1.1_deepSTRAPP_continuous_data_4.4_plot_rates_vs_traits.PNG

vignettes/figures/4_Explore_STRAPP_hypotheses_3.3_Example_cat_3lvl_two_tailed.PNG

vignettes/figures/5_Explore_plot_RTT_2_Example_multinominal.PNG

vignettes/figures/1.2_deepSTRAPP_categorical_3lvl_data_4.2_plot_histograms_1.PNG

vignettes/figures/1.2_deepSTRAPP_categorical_3lvl_data_4.5_plot_updated_densityMaps_2.PNG

vignettes/figures/4_Explore_STRAPP_hypotheses_3.4_Example_cat_3lvl_one_tailed.PNG

vignettes/figures/4_Explore_STRAPP_hypotheses_1.3_Example_continuous_one_tailed.PNG

vignettes/figures/0_deepSTRAPP_categorical_2lvl_data_4.6_plot_BAMM_rates.PNG

vignettes/figures/0_deepSTRAPP_categorical_2lvl_data_4.7_plot_traits_vs_rate_maps_2.PNG

vignettes/figures/1.1_deepSTRAPP_continuous_data_4.1_plot_pvalues.PNG

vignettes/figures/4_Explore_STRAPP_hypotheses_2.3_Example_cat_2lvl_one_tailed.PNG

vignettes/figures/0_deepSTRAPP_categorical_2lvl_data_4.5_plot_updated_densityMaps_1.PNG

vignettes/figures/1.2_deepSTRAPP_categorical_3lvl_data_4.6_plot_BAMM_rates.PNG

vignettes/figures/1.3_deepSTRAPP_biogeographic_data_4.5_plot_updated_densityMaps_1.PNG

vignettes/figures/0_deepSTRAPP_categorical_2lvl_data_4.1_plot_pvalues.PNG

vignettes/figures/1.2_deepSTRAPP_categorical_3lvl_data_4.5_plot_updated_densityMaps_1.PNG

vignettes/figures/1.2_deepSTRAPP_categorical_3lvl_data_4.4_plot_rates_vs_traits.PNG

vignettes/figures/1.1_deepSTRAPP_continuous_data_4.7_plot_traits_vs_rate_maps_1.PNG

vignettes/figures/4_Explore_STRAPP_hypotheses_1.2_Example_continuous_two_tailed_1.PNG

vignettes/figures/1.1_deepSTRAPP_continuous_data_4.6_plot_BAMM_rates.PNG

vignettes/figures/1.3_deepSTRAPP_biogeographic_data_4.4_plot_rates_vs_traits.PNG

vignettes/figures/1.2_deepSTRAPP_categorical_3lvl_data_4.2_plot_histograms_2.PNG

vignettes/figures/1.1_deepSTRAPP_continuous_data_4.3_plot_rates_through_time.PNG

vignettes/figures/4_Explore_STRAPP_hypotheses_3.2_Example_cat_3lvl_overall.PNG

vignettes/figures/1.2_deepSTRAPP_categorical_3lvl_data_4.1_plot_pvalues_2.PNG

vignettes/figures/5_Explore_plot_RTT_1_Example_continuous.PNG

vignettes/tables/whale_ESS_df.csv

data/mammals.rda

data/Ponerinae_biogeo_data_old_calib.rda

data/Ponerinae_trait_tip_data.rda

data/eel_cat_3lvl_data.rda

data/Ponerinae_cat_2lvl_data_old_calib.rda

data/Ponerinae_cat_3lvl_data_old_calib.rda

data/Ponerinae_trait_cont_tip_data_10My.rda

data/Ponerinae_binary_range_table.rda

data/Ponerinae_tree_old_calib.rda

data/BAMM_template_diversification.rda

data/Ponerinae_tree.rda

data/whale_BAMM_object.rda

data/eel_biogeo_data.rda

man/figures/README-plot_histogram_STRAPP_tests_cat_2lvl_eval-1.png

man/figures/README-plot_BAMM_rates_cat_2lvl_eval-3.png

man/figures/README-plot_updated_densityMaps_cat_2lvl_eval-1.png

man/figures/README-plot_trait_vs_rate_maps_cat_2lvl_eval-1.png

man/figures/logo.png

man/figures/README-plot_results_cat_2lvl_eval-1.png

man/figures/README-plot_updated_densityMaps_cat_2lvl_eval-2.png

man/figures/README-plot_rates_through_time_cat_2lvl_eval-1.png

man/figures/README-plot_BAMM_rates_cat_2lvl_eval-2.png

man/figures/README-plot_traits_vs_rates_on_phylogeny_cat_2lvl_eval-1.png

man/figures/README-plot_traits_vs_rates_on_phylogeny_cat_2lvl_eval-2.png

man/figures/deepSTRAPP_workflow.png

man/figures/README-plot_rates_vs_traits_cat_2lvl_eval-1.png

man/figures/README-plot_rates_vs_traits_eval-1.png

man/figures/README-plot_BAMM_rates_cat_2lvl_eval-1.png

man/figures/README-plot_trait_vs_rate_maps_cat_2lvl_eval-2.png

deepSTRAPP documentation built on Jan. 20, 2026, 1:06 a.m.

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deepSTRAPP
Test for Differences in Diversification Rates over Time

Files in deepSTRAPP
Test for Differences in Diversification Rates over Time

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deepSTRAPP Test for Differences in Diversification Rates over Time

Files in deepSTRAPP Test for Differences in Diversification Rates over Time

R Package Documentation

Browse R Packages

We want your feedback!

deepSTRAPP
Test for Differences in Diversification Rates over Time

Files in deepSTRAPP
Test for Differences in Diversification Rates over Time