BAMM_template_diversification
                        Template file for BAMM diversification analyses
BSM_to_phytools_simmap
                        Convert Biogeographic Stochastic Map (BSM) to
                        phytools SIMMAP stochastic map (SM) format
Ponerinae_binary_range_table
                        Dataset providing biogeographic range data for
                        extant ponerine ants
Ponerinae_biogeo_data_old_calib
                        Data summarizing the evolution of geographic
                        ranges in Ponerinae ants using an old
                        ill-calibrated phylogeny for illustrative
                        purposes
Ponerinae_cat_2lvl_data_old_calib
                        Data summarizing the evolution of fake size
                        data in Ponerinae ants using a 2-level factor
                        as categorical trait
Ponerinae_cat_3lvl_data_old_calib
                        Data summarizing the evolution of fake habitat
                        data in Ponerinae ants using a 3-level factor
                        as categorical trait
Ponerinae_trait_cont_tip_data_10My
                        Data summarizing the evolution of a fake
                        continuous trait in Ponerinae ants extracted
                        for 10 Mya
Ponerinae_trait_tip_data
                        Dataset providing fake trait data for extant
                        ponerine ants for illustrative purposes
Ponerinae_tree          Dataset providing the extensive time-calibrated
                        phylogeny of extant ponerine ants
Ponerinae_tree_old_calib
                        Dataset providing the extensive time-calibrated
                        phylogeny of extant ponerine ants using an old
                        calibration for illustrative purposes
compute_STRAPP_test_for_focal_time
                        Compute STRAPP to test for a relationship
                        between diversification rates and trait data
cut_contMap_for_focal_time
                        Cut the phylogeny and continuous trait mapping
                        for a given focal time in the past
cut_densityMap_for_focal_time
                        Cut the phylogeny and posterior probability
                        mapping of a categorical trait for a given
                        focal time in the past
cut_densityMaps_for_focal_time
                        Cut phylogenies and posterior probability
                        mapping of each state for a given focal time in
                        the past
cut_phylo_for_focal_time
                        Cut the phylogeny for a given time in the past
eel_biogeo_data         Data summarizing the evolution of geographic
                        ranges in eels
eel_cat_3lvl_data       Data summarizing the evolution of feeding
                        habits in eels using a 3-level factor as
                        categorical trait
extract_diversification_data_melted_df_for_focal_time
                        Extract diversification data from a BAMM_object
extract_most_likely_ranges_from_densityMaps_for_focal_time
                        Extract biogeographic range data mapped on a
                        phylogeny at a given time in the past
extract_most_likely_states_from_densityMaps_for_focal_time
                        Extract categorical trait data mapped on a
                        phylogeny at a given time in the past
extract_most_likely_trait_values_for_focal_time
                        Extract trait data mapped on a phylogeny at a
                        given time in the past
extract_most_likely_trait_values_from_contMap_for_focal_time
                        Extract continuous trait data mapped on a
                        phylogeny at a given time in the past
is_dev_version          Check whether deepSTRAPP is a development
                        version
mammals                 Phylogeny and body mass data for extant and
                        extinct mammals families/genera from Slater,
                        2013
plot_BAMM_rates         Plot diversification rates and regime shifts
                        from BAMM on phylogeny
plot_STRAPP_pvalues_over_time
                        Plot evolution of p-values of STRAPP tests over
                        time
plot_contMap            Plot continuous trait evolution on the tree
plot_densityMaps_overlay
                        Plot posterior probabilities of states/ranges
                        on phylogeny from densityMaps
plot_histogram_STRAPP_test_for_focal_time
                        Plot histogram of STRAPP test statistics to
                        assess results
plot_histograms_STRAPP_tests_over_time
                        Plot multiple histograms of STRAPP test
                        statistics over time-steps
plot_rates_through_time
                        Plot evolution of diversification rates in
                        relation to trait values over time
plot_rates_vs_trait_data_for_focal_time
                        Plot rates vs. trait data for a given focal
                        time
plot_rates_vs_trait_data_over_time
                        Plot rates vs. trait data over time-steps
plot_traits_vs_rates_on_phylogeny_for_focal_time
                        Plot trait/range evolution vs. diversification
                        rates and regime shifts on phylogeny
plot_traits_vs_rates_on_phylogeny_over_time
                        Plot multiple mapped phylogenies of trait/range
                        evolution vs. diversification rates and regime
                        shifts over time-steps
prepare_diversification_data
                        Run a full BAMM (Bayesian Analysis of
                        Macroevolutionary Mixtures) workflow
prepare_trait_data      Map trait evolution on a time-calibrated
                        phylogeny
run_deepSTRAPP_for_focal_time
                        Run deepSTRAPP to test for a relationship
                        between diversification rates and trait data at
                        a given focal time
run_deepSTRAPP_over_time
                        Run deepSTRAPP to test for a relationship
                        between diversification rates and trait data
                        over multiple time steps
select_best_model_from_BioGeoBEARS
                        Compare model fits with AICc and Akaike's
                        weights
select_best_trait_model_from_geiger
                        Compare trait evolutionary model fits with AICc
                        and Akaike's weights
update_rates_and_regimes_for_focal_time
                        Update diversification rates/regimes mapped on
                        a phylogeny up to a given time in the past
whale_BAMM_object       Dataset summarizing 1000 posterior samples of
                        BAMM for extant whales
