# Test for Differences in Diversification Rates over Time

## Documentation for package ‘deepSTRAPP’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

BAMM_template_diversification | Template file for BAMM diversification analyses
BSMs_to_phytools_simmaps | Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP stochastic map (SM) format
BSM_to_phytools_simmap | Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP stochastic map (SM) format
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_densityMaps_for_focal_time | Cut phylogenies and posterior probability mapping of each state 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_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_contMap | Plot continuous trait evolution on the tree
plot_densityMaps_overlay | Plot posterior probabilities of states/ranges on phylogeny from densityMaps
plot_histograms_STRAPP_tests_over_time | Plot multiple histograms of STRAPP test statistics over time-steps
plot_histogram_STRAPP_test_for_focal_time | Plot histogram of STRAPP test statistics to assess results
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_STRAPP_pvalues_over_time | Plot evolution of p-values of STRAPP tests over time
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
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
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