Package index • deepSTRAPP

Prepare data for deepSTRAPP

All-in-one functions to prepare trait and diversification data to use as inputs for a deepSTRAPP run.

prepare_trait_data(): Map trait evolution on a time-calibrated phylogeny
prepare_diversification_data(): Run a full BAMM (Bayesian Analysis of Macroevolutionary Mixtures) workflow

Core functions to run deepSTRAPP.

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
compute_STRAPP_test_for_focal_time(): Compute STRAPP to test for a relationship between diversification rates and trait data

Plot results from deepSTRAPP runs.

plot_STRAPP_pvalues_over_time(): Plot evolution of p-values of STRAPP tests over time
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 mean rates vs. trait data over time-steps

Plot phylogenies with mapped trait or diversification rates evolution on branches.

plot_contMap(): Plot continuous trait evolution on the tree
plot_densityMaps_overlay(): Plot posterior probabilities of states/ranges on phylogeny from densityMaps
plot_BAMM_rates(): Plot diversification rates and regime shifts from BAMM on phylogeny
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

Format results from external analyses as inputs for a deepSTRAPP run.

convert_contsimmap_to_contMaps(): Convert a contsimmap object into a list of contMaps
aggregate_contMaps(): Aggregate a list of contMaps into a unique mean/median contMap
convert_BSM_to_simmap() convert_BSMs_to_simmaps(): Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP stochastic map (SM) format
convert_simmaps_to_densityMaps(): Convert simmaps into densityMaps suitable for deepSTRAPP
build_BAMM_object(): Build a BAMM object for a deepSTRAPP run
subset_BAMM_object(): Subset a BAMM object before a deepSTRAPP run
prune_BAMM_object(): Prune a BAMM object to a subset of tips

Select best models based on AICc.

select_best_trait_model_from_geiger(): Compare trait evolutionary model fits with AICc and Akaike's weights
select_best_model_from_BioGeoBEARS(): Compare model fits with AICc and Akaike's weights

Extract trait data from contMap(s), densityMaps, simmaps.

extract_most_likely_trait_values_for_focal_time(): Extract most likely trait data mapped on a phylogeny at a given time in the past
extract_all_trait_values_for_focal_time(): Extract all trait data from stochastic maps at a given time in the past
extract_trait_data_melted_df_for_focal_time(): Extract trait data from a trait_data object

Extract diversification rates and regimes from BAMM objects.

extract_diversification_data_melted_df_for_focal_time(): Extract diversification data from a BAMM_object
update_rates_and_regimes_for_focal_time(): Update diversification rates/regimes mapped on a phylogeny up to a given time in the past

Cut different types of mapped phylogenies to a given focal-time.

cut_phylo_for_focal_time(): Cut the phylogeny for a given time in the past
cut_contMap_for_focal_time(): Cut the phylogeny and continuous trait mapping for a given focal time in the past
cut_contMaps_for_focal_time(): Cut the phylogenies and continuous trait mappings of a list of contMaps 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_simmap_for_focal_time(): Cut the phylogeny and categorical trait/range mapping for a given focal time in the past
cut_simmaps_for_focal_time(): Cut the phylogenies and categorical trait/range mappings of a list of simmaps for a given focal time in the past

Datasets used to run examples and display expected results.

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

mammals: Phylogeny and body mass data for extant and extinct mammal families/genera from Slater, 2013
Ponerinae_trait_tip_data: Dataset providing fake trait data for extant ponerine ants for illustrative purposes
Ponerinae_binary_range_table: Dataset providing biogeographic range data for extant ponerine ants

Ponerinae_trait_cont_tip_data_10My: Data summarizing the evolution of a fake continuous trait in Ponerinae ants extracted for 10 Mya
eel_cat_3lvl_data: Data summarizing the evolution of feeding habits in eels using a 3-level factor as categorical trait
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
eel_biogeo_data: Data summarizing the evolution of geographic ranges in eels
Ponerinae_biogeo_data_old_calib: Data summarizing the evolution of geographic ranges in Ponerinae ants using an old ill-calibrated phylogeny for illustrative purposes

BAMM_template_diversification: Template file for BAMM diversification analyses
whale_BAMM_object: Dataset summarizing 1000 posterior samples of BAMM for extant whales