Package index
Prepare data for deepSTRAPP
Prepare trait and diversification data to use as inputs for a deepSTRAPP test.
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prepare_trait_data() - Map trait evolution on a time-calibrated phylogeny
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prepare_diversification_data() - Run a full BAMM (Bayesian Analysis of Macroevolutionary Mixtures) workflow
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run_deepSTRAPP_for_focal_time() - Run deepSTRAPP to test for a relationship between diversification rates and trait data at a given focal time
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run_deepSTRAPP_over_time() - Run deepSTRAPP to test for a relationship between diversification rates and trait data over multiple time steps
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compute_STRAPP_test_for_focal_time() - Compute STRAPP to test for a relationship between diversification rates and trait data
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extract_most_likely_trait_values_for_focal_time() - Extract trait data mapped on a phylogeny at a given time in the past
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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
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extract_most_likely_states_from_densityMaps_for_focal_time() - Extract categorical trait data mapped on a phylogeny at a given time in the past
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extract_most_likely_ranges_from_densityMaps_for_focal_time() - Extract biogeographic range data mapped on a phylogeny at a given time in the past
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extract_diversification_data_melted_df_for_focal_time() - Extract diversification data from a BAMM_object
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update_rates_and_regimes_for_focal_time() - Update diversification rates/regimes mapped on a phylogeny up to a given time in the past
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cut_phylo_for_focal_time() - Cut the phylogeny for a given time in the past
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cut_contMap_for_focal_time() - Cut the phylogeny and continuous trait mapping for a given focal time in the past
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cut_densityMap_for_focal_time() - Cut the phylogeny and posterior probability mapping of a categorical trait for a given focal time in the past
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cut_densityMaps_for_focal_time() - Cut phylogenies and posterior probability mapping of each state for a given focal time in the past
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plot_contMap() - Plot continuous trait evolution on the tree
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plot_densityMaps_overlay() - Plot posterior probabilities of states/ranges on phylogeny from densityMaps
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plot_BAMM_rates() - Plot diversification rates and regime shifts from BAMM on phylogeny
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plot_traits_vs_rates_on_phylogeny_for_focal_time() - Plot trait/range evolution vs. diversification rates and regime shifts on phylogeny
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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
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plot_STRAPP_pvalues_over_time() - Plot evolution of p-values of STRAPP tests over time
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plot_histogram_STRAPP_test_for_focal_time() - Plot histogram of STRAPP test statistics to assess results
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plot_histograms_STRAPP_tests_over_time() - Plot multiple histograms of STRAPP test statistics over time-steps
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plot_rates_through_time() - Plot evolution of diversification rates in relation to trait values over time
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plot_rates_vs_trait_data_for_focal_time() - Plot rates vs. trait data for a given focal time
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plot_rates_vs_trait_data_over_time() - Plot rates vs. trait data over time-steps
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BSM_to_phytools_simmap()BSMs_to_phytools_simmaps() - Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP stochastic map (SM) format
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select_best_trait_model_from_geiger() - Compare trait evolutionary model fits with AICc and Akaike's weights
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select_best_model_from_BioGeoBEARS() - Compare model fits with AICc and Akaike's weights
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Ponerinae_tree - Dataset providing the extensive time-calibrated phylogeny of extant ponerine ants
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Ponerinae_tree_old_calib - Dataset providing the extensive time-calibrated phylogeny of extant ponerine ants using an old calibration for illustrative purposes
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mammals - Phylogeny and body mass data for extant and extinct mammals families/genera from Slater, 2013
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Ponerinae_trait_tip_data - Dataset providing fake trait data for extant ponerine ants for illustrative purposes
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Ponerinae_binary_range_table - Dataset providing biogeographic range data for extant ponerine ants
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Ponerinae_trait_cont_tip_data_10My - Data summarizing the evolution of a fake continuous trait in Ponerinae ants extracted for 10 Mya
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eel_cat_3lvl_data - Data summarizing the evolution of feeding habits in eels using a 3-level factor as categorical trait
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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
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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
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eel_biogeo_data - Data summarizing the evolution of geographic ranges in eels
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Ponerinae_biogeo_data_old_calib - Data summarizing the evolution of geographic ranges in Ponerinae ants using an old ill-calibrated phylogeny for illustrative purposes
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BAMM_template_diversification - Template file for BAMM diversification analyses
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whale_BAMM_object - Dataset summarizing 1000 posterior samples of BAMM for extant whales
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Ponerinae_BAMM_object - Dataset summarizing 1000 posterior samples of BAMM for extant ponerine ants
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Ponerinae_BAMM_object_old_calib - Dataset summarizing 1000 posterior samples of BAMM for extant ponerine ants based on an old time-calibration for illustrative purposes
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Ponerinae_BAMM_object_10My - Dataset summarizing 1000 posterior samples of BAMM for extant ponerine ants updated to 10 My
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Ponerinae_deepSTRAPP_cont_old_calib_0_40 - deepSTRAPP output for fake continuous trait data for old time-calibrated ponerine ant phylogeny over 0 to 40 Mya
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Ponerinae_deepSTRAPP_cat_2lvl_old_calib_0_40 - deepSTRAPP output for fake categorical size data with 2-levels mapped on old time-calibrated ponerine ant phylogeny over 0 to 40 Mya
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Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40 - deepSTRAPP output for fake categorical habitat data with 3-levels mapped on old time-calibrated ponerine ant phylogeny over 0 to 40 Mya
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Ponerinae_deepSTRAPP_biogeo_old_calib_0_40 - deepSTRAPP output for biogeographic ranges mapped on old time-calibrated ponerine ant phylogeny over 0 to 40 Mya