Test for Differences in Diversification Rates over Time
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Documentation for package ‘deepSTRAPP’ version 1.1.0
Help Pages
| aggregate_contMaps | Aggregate a list of contMaps into a unique mean/median contMap |
| BAMM_template_diversification | Template file for BAMM diversification analyses |
| build_BAMM_object | Build a BAMM object for a deepSTRAPP run |
| compute_STRAPP_test_for_focal_time | Compute STRAPP to test for a relationship between diversification rates and trait data |
| convert_BSMs_to_simmaps | Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP stochastic map (SM) format |
| convert_BSM_to_simmap | Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP stochastic map (SM) format |
| convert_contsimmap_to_contMaps | Convert a contsimmap object into a list of contMaps |
| convert_simmaps_to_densityMaps | Convert simmaps into densityMaps suitable for deepSTRAPP |
| 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_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 |
| 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 |
| cut_simmap_for_focal_time | Cut the phylogeny and categorical trait/range mapping for a given focal 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_all_trait_values_for_focal_time | Extract all trait data from stochastic maps at a given time in the past |
| extract_diversification_data_melted_df_for_focal_time | Extract diversification data from a BAMM_object |
| 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_trait_data_melted_df_for_focal_time | Extract trait data from a trait_data object |
| mammals | Phylogeny and body mass data for extant and extinct mammal 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 mean 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 |
| prune_BAMM_object | Prune a BAMM object to a subset of tips |
| 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 |
| subset_BAMM_object | Subset a BAMM object before a deepSTRAPP run |
| 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 |