deepSTRAPP

• See the new vignette handle_uncertainty.

Importing results from external analyses

• New functions to bring analyses run outside deepSTRAPP into the workflow: build_BAMM_object(), subset_BAMM_object() and prune_BAMM_object() for BAMM output; convert_BSM_to_simmap() and convert_BSMs_to_simmaps() for BioGeoBEARS biogeographic stochastic maps; convert_contsimmap_to_contMaps() for contsimmap output; and convert_simmaps_to_densityMaps() to summarise stochastic maps as posterior densities.
• aggregate_contMaps() summarises a list of continuous stochastic maps into a single mean or median contMap.
• See the new vignette import_external_analyses.

Consistency of the statistical method across time steps

• run_deepSTRAPP_over_time() now selects the statistical method once, before any test is run, from all states/ranges described in the complete trait mapping, and applies it at every time step. The method previously depended on the states/ranges still present at each time step, so a trajectory could mix Kruskal-Wallis and Mann-Whitney U p-values on a single curve when a state/range was absent from the deeper time steps. This is not the case anymore, and all p-values across time-steps are prodcued by the same type of test.
• The states/ranges actually observed are now reported: $states_observed and $nb_states_observed per time step, and $states_observed_overall, $states_observed_per_time_steps and $nb_states_observed_per_time_steps in the output of run_deepSTRAPP_over_time().

Other additions

• New extract_all_trait_values_for_focal_time() to extract trait data from every stochastic map at a given time, and extract_trait_data_melted_df_for_focal_time() to return it in long dataframe format.
• New cut_contMaps_for_focal_time(), cut_simmap_for_focal_time() and cut_simmaps_for_focal_time() to cut lists of stochastic maps at a focal time.
• run_deepSTRAPP_for_focal_time() and run_deepSTRAPP_over_time() gain return_updated_Maps to return the mappings cut at each focal time, and run_deepSTRAPP_for_focal_time() gains extract_trait_data_melted_df to return the underlying trait data in long dataframe format.