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deepSTRAPP output for fake categorical habitat data with 3-levels mapped on old time-calibrated ponerine ant phylogeny over 0 to 40 Mya

Source: R/datasets_doc.R
Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40.Rd

deepSTRAPP output for fake categorical habitat data with 3-levels mapped on old time-calibrated ponerine ant phylogeny over 0 to 40 Mya. This object is the typical result of a deepSTRAPP run carried out with run_deepSTRAPP_over_time(). It summaries STRAPP test results and can optionally include trait and diversification rate data frames, STRAPP test outputs, updated trait data objects, and updated BAMM objects, that are required fro downstream plots and analyses.

Usage

data(Ponerinae_deepSTRAPP_cat_3lvl_old_calib_0_40)

Format

A list with 11 elements.

Details

deepSTRAPP output summarizing results of a deepSTRAPP run carried out with run_deepSTRAPP_over_time().

  • $pvalues_summary_df Data.frame with three columns providing test stat $estimate and $p_value obtained for each time step (i.e., $focal_time), that can be passed down to plot_STRAPP_pvalues_over_time() to generate a plot showing the evolution of the test results across time.

  • $time_steps Numerical vector. Time steps at which the STRAPP tests were carried out in the same order as the objects returned in the output lists.

  • $trait_data_type Character string. Specify the type of trait data. Here: "categorical".

  • $trait_data_type_for_stats Character string. The type of trait data used to select statistical method. Here: "multinominal".

  • $rate_type Character string. The type of diversification rates used in the tests. Here: "net_diversification".

Optional summary df for multinominal data, if posthoc_pairwise_tests = TRUE:

  • $pvalues_summary_df_for_posthoc_pairwise_tests Data.frame with five columns providing test stat $estimate, $p_value, and $p_value_adjusted for each $pair of states involved in post hoc Dunn's tests obtained for each time step (i.e., $focal_time). This data.frame can be passed down to plot_STRAPP_pvalues_over_time() to generate a plot showing the evolution of the post hoc test results across time.

Optional melted data.frames:

  • $trait_data_df_over_time Data.frame with three columns providing $trait_value associated with each $tip_ID found along each time step (i.e., $focal_time).

  • $diversification_data_df_over_time Data.frame with six columns providing diversification regimes ($regime_ID) and $rates sorted by $rate_type along tips ($tip_ID) found across all posterior samples ($BAMM_sample_ID) over each time step (i.e., $focal_time).

  • Those data.frames can be passed down to plot_rates_through_time() to generate a plot showing the evolution diversification rates across trait values over time.

Optional objects generated for each time step (i.e., focal_time) and ordered as in $time_steps:

  • $STRAPP_results_over_time List of objects summarizing the results of the STRAPP tests See compute_STRAPP_test_for_focal_time() for a detailed description of the elements in each object. Combined with return_perm_data = TRUE, it allows to plot the histograms of the null distributions used to assess significance of the tests with plot_histogram_STRAPP_test_for_focal_time(). (for a single focal_time) and plot_histograms_STRAPP_tests_over_time() (for multiple time_steps).

  • $updated_trait_data_with_Map_over_time List of objects containing trait data and updated contMap/densityMaps. Updated densityMaps can be plotted with plot_densityMaps_overlay() to display a phylogeny mapped with inferred states with branches cut at each focal_time.

  • $updated_BAMM_objects_over_time List of objects containing rates and regimes ID mapped on phylogeny. Updated BAMM_object can be plotted with plot_BAMM_rates() to display a phylogeny mapped with diversification rates with branches cut at each focal_time.