Skip to contents

Plot multiple histograms of STRAPP test statistics over time-steps

Source: R/plot_histograms_STRAPP_tests_over_time.R
plot_histograms_STRAPP_tests_over_time.Rd

Plot an histogram of the distribution of the test statistics obtained from a deepSTRAPP workflow carried out for each focal time in $time_steps. Main input = output of a deepSTRAPP run over time using run_deepSTRAPP_over_time()).

Returns one histogram for overall tests for each focal time in $time_steps. If plot_posthoc_tests = TRUE, it will return one faceted plot with an histogram per post hoc tests for each focal time in $time_steps.

If a PDF file path is provided in PDF_file_path, the plots will be saved directly in a PDF file, with one page per focal time in $time_steps.

Usage

plot_histograms_STRAPP_tests_over_time(
  deepSTRAPP_outputs,
  display_plots = TRUE,
  plot_posthoc_tests = FALSE,
  PDF_file_path = NULL
)

Arguments

deepSTRAPP_outputs

List of elements generated with run_deepSTRAPP_over_time(), that summarize the results of multiple deepSTRAPP across $time_steps. It needs to include the $STRAPP_results_over_time element with $perm_data_df obtained when setting both return_STRAPP_results = TRUE and return_perm_data = TRUE.

display_plots

Logical. Whether to display the histograms generated in the R console. Default is TRUE.

plot_posthoc_tests

Logical. For multinominal data only. Whether to plot the histograms for the overall Kruskal-Wallis test across all states (plot_posthoc_tests = FALSE), or plot the histograms for all the pairwise post hoc Dunn's tests across pairs of states (plot_posthoc_tests = TRUE). Time-steps at which the data does not yield more than two states/ranges will show a warning and generate no plot. Default is FALSE.

PDF_file_path

Character string. If provided, the plots will be saved in a unique PDF file following the path provided here. The path must end with ".pdf". Each page of the PDF corresponds to a focal time in $time_steps.

Value

By default, the function returns a list of sub-lists of classes gg and ggplot ordered as in $time_steps. Each sub-list corresponds to a ggplot for a given focal_time i that can be displayed on the console with print(output[[i]]). If display_plots = TRUE, the histograms are being displayed on the console one by one while generated.

If using multinominal data and set plot_posthoc_tests = TRUE, the function will return a list of sub-lists of objects ordered as in $time_steps. Each sub-list is a list of the ggplots associated with pairwise post hoc tests carried out for this a given focal_time. For a given focal_time i, to plot each histogram j individually, use print(output_list[[i]][[j]]). To plot all histograms of a given focal_time i at once in a multifaceted plot, as displayed sequentially on the console if display_plots = TRUE, use cowplot::plot_grid(plotlist = output_list[[i]]).

Each plot also displays summary statistics for the STRAPP test associated with the data displayed.

  • The quantile of null statistic distribution at the significant threshold used to define test significance. This is the value found on the red dashed line. The test will be considered significant (i.e., the null hypothesis is rejected) if this value is higher than zero (the black dashed line).

  • The p-value of the STRAPP test which correspond the proportion of cases in which the statistics was lower than expected under the null hypothesis (i.e., the proportion of the histogram found below / on the left-side of the black dashed line).

If a PDF_file_path is provided, the function will also generate a PDF file of the plots with one page per $time_steps. For post hoc tests, this will save the multifaceted plots.

Details

The main input deepSTRAPP_outputs is the typical output of run_deepSTRAPP_over_time(). It provides information on results of a STRAPP tests performed over multiple time-steps.

Histograms are built based on the distribution of the test statistics. Such distributions are recorded in the outputs of a deepSTRAPP run carried out with run_deepSTRAPP_over_time() when return_STRAPP_results = TRUE AND return_perm_data = TRUE. The $STRAPP_results_over_time objects provided within the input are lists that must contain a $perm_data_df element that summarizes test statistics computed across posterior samples.

For multinominal data (categorical or biogeographic data with more than 2 states), it is possible to plot the histograms of post hoc pairwise tests. Set plot_posthoc_tests = TRUE to generate histograms for all the pairwise post hoc Dunn's test across pairs of states. To achieve this, the $STRAPP_results_over_time objects must contain a $posthoc_pairwise_tests$perm_data_array element that summarizes test statistics computed across posterior samples for all pairwise post hoc tests. This is obtained from run_deepSTRAPP_over_time() when setting return_STRAPP_results = TRUE to return the STRAPP results, posthoc_pairwise_tests = TRUE to carry out post hoc tests, and return_perm_data = TRUE to record distributions of test statistics. Time-steps for which the data do not yield more than two states/ranges will show a warning and generate no plot.

See also

Associated functions in deepSTRAPP: run_deepSTRAPP_over_time() plot_histogram_STRAPP_test_for_focal_time()

Author

Maël Doré

Examples