Extract diversification data from a BAMM_object

Extracts regime IDs and tip rates from a BAMM_object that has been updated to provide diversification data for a specific time in the past (i.e. the focal_time). Use update_rates_and_regimes_for_focal_time() to obtain a BAMM_object updated for a given focal_time.

Usage

extract_diversification_data_melted_df_for_focal_time(
  BAMM_object,
  verbose = TRUE
)

Arguments

BAMM_object

Object of class "bammdata", typically generated with update_rates_and_regimes_for_focal_time(), that contains a phylogenetic tree and associated diversification rate mapping across selected posterior samples.

verbose

Logical. Should progression be displayed? A message will be printed for every batch of 100 BAMM posterior samples extracted. Default is TRUE.

Value

Returns a data.frame with six columns.

• $focal_time Integer. The time, in terms of time distance from the present, at which the trait data were extracted. Should be equal for all rows as a unique BAMM_object updated for a unique focal_time is being extracted.

• $BAMM_sample_ID Character string. ID of the posterior samples from which the diversification data are extracted named as 'BAMM_X' where X is the numerical ID.

• $tip_ID Character string. Tip labels of the branches cut-off at focal_time.

  • If keep_tip_labels = TRUE was used in update_rates_and_regimes_for_focal_time(), cut-off branches with a single descendant tip retain their initial tip.label.

  • If keep_tip_labels = FALSE was used in update_rates_and_regimes_for_focal_time(), all cut-off branches are labeled using their tipward node ID.

• $regime_ID Integer. The regime ID on tips at focal_time. IDs are integer. The root process equals "1", then they are incremented from oldest to youngest. Regime IDs are independent across posterior samples.

• $rate_type Character string. Type of rates: "lambda" for speciation rates, "mu" for extinction rates, and "net_diversification" for net diversification rates (lambda - mu).

• $rates Numeric. Rates in \[number of events / branch / evolutionary time\].

Author

Maël Doré

Examples

if (deepSTRAPP::is_dev_version())
{
 # Load the BAMM_object summarizing 1000 posterior samples of BAMM updated for a focal_time of 10 My
 data(Ponerinae_BAMM_object_10My)
 ## This dataset is only available in development versions installed from GitHub.
 # It is not available in CRAN versions.
 # Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.

  # (May take several minutes to run)
 # Extract diversification data
 diversification_data_df <- extract_diversification_data_melted_df_for_focal_time(
     BAMM_object = Ponerinae_BAMM_object_10My,
     verbose = TRUE)
 # Print output
 head(diversification_data_df) 
}