processDivRates: Process Diversification Rates

In RevGadgets: Visualization and Post-Processing of 'RevBayes' Analyses

Process Diversification Rates

Description

Processing the output of a episodic diversification rate analysis with mass-extinction events.

Usage

processDivRates(
  speciation_time_log = "",
  speciation_rate_log = "",
  extinction_time_log = "",
  extinction_rate_log = "",
  fossilization_time_log = "",
  fossilization_rate_log = "",
  burnin = 0.25,
  probs = c(0.025, 0.975),
  summary = "median"
)

Arguments

speciation_time_log	(vector of character strings or single character string; "") Path to speciation times log file(s)
speciation_rate_log	(vector of character strings or single character string; "") Path to speciation rates log file(s)
extinction_time_log	(vector of character strings or single character string; "") Path to extinction times log file(s)
extinction_rate_log	(vector of character strings or single character string; "") Path to extinction rates log file(s)
fossilization_time_log	(vector of character strings or single character string; "") Path to fossilization times log file(s)
fossilization_rate_log	(vector of character strings or single character string; "") Path to fossilization rates log file(s)
burnin	(single numeric value; default = 0) Fraction of generations to discard (if value provided is between 0 and 1) or number of generations (if value provided is greater than 1). Passed to readTrace().
probs	(numeric vector; c(0.025, 0.975)) a vector of length two containing the upper and lower bounds for the confidence intervals.
summary	typically "mean" or "median"; the metric to summarize the posterior distribution. Defaults to "median"

Details

For processing the output of an episodic diversification rate analysis. processDivRates() assumes that the epochs are fixed rather than inferred. Additionally, it assumes that times correspond to rates such that the first rate parameter (i.e. speciation[1]) corresponds to the present. Conversely, the first time parameter (i.e. interval_times[1]) corresponds to the first time interval after the present, moving backwards in time. processDivRates() relies on readTrace and produces a list object that can be read by plotDivRates() to visualize the results. For now, only one log file per parameter type is accepted (i.e. log files from multiple runs must be combined before reading into the function).

Value

List object with processed rate and time parameters.

Examples

# download the example datasets to working directory

url_ex_times <-
   "https://revbayes.github.io/tutorials/intro/data/primates_EBD_extinction_times.log"
dest_path_ex_times <- "primates_EBD_extinction_times.log"
download.file(url_ex_times, dest_path_ex_times)

url_ex_rates <-
   "https://revbayes.github.io/tutorials/intro/data/primates_EBD_extinction_rates.log"
dest_path_ex_rates <- "primates_EBD_extinction_rates.log"
download.file(url_ex_rates, dest_path_ex_rates)

url_sp_times <-
   "https://revbayes.github.io/tutorials/intro/data/primates_EBD_speciation_times.log"
dest_path_sp_times <- "primates_EBD_speciation_times.log"
download.file(url_sp_times, dest_path_sp_times)

url_sp_rates <-
   "https://revbayes.github.io/tutorials/intro/data/primates_EBD_speciation_rates.log"
dest_path_sp_rates <- "primates_EBD_speciation_rates.log"
download.file(url_sp_rates, dest_path_sp_rates)

# to run on your own data, change this to the path to your data file
speciation_time_file <- dest_path_sp_times
speciation_rate_file <- dest_path_sp_rates
extinction_time_file <- dest_path_ex_times
extinction_rate_file <- dest_path_ex_rates

rates <- processDivRates(speciation_time_log = speciation_time_file,
                         speciation_rate_log = speciation_rate_file,
                         extinction_time_log = extinction_time_file,
                         extinction_rate_log = extinction_rate_file,
                         burnin = 0.25)

# remove files
# WARNING: only run for example dataset!
# otherwise you might delete your data!
file.remove(dest_path_sp_times, dest_path_ex_times,
            dest_path_sp_rates, dest_path_ex_rates)

RevGadgets documentation built on May 29, 2024, 10:03 a.m.