calculateShiftBayesFactor: Bayes Factors in support of a shift in diversification rates...

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

Bayes Factors in support of a shift in diversification rates over a given time interval.

Description

This function computes the Bayes Factor in favor of a rate-shift between time t1 and t2 (t1 < t2). The default assumption (suitable to standard HSMRF and GMRF models) is that the prior probability of a shift is 0.5.

Usage

calculateShiftBayesFactor(
  rate_trace,
  time_trace,
  rate_name,
  time_name,
  t1,
  t2,
  prior_prob = 0.5,
  decrease = TRUE,
  return_2lnBF = TRUE
)

Arguments

rate_trace	(list; no default) The processed Rev output of the rate of interest through time for computation (output of readTrace()).
time_trace	(list; no default) The processed Rev output of the change/interval times of the rate of interest through time for computation (output of readTrace()).
rate_name	(character; no default) The name of the parameter (e.g. "speciation") for which Bayes Factor is to be calculated.
time_name	(character; no default) The name of the interval times (e.g. "interval_times) for the rate change times.
t1	(numeric; no default) Support will be assessed for a shift between time t1 and time t2 (t1 < t2).
t2	(numeric; no default) Support will be assessed for a shift between time t1 and time t2 (t1 < t2).
prior_prob	(numeric; 0.5) The prior probability of a shift over this interval (default of 0.5 applies to standard HSMRF- and GMRF-based models).
decrease	(logical; default TRUE) Should support be assessed for a decrease in the parameter (if TRUE) or an increase (if FALSE) between t1 and t2?
return_2lnBF	(logical; TRUE) Should the 2ln(BF) be returned (if TRUE) or simply the BF (if FALSE)?

Value

The Bayes Factor.

References

Kass and Raftery (1995) Bayes Factors. JASA, 90 (430), 773-795.

Examples

#' # download the example datasets to working directory
url_times <-
   "https://revbayes.github.io/tutorials/intro/data/primates_EBD_speciation_times.log"
dest_path_times <- "primates_EBD_speciation_times.log"
download.file(url_times, dest_path_times)

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

# to run on your own data, change this to the path to your data file
speciation_time_file <- dest_path_times
speciation_rate_file <- dest_path_rates

speciation_times <- readTrace(speciation_time_file, burnin = 0.25)
speciation_rate <- readTrace(speciation_rate_file, burnin = 0.25)

calculateShiftBayesFactor(speciation_rate,
                          speciation_times,
                          "speciation",
                          "interval_times",
                          0.0,40.0,
                          decrease=FALSE)

# remove file
# WARNING: only run for example dataset!
# otherwise you might delete your data!
file.remove(dest_path_times, dest_path_rates)

revbayes/RevGadgets documentation built on Jan. 19, 2024, 3:29 p.m.