posteriorSamplesToParametricPrior: Priors from MCMC samples

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

Priors from MCMC samples

Description

Turn posterior samples collected by MCMC into a parametric prior distribution.

Usage

posteriorSamplesToParametricPrior(
  samples,
  distribution,
  variance_inflation_factor = 2
)

Arguments

samples	(numeric vector; no default) MCMC samples for a single parameter.
distribution	(character; no default) The distribution to fit. Options are gamma for strictly positive parameters and normal for unbounded parameters.
variance_inflation_factor	(single numeric value; default = 2.0) Makes the prior variance larger than the variance of the posterior

Details

The distributions are fit by the method of moments. The function allows inflating the prior variance relative to the posterior being supplied.

Value

Numeric vector of parameters with names (to avoid rate/scale and var/sd confusion).

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

primates <- 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)

speciation_rates <-
       dplyr::pull(primates[which(primates$item == "speciation rate"),],
                  "value")
speciation_1_gamma_prior <-
          posteriorSamplesToParametricPrior(speciation_rates,"gamma")

# 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.