plotMassExtinctions {RevGadgets}

Plot Mass Extinction Support

Description

Plots the support (as 2ln Bayes factors) for mass extinctions.

Usage

plotMassExtinctions(
  mass_extinction_trace,
  mass_extinction_times,
  mass_extinction_name,
  prior_prob,
  return_2lnBF = TRUE
)

Arguments

mass_extinction_trace

(list; no default) The processed Rev output of the mass extinction probabilities (output of readTrace()).

mass_extinction_times

(numeric; no default) Vector of the fixed grid of times at which mass extinctions were allowed to occur.

mass_extinction_name

(character; no default) The name of the mass extinction probability parameter (e.g. "mass_extinction_probabilities") for which support is to be calculated/plotted.

prior_prob

(numeric; no default) The per-interval prior probability of a mass extinction (one minus the p parameter in RevBayes' dnReversibleJumpMixture()).

return_2lnBF

(logical; TRUE) Should the 2ln(BF) be returned (if TRUE) or simply the BF (if FALSE)?

Details

Works only for analyses with a fixed grid where mass extinctions may occur.

The return object can be manipulated. For example, you can change the axis labels, the color palette, whether the axes are to be linked, or the overall plotting style/theme, just as with any ggplot object.

Value

A ggplot object

References

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

Examples

# download the example dataset to working directory
url <-
  "https://revbayes.github.io/tutorials/intro/data/crocs_mass_extinction_probabilities.log"
dest_path <- "crocs_mass_extinction_probabilities.log"
download.file(url, dest_path)

# to run on your own data, change this to the path to your data file
mass_extinction_probability_file <- dest_path

mass_extinction_probabilities <-
              readTrace(mass_extinction_probability_file,burnin = 0.25)

# prior probability of mass extinction at any time
prior_n_expected <- 0.1
n_intervals <- 100
prior_prob <- prior_n_expected/(n_intervals-1)

# times when mass extinctions were allowed
tree_age <- 243.5
interval_times <- tree_age * seq(1/n_intervals,(n_intervals-1) /
                                                   n_intervals,1/n_intervals)

# then plot results:
p <- plotMassExtinctions(mass_extinction_trace=mass_extinction_probabilities,
                         mass_extinction_times=interval_times,
                         mass_extinction_name="mass_extinction_probabilities"
                         ,prior_prob);p

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