sample.congruence.class.posterior: Stochastic exploration of congruent models for all samples in...

In CRABS: Congruent Rate Analyses in Birth-Death Scenarios

Stochastic exploration of congruent models for all samples in the posterior

Description

This function takes a posterior sample as input: a list of CRABS objects. It will then iterate over the samples, and for each posterior sample it will sample from the posterior class. It will sample using the sample.basic.models function, and all additional parameters are passed to sample.basic.models.

Usage

sample.congruence.class.posterior(
  posterior,
  num.samples,
  rate.type = "extinction",
  mu0.equal = FALSE,
  rate0 = NULL,
  ...
)

Arguments

posterior	a list of CRABS model objects
num.samples	The number of samples to be drawn
rate.type	either "extinction", "speciation", "both" or "joint"
mu0.equal	whether to propose alternative mu starting at mu0 equal to the posterior sample. default to FALSE
rate0	rate0 allows the user to fix the extinction rate at the present to a single value. defaults to NULL, for drawing it randomly
...	Arguments passed on to sample.basic.models times the time knots model "MRF" for pure MRF model, otherwise MRF has a trend of type "exponential","linear", or "episodic<n>" direction "increase" or "decrease" (measured in past to present) noisy If FALSE, no MRF noise is added to the trajectory MRF.type "HSMRF" or "GMRF", type for stochastic noise. monotonic Whether the curve should be forced to always move in one direction. fc.mean Determines the average amount of change when drawing from the model. rate0.median When not specified, rate at present is drawn from a lognormal distribution with this median. rate0.logsd When not specified, rate at present is drawn from a lognormal distribution with this sd mrf.sd.scale scale the sd of the mrf process up or down. defaults to 1.0 min.rate The minimum rate (rescaling fone after after drawing rates). max.rate The maximum rate (rescaling fone after after drawing rates).

Value

A named list with congruent rates.

Examples

data(primates_ebd_log)

posterior <- read.RevBayes(primates_ebd_log, max_t = 65, n_samples = 10)

samples <- sample.congruence.class.posterior(posterior, 
                                             num.samples = 5,
                                             rate.type = "extinction",
                                             rate0.median = 0.1,
                                             model = "MRF",
                                             max.rate = 1.0)

print(samples)

CRABS documentation built on Oct. 24, 2023, 5:06 p.m.