rwty (version 1.0.3)

makeplot.all.params: Plotting all parameters

Description

Plots all parameter values, including tree topologies (see makeplot.topology) over the length of the MCMC chain

Usage

makeplot.all.params(
  chains,
  burnin = 0,
  facet = TRUE,
  free_y = FALSE,
  strip = 1
)

Value

param.plot Returns a list of ggplot objects.

Arguments

chains

A set of rwty.chain objects

burnin

The number of trees to omit as burnin.

facet

Boolean denoting whether to make a facet plot.

free_y

TRUE/FALSE to turn free y scales on the facetted plots on or off (default FALSE). Only works if facet = TRUE.

strip

Number indicating which column to strip off (i.e., strip=1 removes first column, which is necessary for most MCMC outputs in which the first column is just the generation). You can skip multiple columns by passing a vector of columns to skip, e.g., strip=c(1,4,6).

Examples

if (FALSE) {
data(fungus)
makeplot.all.params(fungus, burnin=20)
}