makeplot.all.params: Plotting all parameters

In rwty: R We There Yet? Visualizing MCMC Convergence in Phylogenetics

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
)

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).

Value

param.plot Returns a list of ggplot objects.

Examples

## Not run: 
data(fungus)
makeplot.all.params(fungus, burnin=20)

## End(Not run)

rwty documentation built on April 3, 2025, 9:20 p.m.