makeplot.all.params: Plotting all parameters

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

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 May 2, 2019, 4 p.m.