makeplot.topology: Plotting parameters

In danlwarren/RWTY: R We There Yet? Visualizing MCMC Convergence in Phylogenetics

Description

Plots a trace of topological distances of trees over the length of the MCMC chain. The plot shows the path distance of each tree in each chain from the last tree of the burnin of the first chain. If burnin is set to zero, then distances are calculated from the first tree of the first chain. If required, the behaviour can be changed to plot the path distance of each tree from the last tree of the burnin of each chain, using the independent.chains option. This is not recommended in most cases.

Usage

makeplot.topology(chains, burnin = 0, facet = TRUE, free_y = FALSE,
  independent.chains = FALSE, treedist = "PD", approx.ess = TRUE)

Arguments

chains	A set of rwty.chain objects.
burnin	The number of trees to omit as burnin.
facet	TRUE/FALSE denoting whether to make a facet plot (default TRUE)
free_y	TRUE/FALSE to turn free y scales on the facetted plots on or off (default FALSE). Only works if facet = TRUE.
independent.chains	TRUE/FALSE if FALSE (the default) then the plots show the distance of each tree from the last tree of the burnin of the first chain. If TRUE, the plots show the distance of each tree from the first tree of the chain in which that tree appears. The TRUE option should only be used in the case that different chains represent analyses of different genes or datasets.
treedist	the type of tree distance metric to use, can be 'PD' for path distance or 'RF' for Robinson Foulds distance
approx.ess	TRUE/FALSE do you want the approximate topological ess to be calculated and displayed for each chain?

Value

topology.trace.plot Returns a ggplot object.

Examples

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

## End(Not run)

danlwarren/RWTY documentation built on Sept. 5, 2021, 8:35 p.m.