makeplot.treespace: Plot chains in treespace.

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

Description

This function will take list of rwty.chains objects and produce plots of chains in treespace.

Usage

makeplot.treespace(chains, burnin = 0, n.points = 100,
  fill.color = NA)

Arguments

chains	A list of one or more rwty.chain objects
burnin	The number of samples to remove from the start of the chain as burnin
n.points	The number of points on each plot
fill.color	The name of any column in your parameter file that you would like to use as a fill colour for the points of the plot.

Value

A list of two ggplot objects: one plots the points in treespace, the other shows a heatmap of the same points

Examples

## Not run: 
data(fungus)

p <- makeplot.treespace(fungus, burnin = 20, fill.color = 'LnL')
# Treespace plot for all the fungus data

# NB: these data indicate significant problems: the chains are sampling very 
# different parts of tree space.
#
# View the points plotted in treespace (these data indicate significant problems)
p$treespace.points.plot

# View the heatmap of the same data
# Note that this data is so pathologically bad that the heatmap is not
# very useful. It is more useful on better behaved datasets
p$treespace.heatmap

# we can also plot different parameters as the fill colour.
# e.g. we can plot the first two fungus chains with likelihood as the fill
makeplot.treespace(fungus[1:2], burnin = 100, fill.color = 'LnL')

# or with tree length as the fill
makeplot.treespace(fungus[1:2], burnin = 100, fill.color = 'TL')

# you can colour the plot with any parameter in your ptable
# to see which parameters you have you can simply do this:
names(fungus[[1]]$ptable)

## End(Not run)

rwty documentation built on May 2, 2019, 4 p.m.