| makeplot.pseudo.ess {rwty} | R Documentation |
Plot the pseudo ESS of tree topologies from MCMC chains.
Description
This function takes a list of rwty.chain objects, and plots the pseudo ESS of the tree topologies from each chain, after removing burnin. Each caulcation is repeated n times, where in each replicate a random tree from the chain is chosen as a 'focal' tree. The calculation works by calculating the path distance of each tree in the chain from the focal tree, and calculating the ESS of the resulting vector of phylogenetic distances using the effectiveSize function from the coda package. NB this function requires the calculation of many tree distances, so can take some time.
Usage
makeplot.pseudo.ess(chains, burnin = 0, n = 20)
Arguments
chains |
A list of rwty.chain objects. |
burnin |
The number of trees to eliminate as burnin |
n |
The number of replicate analyses to do |
Value
pseudo.ess.plot A ggplot2 plot object, in which each chain is represented by a point which represents the median pseudo ESS from the n replicates, and whiskers representing the upper and lower 95
Examples
## Not run:
data(fungus)
makeplot.pseudo.ess(fungus, burnin = 20, n = 10)
## End(Not run)