plot_pvo: Plots estimates of species traits distribution

In bite: Bayesian Integrative Models of Trait Evolution

Description

Density plot representing estimated species trait distributions under a jive model. This function plots the mean or median density distribution and the HPD distributions assuming that the trait is normally distributed

Usage

plot_pvo(phy, traits, map = NULL, mcmc.log, tip = NA, burnin = 0.1,
  conf = 0.95, stat = "median", trait.lab = "x", col = NULL,
  lab = TRUE, lolipop = c(0.4, 0.4), cex.tip = par("cex"),
  var.f = NULL, ...)

Arguments

phy	phylogenetic tree provided as either a simmap or a phylo object
traits	trait data used to perform the jive analysis. This has to be of the same form as the one used in make_jive
map	map used to perform the jive analysis. This has to be of the same form as the one used in make_jive
mcmc.log	the output file of a mcmc_bite run
tip	A string giving the species to be plotted. If tip == NA, the posterior distribution of every tip is plotted along with the phylogenetic tree
burnin	The size of the burnin in number of iterations or the proportion of iteration you want to remove
conf	A number of [0,1] giving the confidence level desired.
stat	A character giving the function to be used to estimate species mean and variance from the posterior distributions. Must be one of be "mean" and "median"
trait.lab	a charachter specifying the axis label for the traits
col	color of the density filling. Must be of size two for estimates and HPD. If col and border are NULL, two random colors are assigned
lab	logical indicating whether to show species name in the plot. Only evaluated if tip =! NA
lolipop	size and width of the lolipops representing samples
cex.tip	size of the tips
var.f	alternative distribution used to model intraspecific variation of the form function(n, pars). The function must return n samples from the given distribution.
...	Additional parameters that can be parsed to plot

Author(s)

Theo Gaboriau

Examples

## Load test data
data(Anolis_traits)
data(Anolis_tree)
data(Anolis_map)
# Run a simple MCMC chain
my.jive <- make_jive(Anolis_tree, Anolis_traits[,-3],  model.priors=list(mean="BM", logvar = "OU"))
bite_ex <- tempdir()
logfile <- sprintf("%s/my.jive_mcmc.log", bite_ex)
mcmc_bite(my.jive, log.file=logfile, sampling.freq=1, print.freq=1, ngen=500) 
# import the results in R
res <- read.csv(logfile, header = TRUE, sep = "\t")
 plot_pvo(phy = Anolis_tree, traits = Anolis_traits, tip = NA, mcmc.log = res)

bite documentation built on April 22, 2020, 5:09 p.m.