mcmc.plot: plot the output from transformPhylo.MCMC

In PuttickMacroevolution/motmot: Models of Trait Macroevolution on Trees

Description

Plots a histogram of the estimated parameter and a trace of the results

Usage

mcmc.plot(
  mcmc.input,
  y.limit = NULL,
  x.limit = NULL,
  label.text = NULL,
  cex.axis = 1,
  cex.labels = 0.7,
  col.hist = "green4",
  col.trace = "navy"
)

Arguments

mcmc.input	an object of class "mcmc.motmot" output from transformPhylo.MCMC
y.limit	the limits for the y axes for the plots
x.limit	the limits for the x axes for the plots
label.text	the labels for the two plots defaults to '(a)' etc., for the histogram and '(b)' etc., for the trace plot
cex.axis	character expansion for the plot axis labels
cex.labels	character expansion for the plot axis names
col.hist	colour for the histogram bars
col.trace	colour for the trace plot

Value

Two plots showing the histogram of the estimated parameter value and a trace of the MCMC estimation

Author(s)

Mark Puttick

Examples

library(motmot)
data(anolis.tree)
data(anolis.data)
attach(anolis.data)
male.length <- matrix(Male_SVL, dimnames=list(rownames(anolis.data)))
sortedData <- sortTraitData(anolis.tree, male.length)
phy <- sortedData$phy
male.length <- sortedData$trait
phy.clade <- extract.clade(phy, 182)
male.length.clade <- as.matrix(male.length[match(phy.clade$tip.label, rownames(male.length)),])
## not run
# please note, this model will be need to run for longer to achieve convergence
# lambda.mcmc <- transformPhylo.MCMC(y=male.length.clade, phy=phy.clade, 
# model="lambda", mcmc.iteration=100, burn.in=0.1)
# mcmc.plot(lambda.mcmc)

PuttickMacroevolution/motmot documentation built on June 5, 2020, 7 p.m.