estimateCauchy: Estimate Cauchy Distribution for MCMCtree

In MCMCtreeR: Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees

Description

Estimate the offset and scale paramaters of a soft-tailed cauchy distribution and output trees for MCMCtree input

Usage

estimateCauchy(minAge, maxAge, phy, monoGroups, scale = 1.5,
  offset = 50, estimateScale = TRUE, minProb = 0, maxProb = 0.975,
  plot = FALSE, pdfOutput = "cauchyPlot.pdf", writeMCMCtree = FALSE,
  MCMCtreeName = "cauchyInput.tre")

Arguments

minAge	vector of minimum age bounds for nodes matching order in monoGroups
maxAge	vector of maximum age bounds for nodes matching order in monoGroups
phy	fully resolved phylogeny in ape format
monoGroups	list with each element containing species that define a node of interest
scale	scale value for cauchy distribution (default = 1.5) (c in PAML manual page 49)
offset	offset value for cauchy distribution (default = 50) (p in PAML manual page 49)
estimateScale	logical specifying whether to estimate scale with a given shape value (default = TRUE)
minProb	probability of left tail (minimum bound) - default to hard minimum (minProb=0)
maxProb	probability of right tail (maximum bound. default = 0.975)
plot	logical specifying whether to plot to PDF
pdfOutput	pdf output file name
writeMCMCtree	logical whether to write tree in format that is compatible with MCMCTree to file
MCMCtreeName	MCMCtree.output file name

Value

list containing node estimates for each distribution

• "parameters" estimated parameters for each node

• "apePhy" phylogeny in ape format with node labels showing node distributions

• "MCMCtree" phylogeny in MCMCtree format

• "nodeLabels" node labels in MCMCtreeR format

If plot=TRUE plot of distributions in file 'pdfOutput' written to current working directory

If writeMCMCtree=TRUE tree in MCMCtree format in file "MCMCtreeName" written to current working directory

Author(s)

Mark Puttick data(apeData) attach(apeData) ## extract taxon descending from calibrated nodes 8, 10, 11, 13 ## these nodes can be visualised using plot.phylo ## and nodelabels from ape monophyleticGroups <- tipDes(apeData$apeTree, c(8,10,11,13)) minimumTimes <- c("nodeOne"=15, "nodeTwo"=6, "nodeThree"=8, "nodeFour"=13) / 10 maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12, "nodeThree"=12, "nodeFour" = 20) / 10 estimateCauchy(minAge=minimumTimes, maxAge=maximumTimes, monoGroups=monophyleticGroups, offset=0.5, phy=apeTree, plot=FALSE)$MCMCtree

MCMCtreeR documentation built on May 22, 2019, 1:03 a.m.