estimateBound: Estimate a Uniform Distribution for MCMCtree

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

Description

Estimate the paramaters of a soft-bounded uniform distribution and output trees for MCMCtree input

Usage

estimateBound(
  minAge,
  maxAge,
  minProb = 0.025,
  rightTail = 0.025,
  phy,
  monoGroups,
  writeMCMCtree = FALSE,
  plot = TRUE,
  MCMCtreeName = "bound.tre",
  pdfOutput = "uniformPlot.pdf"
)

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
minProb	probability of left tail (minimum bound) - default to hard minimum (minProb=0)
rightTail	probability of right tail (maximum bound default = 0.975)
phy	fully resolved phylogeny in ape format
monoGroups	list with each element containing species that define a node of interest
writeMCMCtree	logical whether to write tree in format that is compatible with MCMCTree to file
plot	logical specifying whether to plot to PDF
MCMCtreeName	MCMCtree.output file name
pdfOutput	pdf 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 MCMCtreeR 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

Examples

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$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
estimateBound(minAge=minimumTimes, maxAge=maximumTimes, 
monoGroups=monophyleticGroups, phy=apeTree, plot=FALSE)$MCMCtree

PuttickMacroevolution/MCMCtreeR documentation built on Nov. 24, 2019, 5:22 a.m.