estimateUpper: Estimate Upper Age for MCMCtree analysis

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

Description

Estimate the upper age distribution and output trees for MCMCtree input

Usage

estimateUpper(
  maxAge,
  rightTail = 0.025,
  phy,
  monoGroups,
  writeMCMCtree = FALSE,
  MCMCtreeName = "estimateUpper.tre"
)

Arguments

maxAge	vector of maximum age bounds for nodes matching order in monoGroups
rightTail	probability of right tail (maximum bound default = 0.025)
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
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

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
estimateUpper(maxAge=maximumTimes, monoGroups=monophyleticGroups,
rightTail=0.025, phy=apeTree)

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