estimateFixed: Fixed Age for MCMCtree analysis input

Description Usage Arguments Value Author(s) Examples

Description

Produce fixed age trees for MCMCtree analysis

Usage

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estimateFixed(minAge, phy, monoGroups, writeMCMCtree = FALSE,
  MCMCtreeName = "estimateFixed.tre")

Arguments

minAge

vector of fixed 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

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

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

Author(s)

Mark Puttick

Examples

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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$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
estimateFixed(minAge=minimumTimes[1],
monoGroups=monophyleticGroups[[1]], phy=apeTree)$MCMCtree

PuttickMacroevolution/MCMCtreeR documentation built on June 11, 2019, 1:47 p.m.