estimateFixed: Fixed Age for MCMCtree analysis input

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

Description

Produce fixed age trees for MCMCtree analysis

Usage

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

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

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