Description Usage Arguments Value Author(s) Examples
View source: R/estimateUpper.R
Estimate the upper age distribution and output trees for MCMCtree input
1 2 3 4 5 6 7 8 | estimateUpper(
maxAge,
rightTail = 0.025,
phy,
monoGroups,
writeMCMCtree = FALSE,
MCMCtreeName = "estimateUpper.tre"
)
|
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 |
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
Mark Puttick
1 2 3 4 5 6 7 8 9 10 11 12 | 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)
|
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