| estimateSkewT {MCMCtreeR} | R Documentation |
Estimate Skew-t Distribution for MCMCtree analysis
Description
Estimate the shape, scale, and location paramaters of a Skew-t distribution and output trees for MCMCtree input
Usage
estimateSkewT(minAge, maxAge, monoGroups, phy, shape = 50, scale = 1.5,
df = 1, addMode = 0, maxProb = 0.975, minProb = 0.003,
estimateScale = TRUE, estimateShape = FALSE, estimateMode = FALSE,
plot = FALSE, pdfOutput = "skewTPlot.pdf", writeMCMCtree = FALSE,
MCMCtreeName = "skewTInput.tre")
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 |
monoGroups |
list with each element containing species that define a node of interest |
phy |
fully resolved phylogeny in ape format |
shape |
shape value for skew-t distribution (default = 50) |
scale |
scale value for skew-t distribution (default = 1.5) |
df |
degrees of freedom for skew-t distribution (default = 1) |
addMode |
addition to the minimum age to give the location of the distribution |
maxProb |
probability of right tail (maximum bound default = 0.975) |
minProb |
probability of left tail (maximum bound default = 0.003) |
estimateScale |
logical specifying whether to estimate scale with a given shape value (default = TRUE) |
estimateShape |
logical specifying whether to estimate shape with a given scale value (default = FALSE) |
estimateMode |
logical speciftying whether to estimate the scale that produces probabilities of each tail that corresponds roughly to the values given by minProb (lower tail) and maxProb (upper tail) |
plot |
logical specifying whether to plot to PDF |
pdfOutput |
pdf output file name |
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
See Also
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$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
estimateSkewT(minAge=minimumTimes, maxAge=maximumTimes,
monoGroups=monophyleticGroups, phy=apeTree, plot=FALSE)$MCMCtree