estimateSkewT: Estimate Skew-t Distribution for MCMCtree analysis

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

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

qst

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

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