MCMCtreePhy: MCMCtreePhy

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

Description

Wrapper function to estimate node distributions and add them to tree and output MCMCtree format phylogeny file. If parameter values are in vectors shorter than the number of nodes they are recycled.

Usage

MCMCtreePhy(phy, minAges, maxAges, monoGroups, method = c("cauchy",
  "upper", "bound", "gamma", "skewNormal", "skewT", "fixed"),
  offset = 0.1, df = 1, shape = 50, scale = 1.5, minProb = 1e-08,
  addMode = 0, maxProb = 0.975, rightTail = 0.025, alpha = 188,
  beta = 100, estimateScale = TRUE, estimateShape = FALSE,
  estimateMode = FALSE, estimateAlpha = TRUE, estimateBeta = FALSE,
  plot = FALSE, pdfOutput = "nodeDistributions.pdf",
  writeMCMCtree = TRUE, MCMCtreeName = "output.tre")

Arguments

phy	fully resolved phylogeny in ape format
minAges	vector of minimum age bounds for nodes matching order in monoGroups
maxAges	vector of maximum age bounds for nodes matching order in monoGroups
monoGroups	list with each element containing species that define a node of interest
method	vector of the type of calibration distribution for each node
offset	offset value for distribution (default = 50)
df	degrees of freedom for skew-t distribution (default = 1)
shape	shape value for skew-t distribution (default = 50)
scale	scale value for distribution (default = 1.5)
minProb	probability of left tail (minimum bound) - default to hard minimum (minProb=0)
addMode	addition to the minimum age to give the location of the distribution
maxProb	probability of right tail (maximum bound. default = 0.975)
rightTail	probability of right tail (maximum bound default = 0.025)
alpha	alpha value for gamma distribution (default = 188)
beta	beta value for gamma distribution (default = 2690)
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
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)
estimateAlpha	logical specifying whether to estimate alpha with a given beta value (default = TRUE)
estimateBeta	logical specifying whether to estimate beta with a given alpha value (default = FALSE)
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

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
# Cauchy, upper age, bound, and gamma applied individually to each node
MCMCtreePhy(phy=apeTree, minAge=minimumTimes, maxAge=maximumTimes, 
monoGroups=monophyleticGroups, plot=FALSE, 
method=c("cauchy", "upper", "bound", "gamma"), writeMCMCtree=FALSE)

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