mcmcTreePhy: mcmcTreePhy

Description Usage Arguments Value Examples

View source: R/mcmcTreePhy.R

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

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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, alphaInput = 188, betaInput = 100,
  estimateScale = T, estimateShape = F, estimateMode = F,
  estimateAlpha = TRUE, estimateBeta = FALSE, plot = FALSE,
  plotPDF = "nodeDistributions.pdf", writeMCMCTree = TRUE,
  writeTreeName = "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

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)

estimateScale

logical specifying whether to estimate scale with a given shape value (default = TRUE)

estimateShape

logical specifying whether to estimate beta with a given alpha 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)

estimateAlpha

logical specifying whether to estimate alpha with a given beta value (default = TRUE)

plot

logical specifying whether to plot to PDF

writeMCMCTree

logical whether to write tree in format that is compatible with mcmcTree to file

alpha

alpha value for gamma distribution (default = 188)

beta

beta value for gamma distribution (default = 2690)

pdfOutput

pdf output file name

mcmcTreeName

mcmcTree output file name

Value

list containing node estimates for each distribution

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

Examples

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PuttickMacroevolution/MCMCTreeR documentation built on Nov. 20, 2017, 2:22 p.m.