Estimate the offset and scale paramaters of a soft-tailed cauchy distribution and output trees for MCMCtree input
estimateCauchy(minAge, maxAge, phy, monoGroups, scale = 1.5,
offset = 50, estimateScale = TRUE, minProb = 0, maxProb = 0.975,
plot = FALSE, pdfOutput = "cauchyPlot.pdf", writeMCMCtree = FALSE,
MCMCtreeName = "cauchyInput.tre")vector of minimum age bounds for nodes matching order in monoGroups
vector of maximum age bounds for nodes matching order in monoGroups
fully resolved phylogeny in ape format
list with each element containing species that define a node of interest
scale value for cauchy distribution (default = 1.5) (c in PAML manual page 49)
offset value for cauchy distribution (default = 50) (p in PAML manual page 49)
logical specifying whether to estimate scale with a given shape value (default = TRUE)
probability of left tail (minimum bound) - default to hard minimum (minProb=0)
probability of right tail (maximum bound. default = 0.975)
logical specifying whether to plot to PDF
pdf output file name
logical whether to write tree in format that is compatible with MCMCTree to file
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