# estimateSkewNormal: Estimate Skew Normal 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 normal distribution and output trees for MCMCtree input

## Usage

 ```1 2 3 4 5``` ```estimateSkewNormal(minAge, maxAge, monoGroups, phy, shape = 50, scale = 1.5, addMode = 0, maxProb = 0.975, minProb = 0.003, estimateScale = TRUE, estimateShape = FALSE, estimateMode = FALSE, plot = FALSE, pdfOutput = "skewNormalPlot.pdf", writeMCMCtree = FALSE, MCMCtreeName = "skewNormalInput.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 normal distribution (default = 50) `scale` scale value for skew normal distribution (default = 1.5) `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

`qst`
 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13``` ```data(apeData) attach(apeData) monophyleticGroups <- list() ## 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 estimateSkewNormal(minAge=minimumTimes, maxAge=maximumTimes, monoGroups=monophyleticGroups, phy=apeTree, plot=FALSE) ```