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Estimate Skew Normal for MCMCtree analysis

estimateSkewNormal.Rd

Estimate the shape, scale, and location paramaters of a skew normal distribution and output trees for MCMCtree input

Usage

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

See also

qst

Author

Mark Puttick

Examples

data(apeData)
attach(apeData)
#> The following objects are masked from apeData (pos = 3):
#> 
#>     apeTree, maximumTimes, minimumTimes, monophyleticGroups
#> The following objects are masked from apeData (pos = 4):
#> 
#>     apeTree, maximumTimes, minimumTimes, monophyleticGroups
#> The following objects are masked from apeData (pos = 5):
#> 
#>     apeTree, maximumTimes, minimumTimes, monophyleticGroups
#> The following objects are masked from apeData (pos = 6):
#> 
#>     apeTree, maximumTimes, minimumTimes, monophyleticGroups
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)
#> [1] "warning - minProb parameter value recycled"
#> [1] "warning - maxProb parameter value recycled"
#> [1] "warning - estimateScale argument recycled"
#> [1] "warning - estimateShape argument recycled"
#> [1] "warning - estimateMode argument recycled"
#> [1] "warning - shape parameter value recycled"
#> [1] "warning - addMode parameter value recycled"
#> Warning: Length of node.label does not match number of nodes.
#> $parameters
#>        location scale shape
#> node_1      1.5  0.67    50
#> node_2      0.6  0.27    50
#> node_3      0.8  0.18    50
#> node_4      1.3  0.31    50
#> 
#> $apePhy
#> 
#> Phylogenetic tree with 7 tips and 6 internal nodes.
#> 
#> Tip labels:
#>   human, chimpanzee, bonobo, gorilla, orangutan, sumatran, ...
#> Node labels:
#>   'SN[1.5~0.67~50]', NA, 'SN[0.6~0.27~50]', 'SN[0.8~0.18~50]', NA, 'SN[1.3~0.31~50]'
#> 
#> Rooted; no branch lengths.
#> 
#> $MCMCtree
#>      
#> 1 7 1
#>                                                                                                                                             
#> 1 ((((human,(chimpanzee,bonobo))'SN(0.8,0.18,50)',gorilla)'SN(0.6,0.27,50)',(orangutan,sumatran)'SN(1.3,0.31,50)'),gibbon)'SN(1.5,0.67,50)';
#>                
#> 1 //end of file
#> 
#> $nodeLabels
#> [1] "'SN[1.5~0.67~50]'" "'SN[0.6~0.27~50]'" "'SN[0.8~0.18~50]'"
#> [4] "'SN[1.3~0.31~50]'"
#>