MCMCtreePhy

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

Mark Puttick

Examples

data(apeData)
attach(apeData)
#> 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
#> The following objects are masked from apeData (pos = 7):
#> 
#>     apeTree, maximumTimes, minimumTimes, monophyleticGroups
#> The following objects are masked from apeData (pos = 8):
#> 
#>     apeTree, maximumTimes, minimumTimes, monophyleticGroups
#> The following objects are masked from apeData (pos = 9):
#> 
#>     apeTree, maximumTimes, minimumTimes, monophyleticGroups
#> The following objects are masked from apeData (pos = 10):
#> 
#>     apeTree, maximumTimes, minimumTimes, monophyleticGroups
## 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)
#> Warning: Length of node.label does not match number of nodes.
#> Warning: Length of node.label does not match number of nodes.
#> Warning: Length of node.label does not match number of nodes.
#> Warning: Length of node.label does not match number of nodes.
#> $node_1
#>         tL   p     c     pL
#> node_1 1.5 0.1 0.085 1e-300
#> 
#> $node_2
#>         tU    pR
#> node_1 1.2 0.025
#> 
#> $node_3
#>         tL  tU     pL    pU
#> node_1 0.8 1.2 1e-300 0.025
#> 
#> $node_4
#>        alpha beta
#> node_1   140  100
#>