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Fixed Age for MCMCtree analysis input

estimateFixed.Rd

Produce fixed age trees for MCMCtree analysis

Usage

estimateFixed(
  minAge,
  phy,
  monoGroups,
  writeMCMCtree = FALSE,
  MCMCtreeName = "estimateFixed.tre"
)

Arguments

minAge

vector of fixed age bounds for nodes matching order in monoGroups

phy

fully resolved phylogeny in ape format

monoGroups

list with each element containing species that define a node of interest

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 MCMCtreeR format

  • "nodeLabels" node labels in MCMCtreeR format

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 = 3):
#> 
#>     apeTree, maximumTimes, minimumTimes, monophyleticGroups
#> The following objects are masked from apeData (pos = 4):
#> 
#>     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$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
estimateFixed(minAge=minimumTimes[1],
monoGroups=monophyleticGroups[[1]], phy=apeTree)$MCMCtree
#> Warning: Length of node.label does not match number of nodes.
#>      
#> 1 7 1
#>                                                                                                             
#> 1 ((((human,(chimpanzee,bonobo)'=1.5')'=1.5',gorilla)'=1.5',(orangutan,sumatran)'=1.5')'=1.5',gibbon)'=1.5';
#>                
#> 1 //end of file