Rev Language Reference


readTreeTrace

Usage

readTreeTrace(String file, String treetype, Clade outgroup, String separator, Probability burnin, Natural thinning, Bool nexus, Natural nruns)

Arguments

file : String (pass by value)
The name of the tree trace file(s), or directories containing them.
treetype : String (pass by value)
The type of trees.
Default : clock
Options : clock|non-clock
outgroup : Clade (pass by const reference)
The clade (consisting of one or more taxa) used as an outgroup.
Default : NULL
separator : String (pass by value)
The separator/delimiter between values in the file.
Default :
burnin : Probability (pass by value)
The fraction/number of samples to discard as burnin.
Default : 0.25
thinning : Natural (pass by value)
The frequency of samples to read, i.e., we will only used every n-th sample where n is defined by this argument.
Default : 1
nexus : Bool (pass by value)
Whether the file to read is in NEXUS format.
Default : FALSE
nruns : Natural (pass by value)
The number of trace files with the same basename (i.e. the number of filenames with pattern _run_.trees
Default : 1

Return Type