Rev Language Reference



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


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
unroot_nonclock : Bool (pass by value)
Remove a degree-2 root node and set the tree unrooted, if treetype is non-clock.
Default : TRUE
outgroup : Clade (pass by const reference)
The clade (consisting of one or more taxa) used as an outgroup.
Default : NULL
separator/delimiter : String (pass by value)
The field separator character. Values on each line of the file are separated by this character. If sep = "" the separator is 'white space', that is one or more spaces, tabs, newlines or carriage returns.
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
offset : Natural (pass by value)
The offset of the first sample to read, i.e., how many samples should we skip before we take the first sample.
Default : 0
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