Rev Language Reference

readTreeTrace(String file, String treetype, Bool unroot_nonclock, Clade outgroup, String separator/delimiter, Integer 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 :	Integer (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

TraceTree

Either a file name or a directory must be provided as argument. If a folder is provided, all the files that contain trees in that directory are read in the same object. `tree_trace = readTreeTrace(..., nruns = 1)` returns a `TraceTree` object. `tree_trace = readTreeTrace(..., nruns > 1)` returns a `TraceTree[]` object, in which `tree_trace[n]` corresponds to the trace of run `n`. The resulting `TraceTree` object stores every `thinning`th sample from a file, starting at the sample numbered `offset + 1`.

# read a tree trace
tree_trace = readTreeTrace("my_filename.tree", treetype="clock", burnin=0.5)

# make a summary maximum clade credibility (MCC) tree
mcc_tree = mccTree(trace=tree_trace, file="mcc.tree")

• readAncestralStateTrace
• readTrace
• readTrees
• TraceTree