prt: Print tree in table format
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/BioGeoBEARS_readwrite_v1.R

Learning and using APE's tree structure can be difficult and confusing because much of the information is implicit. This function prints the entire tree to a table, and makes much of the implicit information explicit. It is not particularly fast, but it is useful.

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  prt(t, printflag = TRUE, relabel_nodes = FALSE,
    time_bp_digits = 7, add_root_edge = TRUE,
    get_tipnames = FALSE, fossils_older_than = 0.6)

`t`	A `phylo` tree object.
`printflag`	Should the table be printed to screen? Default TRUE.
`relabel_nodes`	Manually renumber the internal nodes, if desired. Default FALSE.
`time_bp_digits`	The number of digits to print in the time_bp (time before present) column. Default=7.
`add_root_edge`	Should a root edge be added? Default `TRUE`.
`get_tipnames`	Should the list of tipnames descending from each node be printed as a string in another column? This is slow-ish, but useful for matching up nodes between differing trees. Default `FALSE`.
`fossils_older_than`	Tips that are older than `fossils_older_than` will be marked as `TRUE` in a column called `fossil`. This is not currently set to 0, because Newick files can have slight precision issues etc. that mean not all tips quite come to zero. You can attempt to fix this with `average_tr_tips` (but make sure you do not inappropriately average in fossils!!).

See http://ape.mpl.ird.fr/ape_development.html for the official documentation of R tree objects.

dtf A data.frame holding the table. (Similar to the printout of a phylo4 object.)

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

http://ape.mpl.ird.fr/ape_development.html

Matzke_2012_IBS

phylo, average_tr_tips

test=1

Loading required package: rexpokit
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

Loading required package: Rcpp
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges