postorder_nodes_phylo4_return_table: Get a table of node numbers, including DIVA node numbers

In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

Description

Various programs (annoyingly) label internal nodes in different ways. This function shows the corresponding node numbers for several different systems. This table can then be used to translate, when the user wishes to plot the output from various programs on the nodes of a tree. In particular, the last column contains the DIVA node-numbering scheme (Ronquist (1996), Ronquist (1997)).

Usage

  postorder_nodes_phylo4_return_table(tr4)

Arguments

tr4	A tree object in phylo or phylo4 format.

Details

There are many ways of numbering nodes in a tree. This returns a matrix containing (column 1) R's native internal numbering scheme, and (column 2) the node numbers in the downpass numbering used by C++ LAGRANGE, in particular in their .bgkey output file. Note that this is different from ape's pruningwise downpass ordering (see get_pruningwise_nodenums).

The python version of LAGRANGE labels internal nodes differently (sigh), but they are in the same order at least, so can just be renumbered from 1 to tr$Nnode to get them to match the C++ LAGRANGE node numbering.

DIVA has yet a different node numbering scheme; see postorder_nodes_phylo4_return_table

Value

postorder_table A data.frame showing the various corresponding node numbers.

Note

Go BEARS!

Author(s)

Nicholas J. Matzke [e-mail]

References

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster https://code.google.com/p/lagrange/

Ronquist1996_DIVA

Ronquist_1997_DIVA

Matzke_2012_IBS

ReeSmith2008

See Also

get_pruningwise_nodenums, get_lagrange_nodenums, prt

Examples

test=1

Example output

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

BioGeoBEARS documentation built on May 29, 2017, 8:36 p.m.