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)).
A tree object in
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
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_table A data.frame showing the various
corresponding node numbers.
Nicholas J. Matzke [email protected]
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
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