map_LG_MLstates_to_tree: Map states to the nodes on a phylogeny

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

Description

What it says.

Usage

  map_LG_MLstates_to_tree(MLstates_LGcpp, tr, tipranges,
    removechar = NULL, type = "C++",
    statesColors_table = "default", bgcol = "green3",
    areanames = "default", newplot = TRUE, ...)

Arguments

MLstates_LGcpp	A data.frame containing the node numbers, states, and states probabilities.
tr	An ape phylo object
tipranges	Tipranges object
removechar	The character to remove, if needed.
type	The type of LAGRANGE input (default C++)
statesColors_table	If not default, a table with a color for each area combination.
bgcol	The background color
areanames	The area names, if different from those in the tipranges object
newplot	Default TRUE; should there be a new plot, or should the splits be added to another plot?
...	Additional arguments to standard functions

Value

MLstates_LGcpp The states table, ordered appropriately.

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/

Matzke_2012_IBS

ReeSmith2008

See Also

get_lagrange_nodenums, LGpy_splits_fn_to_table, LGcpp_splits_fn_to_table

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.