map_LG_MLstates_to_tree: Map states to the nodes on a phylogeny

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

View source: R/BioGeoBEARS_plots_v1.R

Description

What it says.

Usage

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  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 [email protected]

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

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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.