map_LG_MLsplits_to_tree: Take the table of ML splits and node number and map on tree...

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

View source: R/BioGeoBEARS_plots_v1.R

Description

Given a table of splits probabilities from LGcpp_splits_fn_to_table, map the splits on the tree.

Usage

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  map_LG_MLsplits_to_tree(MLsplits_LGcpp, tr,
    tiprange_names, removechar = NULL, type = "C++")

Arguments

MLsplits_LGcpp

A data.frame containing the node numbers, splits, and split probabilities.

tr

An ape phylo object

tiprange_names

The geographic ranges at the tips (i.e. the input data)

removechar

The character to remove, if needed.

type

The type of LAGRANGE input (default C++)

Details

See get_lagrange_nodenums for connecting these node numbers to APE node numbers.

Value

MLsplits_LGcpp A data.frame containing the node numbers, ML splits, and split probabilities; reordered for this plot.

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.