make_spmat_row: Construct a (text) cell of the cladogenesis/speciation matrix
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

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

Given the identity of the states/geographic ranges on the left branch (Lstates), right branch (Rstates), and ancestral areas (ancareas_txt_tmp), construct the (text version) of the row of transition probabilities. This means that each nonzero cell gets a v for a vicariance event, a y for a sympatric speciation/range-copying event, a j for a founder-event/jump speciation event, and an s for a sympatric-subset event.

1 2	make_spmat_row(Lstates, Rstates, ancareas_txt_tmp, splitval = "", code_for_overlapping_subsets = NA)

`Lstates`	A string listing the possible left states, which will be split by `splitval`.
`Rstates`	A string listing the possible right states, which will be split by `splitval`.
`ancareas_txt_tmp`	A string listing the possible ancestral states, which will be split by `splitval`.
`splitval`	The character to split on.
`code_for_overlapping_subsets`	Hypothetically, there is no reason that a vicariance event could happen, e.g. ABC–>AB, BC. This is disallowed in `LAGRANGE` BioGeoBEARS defaults, and, if one is going to employ the construct of discrete areas in the first place, overlaps should probably be avoided. But this parameter will allow experimentation. Here, `code_for_overlapping_subsets=NA` equals the default, and any other value means that overlapping vicariance events are included, with a number describing the number of areas in the overlap. Users could then manually convert this to a probability according to some function.

This function is utilized by apply in other functions (e.g. ) in an attempt to speed up calculation over rows. However, processing of text formulas via apply will never be fast enough for large matrices; see cladoRcpp for optimized functions.

This text-based matrix later gets evaluated by other functions to calculate the numerical probabilities. I.e., if j=0 and the other forms of speciation have weights equal to each other, this is the LAGRANGE cladogenesis model.

returncell The text specifying the type of transition.

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

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

Matzke_2012_IBS

ReeSmith2008

size_species_matrix, make_relprob_matrix_bi

testval=1

Loading required package: rexpokit
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges