BioGeoBEARS (version 0.2.1)

make_relprob_matrix_bi: Make a relative probability matrix for a single speciation (bifurcation) event

Description

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.

Usage

make_relprob_matrix_bi(states_list = default_states_list(), split_ABC = FALSE, splitval = "", code_for_overlapping_subsets = NA, printwarn = 1)

Arguments

states_list

A list of states, where each state consists of a list of areas. A default example list is provided.

split_ABC

TRUE or FALSE If TRUE then each state/range in the input geographic ranges (states_list) will be split on the argument contained in split.

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.

printwarn

If printwarn>0 (printwarn=1 by default), then print to screen a message describing the size of the cladogenesis matrix.

Value

probmat A matrix of strings, where each cell contains the parameters describing the conditional probability of that ancestor-->(Left descendant,Right descendant) range inheritance scenario.

Details

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.

NOTE: This function is veeeeeeery slow, even for only 3 areas (i.e. 2^3=8 geographic ranges). It is mostly useful for illustration. See cladoRcpp for drastic improvements in calculating cladogenesis models.

References

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

Matzke_2012_IBS

ReeSmith2008

See Also

size_species_matrix, make_spmat_row

Examples

testval=1
probmat = make_relprob_matrix_bi(states_list=list("_",
c("A"), c("B"), c("C"), c("A","B"), c("B","C"), c("A","C"),
c("A","B","C")), split_ABC=FALSE, splitval="",
code_for_overlapping_subsets=NA, printwarn=1)
probmat