size_species_matrix: Calculate the dimensions of the cladogenesis/speciation...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

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

This function calculates the dimensions of the cladogenesis/speciation matrix describing the transition probabilities between ancestral geographic ranges and descendant geographic range pairs on Left (L) and Right (R) branches.

1 2	size_species_matrix(states_list = default_states_list(), printwarn = 1)

`states_list`	A list of states, where each state consists of a list of areas. A default example list is provided.
`printwarn`	If `printwarn>0` (`printwarn=1` by default), then print to screen a message describing the size of the cladogenesis matrix.

Under a cladogenesis model of geographic range change, the model will give the conditional probability of each possible combination of geographic ranges on the Left (L) and Right (R) descendant branches, conditional on a particular ancestral state. A matrix representing these transitions will have numstates ancestral states, and numstates*numstates possible descendant pairs. Many of these will have 0 conditional probability under the model, but, for visualization or experimental purposes it can be useful to display them all.

However, because numstates = 2^numareas under default conditions, and the number of cells the processor has to consider (without optimization tricks) is numstates^3, this transition matrix can very quickly become cumbersome to explicitly calculate or display. size_species_matrix allows the user to check this ahead of time.

See numstates_from_numareas for the details of calculating numstates.

At various points in BioGeoBEARS code, the text and numeric versions of the cladogenesis matrix are named spmat and spPmat, respectively.

spmat_dimensions The dimensions of the cladogenesis matrix.

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

make_relprob_matrix_de, make_spmat_row

testval=1
spmat_dimensions = size_species_matrix(
states_list=list("_", c("A"), c("B"), c("C"), c("A","B"),
c("B","C"), c("A","C"), c("A","B","C")), printwarn=1)
spmat_dimensions