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.
A list of states, where each state consists of a list of areas. A default example list is provided.
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,
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.
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
size_species_matrix allows the user to
check this ahead of time.
the details of calculating
At various points in
BioGeoBEARS code, the text
and numeric versions of the cladogenesis matrix are named
spmat_dimensions The dimensions of the
Nicholas J. Matzke email@example.com
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