Convert a cladogenesis/speciation transition matrix
(specifying the probability of each Left/Right descendant
range pair, conditional on each ancestral state) of
numstates^2 to a
square transition matrix of dimensions
numstates, representing the probability of a
transition when only one daughter survives in the tree.
A matrix of text, describing each of the allowed range-inheritance events. Assumes that column names are in the "A|B" format.
The value to split Left/Right pairs on (e.g., "A|B" –> "A", "B")
This matrix could be used to quantify the probability of range-change along a branch due to unobserved speciation events; all that would be required would be an estimate of the number of unobserved speciation events on the branch, and treating this as a Poisson process. (Note: this assumes that the probability of either branch surviving is identical, which might not be the case. See the GeoSSE (Goldberg et al. (2011)) and ClaSSE ("Goldberg et al. (2012)) for the beginnings of work on this, with 2 and 3 geographic areas, respectively.
newmat A new square matrix.
Nicholas J. Matzke email@example.com
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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 newmat = make_relprob_txtmatrix_sp1(probmat=probmat, split="\\\\|") newmat
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