make_relprob_nummatrix_sp1: Convert a observed-speciation transition matrix to an...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

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

Convert a cladogenesis/speciation transition matrix (specifying the probability of each Left/Right descendant range pair, conditional on each ancestral state) of dimensions numstates by numstates^2 to a square transition matrix of dimensions numstates by numstates, representing the probability of a transition when only one daughter survives in the tree.

1 2	make_relprob_nummatrix_sp1(probmat, spPmat, split = "\\\|")

`probmat`	A matrix of text, describing each of the allowed range-inheritance events. Assumes that column names are in the "A\|B" format.
`spPmat`	A matrix of numbers, where each cell contains the conditional probability of that ancestor–>(Left descendant,Right descendant) range inheritance scenario.
`split`	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.

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster https://code.google.com/p/lagrange/ http://tigger.uic.edu/~eeg/code/code.html

Goldberg_etal_2011_GeoSSE

Goldberg_Igic_2012_ClaSSE

Matzke_2012_IBS

ReeSmith2008

make_relprob_matrix_bi, make_relprob_txtmatrix_sp1, paste_rows_without_zeros

testval=1
spmat = 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)
spmat

spPmat = symbolic_to_relprob_matrix_sp(spmat, cellsplit="\\\\+",
mergesym="*", ys=1, j=0, v=1, maxent_constraint_01=0.0001,
maxent_constraint_01v=0.0001, max_numareas=3)
spPmat

newmat = make_relprob_nummatrix_sp1(probmat=spmat, spPmat=spPmat, split="\\\\|")
newmat