This is a C++ implementation of
rcpp_calc_anclikes_sp_rowsums. It should
be substantially faster, as it requires only one pass
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Transition probability matrix in COO-like format as 4 columns: ancestral index, left index, right index, conditional probability given ancestral states. (assuming likelihood of descendants is 1). Indexes are 0-based. Keep in mind that cladogenesis matrices exclude the null state (a range of 0 areas), so if your states list starts with the null range (as is typical/default in DEC-style models) then to get the R 1-based state indices requires e.g. COO_weights_columnar[] + 2.
The user should provide the number of
states (WITHOUT counting the null range), in case they
are not all present in
Should the probability matrix output be printed to screen? (useful for debugging, but can be dramatically slow in R.app for some reason for even moderate numbers of states; perhaps overrunning the line length...)
rowsums A vector of size (numstates) giving the
sum of the relative probabilites of each combination of
descendant states, assuming the probabilities of the
left- and right-states are all equal (set to 1). This is
thus the sum of the weights, and dividing by this
normalization vector means that the each row of the
speciation probability matrix will sum to 1. Default
assumes the weights sum to 1 but this is not usually the
case. Rsp_rowsums need only be calculated once per
tree+model combination, stored, and then re-used for each
node in the tree, yielding significant time savings.
Nicholas Matzke [email protected]
Matzke N (2012). "Founder-event speciation in BioGeoBEARS package dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses." _Frontiers of Biogeography_, *4*(suppl. 1), pp. 210. ISSN 1948-6596, Poster abstract published in the Conference Program and Abstracts of the International Biogeography Society 6th Biannual Meeting, Miami, Florida. Poster Session P10: Historical and Paleo-Biogeography. Poster 129B. January 11, 2013, <URL: http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster>.
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# For the basic logic of a probablistic cladogenesis model, see ?rcpp_calc_anclikes_sp # For examples of running the functions, see the comparison of all functions at: # ?cladoRcpp
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