rcpp_calc_rowsums_for_COOweights_columnar: Calculate sum of weights for each ancestral state
In wrathematics/cladoRcpp: C++ implementations of phylogenetic calculations

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

This is a C++ implementation of rcpp_calc_anclikes_sp_rowsums. It should be substantially faster, as it requires only one pass through COO_weights_columnar.

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  rcpp_calc_rowsums_for_COOweights_columnar(COO_weights_columnar,
    numstates = 1 + max(sapply(X = COO_weights_columnar, FUN = max)[1:3]),
    printmat = TRUE)

`COO_weights_columnar`	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.
`numstates`	The user should provide the number of states (WITHOUT counting the null range), in case they are not all present in `COO_weights_columnar`. If empty, the function assumes that the highest index represents the last state, and adds 1 to get the number of states. This may be a hazardous assumption.
`printmat`	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 matzke@berkeley.edu

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>.

rcpp_calc_anclikes_sp

# 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

wrathematics/cladoRcpp documentation built on May 4, 2019, 9:48 a.m.