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

Calculates the split likelihoods using
`COO_weights_columnar`

, i.e. the weights as produced
by `rcpp_calc_anclikes_sp_COOweights_faster`

.

1 2 3 | ```
rcpp_calc_splitlikes_using_COOweights_columnar(Rcpp_leftprobs,
Rcpp_rightprobs, COO_weights_columnar, Rsp_rowsums,
printmat = TRUE)
``` |

`Rcpp_leftprobs` |
Probabilities of the states at the base of the left descendant branch |

`Rcpp_rightprobs` |
Probabilities of the states at the base of the right descendant branch |

`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. 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[[1]] + 2. |

`Rsp_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. |

`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...) |

`splitlikes`

Vector of the probabilities of each
allowed split

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>.

1 2 3 4 5 | ```
# 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
``` |

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.