# cladoRcpp: C++ implementations of phylogenetic cladogenesis calculations

This package implements in C++/Rcpp various cladogenesis-related calculations that are slow in pure R. These include the calculation of the probability of various scenarios for the inheritance of geographic range at the divergence events on a phylogenetic tree, and other calculations necessary for models which are not continuous-time markov chains (CTMC), but where change instead occurs instantaneously at speciation events. Typically these models must assess the probability of every possible combination of (ancestor state, left descendent state, right descendent state). This means that there are up to (# of states)^3 combinations to investigate, and in biogeographical models, there can easily be hundreds of states, so calculation time becomes an issue. C++ implementation plus clever tricks (many combinations can be eliminated a priori) can greatly speed the computation time over naive R implementations. CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it! Type: citation(package="cladoRcpp") to get the citation information.

- Author
- Nicholas J. Matzke [aut, cre, cph]
- Date of publication
- 2014-05-18 07:22:44
- Maintainer
- Nicholas J. Matzke <matzke@berkeley.edu>
- License
- GPL (>= 2)
- Version
- 0.14.4
- URLs

## Man pages

- areas_list_to_states_list_old
- Convert a list of areas to a list of geographic ranges...
- cladoRcpp-package
- Phylogenetic probability calculations using Rcpp
- numstates_from_numareas
- Calculate the number of states, given a certain number of...
- rcpp_areas_list_to_states_list
- Make a list of 0-based indices of possible combinations of...
- rcpp_calc_anclikes_sp
- Calculate probability of ancestral states below a speciation...
- rcpp_calc_anclikes_sp_COOprobs
- Faster version of rcpp_calc_anclikes_sp
- rcpp_calc_anclikes_sp_COOweights_faster
- Even faster version of rcpp_calc_anclikes_sp
- rcpp_calc_anclikes_sp_prebyte
- Calculate probability of ancestral states below a speciation...
- rcpp_calc_anclikes_sp_rowsums
- Calculate the number of cladogenesis events of nonzero...
- rcpp_calc_anclikes_sp_using_COOprobs
- Calculate ancestral likelihoods given a COO-like probability...
- rcpp_calc_rowsums_for_COOweights_columnar
- Calculate sum of weights for each ancestral state
- rcpp_calc_splitlikes_using_COOweights_columnar
- Calculate the split likelihoods using 'COO_weights_columnar'
- Rcpp_combn_zerostart
- Get all the combinations of descendent state pairs, in...
- rcpp_convolve
- Run C++ version of convolve(x,y, conj=TRUE, type="open")
- rcpp_mult2probvect
- Get the product of multiplying each pair of values in a...
- rcpp_states_list_to_DEmat
- C++ conversion of a states list to a dispersal-extinction...
- strsplit3
- String splitting shortcut

## Files in this package

cladoRcpp |

cladoRcpp/inst |

cladoRcpp/inst/REFERENCES.bib |

cladoRcpp/src |

cladoRcpp/src/calc_anclikes_sp.cpp |

cladoRcpp/src/basics.h |

cladoRcpp/src/calc_anclikes_sp.h |

cladoRcpp/src/basics.cpp |

cladoRcpp/NAMESPACE |

cladoRcpp/NEWS |

cladoRcpp/R |

cladoRcpp/R/cladoRcpp.R |

cladoRcpp/R/cladoRcpp-package.R |

cladoRcpp/MD5 |

cladoRcpp/DESCRIPTION |

cladoRcpp/man |

cladoRcpp/man/rcpp_calc_anclikes_sp_COOprobs.Rd |

cladoRcpp/man/rcpp_mult2probvect.Rd |

cladoRcpp/man/Rcpp_combn_zerostart.Rd |

cladoRcpp/man/strsplit3.Rd |

cladoRcpp/man/cladoRcpp-package.Rd |

cladoRcpp/man/rcpp_calc_rowsums_for_COOweights_columnar.Rd |

cladoRcpp/man/areas_list_to_states_list_old.Rd |

cladoRcpp/man/rcpp_areas_list_to_states_list.Rd |

cladoRcpp/man/rcpp_states_list_to_DEmat.Rd |

cladoRcpp/man/rcpp_calc_anclikes_sp_COOweights_faster.Rd |

cladoRcpp/man/rcpp_calc_anclikes_sp.Rd |

cladoRcpp/man/rcpp_calc_splitlikes_using_COOweights_columnar.Rd |

cladoRcpp/man/numstates_from_numareas.Rd |

cladoRcpp/man/rcpp_convolve.Rd |

cladoRcpp/man/rcpp_calc_anclikes_sp_prebyte.Rd |

cladoRcpp/man/rcpp_calc_anclikes_sp_using_COOprobs.Rd |

cladoRcpp/man/rcpp_calc_anclikes_sp_rowsums.Rd |