Package: cladoRcpp 0.15.1

cladoRcpp: C++ Implementations of Phylogenetic Cladogenesis Calculations

Various cladogenesis-related calculations that are slow in pure R are implemented in C++ with Rcpp. 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.

Authors:Nicholas J. Matzke [aut, cre, cph]

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NEWS

# Install 'cladoRcpp' in R:
install.packages('cladoRcpp', repos = c('https://nmatzke.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/nmatzke/cladorcpp/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

16 exports 0.94 score 2 dependencies 236 scripts 332 downloads

Last updated 3 months agofrom:bc5198f075. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 25 2024
R-4.5-win-x86_64OKAug 25 2024
R-4.5-linux-x86_64OKAug 25 2024
R-4.4-win-x86_64OKAug 25 2024
R-4.4-mac-x86_64OKAug 25 2024
R-4.4-mac-aarch64OKAug 25 2024
R-4.3-win-x86_64OKAug 25 2024
R-4.3-mac-x86_64OKAug 25 2024
R-4.3-mac-aarch64OKAug 25 2024

Exports:areas_list_to_states_list_oldnumstates_from_numareasrcpp_areas_list_to_states_listrcpp_calc_anclikes_sprcpp_calc_anclikes_sp_COOprobsrcpp_calc_anclikes_sp_COOweights_fasterrcpp_calc_anclikes_sp_prebytercpp_calc_anclikes_sp_rowsumsrcpp_calc_anclikes_sp_using_COOprobsrcpp_calc_rowsums_for_COOweights_columnarrcpp_calc_splitlikes_using_COOweights_columnarRcpp_combn_zerostartrcpp_convolvercpp_mult2probvectrcpp_states_list_to_DEmatstrsplit3

Dependencies:RcppRcppArmadillo

Readme and manuals

Help Manual

Help pageTopics
Phylogenetic probability calculations using RcppcladoRcpp-package cladorcpp-package cladoRcpp cladorcpp
Convert a list of areas to a list of geographic ranges (states); original R versionareas_list_to_states_list_old
Calculate the number of states, given a certain number of areasnumstates_from_numareas
Make a list of 0-based indices of possible combinations of input areasrcpp_areas_list_to_states_list
Calculate probability of ancestral states below a speciation event, given probabilities of the states on each descendant branchrcpp_calc_anclikes_sp
Faster version of rcpp_calc_anclikes_sprcpp_calc_anclikes_sp_COOprobs
Even faster version of rcpp_calc_anclikes_sprcpp_calc_anclikes_sp_COOweights_faster
Calculate probability of ancestral states below a speciation event, given probabilities of the states on each descendant branchrcpp_calc_anclikes_sp_prebyte
Calculate the number of cladogenesis events of nonzero probability for each ancestral statercpp_calc_anclikes_sp_rowsums
Calculate ancestral likelihoods given a COO-like probability matrixrcpp_calc_anclikes_sp_using_COOprobs
Calculate sum of weights for each ancestral statercpp_calc_rowsums_for_COOweights_columnar
Calculate the split likelihoods using 'COO_weights_columnar'rcpp_calc_splitlikes_using_COOweights_columnar
Get all the combinations of descendent state pairs, in 0-based index formRcpp_combn_zerostart
Run C++ version of convolve(x,y, conj=TRUE, type="open")rcpp_convolve
Get the product of multiplying each pair of values in a vector (cross-product)rcpp_mult2probvect
C++ conversion of a states list to a dispersal-extinction matrix (DEmat)rcpp_states_list_to_DEmat
String splitting shortcutstrsplit3