R: C++ Implementations of Phylogenetic Cladogenesis Calculations

# C++ Implementations of Phylogenetic Cladogenesis Calculations

## Documentation for package ‘cladoRcpp’ version 0.15.1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

cladoRcpp-package | Phylogenetic probability calculations using Rcpp
cladorcpp-package | Phylogenetic probability calculations using Rcpp
areas_list_to_states_list_old | Convert a list of areas to a list of geographic ranges (states); original R version
cladoRcpp | Phylogenetic probability calculations using Rcpp
cladorcpp | Phylogenetic probability calculations using Rcpp
numstates_from_numareas | Calculate the number of states, given a certain number of areas
rcpp_areas_list_to_states_list | Make a list of 0-based indices of possible combinations of input areas
rcpp_calc_anclikes_sp | Calculate probability of ancestral states below a speciation event, given probabilities of the states on each descendant branch
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 event, given probabilities of the states on each descendant branch
rcpp_calc_anclikes_sp_rowsums | Calculate the number of cladogenesis events of nonzero probability for each ancestral state
rcpp_calc_anclikes_sp_using_COOprobs | Calculate ancestral likelihoods given a COO-like probability matrix
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 0-based index form
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 vector (cross-product)
rcpp_states_list_to_DEmat | C++ conversion of a states list to a dispersal-extinction matrix (DEmat)
strsplit3 | String splitting shortcut