C++ Implementations of Phylogenetic Cladogenesis Calculations

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Documentation for package ‘cladoRcpp’ version 0.15.1

• DESCRIPTION file.
• Package NEWS.

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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