cladoRcpp: C++ implementations of phylogenetic cladogenesis calculations

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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

View on CRAN

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