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cladoRcpp
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Download and install cladoRcpp package within the R console
Install from CRAN:
install.packages("cladoRcpp")
Install from Github:
library("remotes")
install_github("cran/cladoRcpp")
Install by package version:
library("remotes")
install_version("cladoRcpp", "0.15.1")
Attach the package and use:
library("cladoRcpp")
Maintained by
Nicholas J. Matzke
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2013-04-04
Latest Update: 2018-11-21
Description:
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.
How to cite:
Nicholas J. Matzke (2013). cladoRcpp: C++ Implementations of Phylogenetic Cladogenesis Calculations. R package version 0.15.1, https://cran.r-project.org/web/packages/cladoRcpp
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Functions, R codes and Examples using
the cladoRcpp R package
Some associated functions: 00-cladoRcpp-package . Rcpp_combn_zerostart . areas_list_to_states_list_old . numstates_from_numareas . rcpp_areas_list_to_states_list . rcpp_calc_anclikes_sp . rcpp_calc_anclikes_sp_COOprobs . rcpp_calc_anclikes_sp_COOweights_faster . rcpp_calc_anclikes_sp_prebyte . rcpp_calc_anclikes_sp_rowsums . rcpp_calc_anclikes_sp_using_COOprobs . rcpp_calc_rowsums_for_COOweights_columnar . rcpp_calc_splitlikes_using_COOweights_columnar . rcpp_convolve . rcpp_mult2probvect . rcpp_states_list_to_DEmat . strsplit3 .
Some associated R codes: cladoRcpp-package.R . cladoRcpp.R . Full cladoRcpp package functions and examples
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