This is a customized version of the fast C++ backend for the PCMBase R-package. This version adds a C++ implementation for the Early Burst (EB) phylogenetic comparative model.
The package needs a C++ 11 or later compiler and Rcpp to be installed in your R-environment. Once this is done, you can install the most recent version of the package from github:
devtools::install_github("MehediHasanSM/PCMBaseCppCustom", force = TRUE)To give credit to the PCMBase package in a publication, please cite the following articles:
Mitov, V., & Stadler, T. (2018). Parallel likelihood calculation for phylogenetic comparative models: The SPLITT C++ library. Methods in Ecology and Evolution, 2041–210X.13136. http://doi.org/10.1111/2041-210X.13136
Mitov, V., Bartoszek, K., Asimomitis, G., & Stadler, T. (2019). Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts. Theor. Popul. Biol. https://doi.org/10.1016/j.tpb.2019.11.005
The PCMBaseCppCustom R-package uses the following R-packages and C++ libraries:
- For tree processing in C++: The SPLITT library (Mitov and Stadler 2018);
- For data processing in R: data.table v1.17.8 (Dowle and Srinivasan 2019);
- For algebraic manipulation: The Armadillo C++ template library (Sanderson and Curtin 2016) and its port to R RcppArmadillo v14.6.0.1 (Eddelbuettel et al. 2019);
- For unit-testing: testthat v3.2.3 (Wickham 2019), covr v3.6.4 (Hester 2018);
- For documentation and web-site generation: roxygen2 v7.3.2 (Wickham, Danenberg, and Eugster 2018), pkgdown v2.1.3 (Wickham and Hesselberth 2018);
Dowle, Matt, and Arun Srinivasan. 2019. Data.table: Extension of ‘Data.frame‘. https://CRAN.R-project.org/package=data.table.
Eddelbuettel, Dirk, Romain Francois, Doug Bates, and Binxiang Ni. 2019. RcppArmadillo: ’Rcpp’ Integration for the ’Armadillo’ Templated Linear Algebra Library. https://CRAN.R-project.org/package=RcppArmadillo.
Hester, Jim. 2018. Covr: Test Coverage for Packages. https://CRAN.R-project.org/package=covr.
Mitov, Venelin, and Tanja Stadler. 2018. “Parallel likelihood calculation for phylogenetic comparative models: The SPLITT C++ library.” Methods in Ecology and Evolution, December, 2041–210X.13136.
Sanderson, Conrad, and Ryan Curtin. 2016. “Armadillo: a template-based C++ library for linear algebra.” Journal of Open Source Software 1 (2).
Wickham, Hadley. 2019. Testthat: Unit Testing for r. https://CRAN.R-project.org/package=testthat.
Wickham, Hadley, Peter Danenberg, and Manuel Eugster. 2018. Roxygen2: In-Line Documentation for r. https://CRAN.R-project.org/package=roxygen2.
Wickham, Hadley, and Jay Hesselberth. 2018. Pkgdown: Make Static HTML Documentation for a Package. https://CRAN.R-project.org/package=pkgdown.