Estimate Growth Rates from Phylogenetic Trees R package cloneRate version 0.2.3 Quickly estimate the net growth rate of a population or clone whose growth can be approximated by a birth-death branching process. Input should be phylogenetic tree(s) of clone(s) with edge lengths corresponding to either time or mutations. Based on coalescent results in Johnson et al. (2023) <doi:10.1093/bioinformatics/btad561>. Simulation techniques as well as growth rate methods build on prior work from Lambert A. (2018) <doi:10.1016/j.tpb.2018.04.005> and Stadler T. (2009) <doi:10.1016/j.jtbi.2009.07.018>. Software Depends: R (>= 3.6.0) Imports: ape (>= 4.0), methods, Rcpp (>= 0.12.0), Rmpfr (>= 0.8), rstan (>= 2.18.1), rstantools (>= 2.3.1) LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: car, covr, ggplot2, ggsurvfit, knitr, parallel, rmarkdown, survival, testthat (>= 3.0.0) Brian Johnson <brian.d.johnson97@gmail.com> Comprehensive R Archive Network (CRAN) Brian Johnson [cre, aut, cph] (ORCID: <https://orcid.org/0000-0002-9477-4677>), Yubo Shuai [aut, cph], Jason Schweinsberg [aut, cph] (ORCID: <https://orcid.org/0000-0002-4152-0059>), Kit Curtius [aut, cph] (ORCID: <https://orcid.org/0000-0002-2678-0960>) MIT + file LICENSE (https://CRAN.R-project.org/package=cloneRate/LICENSE) 2023-09-22 application/tgz https://CRAN.R-project.org/package=cloneRate doi:10.32614/CRAN.package.cloneRate