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>.
Version: 0.2.3 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) Published: 2023-09-22 DOI: 10.32614/CRAN.package.cloneRate Author: Brian Johnson [cre, aut, cph], Yubo Shuai [aut, cph], Jason Schweinsberg [aut, cph], Kit Curtius [aut, cph] Maintainer: Brian Johnson <brian.d.johnson97 at gmail.com> BugReports: https://github.com/bdj34/cloneRate/issues License: MIT + file LICENSE URL: https://github.com/bdj34/cloneRate, https://bdj34.github.io/cloneRate/ NeedsCompilation: yes SystemRequirements: GNU make Citation: cloneRate citation info Materials: README NEWS CRAN checks: cloneRate resultsRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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