cloneRate: Estimate Growth Rates from Phylogenetic Trees
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 results |
Documentation:
| Reference manual: | cloneRate.pdf |
| Vignettes: |
Analysis of human blood data Validating growth rate estimates via simulation |
Downloads:
| Package source: | cloneRate_0.2.3.tar.gz |
| Windows binaries: | r-devel: cloneRate_0.2.3.zip, r-release: cloneRate_0.2.3.zip, r-oldrel: cloneRate_0.2.3.zip |
| macOS binaries: | r-release (arm64): cloneRate_0.2.3.tgz, r-oldrel (arm64): cloneRate_0.2.3.tgz, r-release (x86_64): cloneRate_0.2.3.tgz, r-oldrel (x86_64): cloneRate_0.2.3.tgz |
Linking:
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