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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 |
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 |
Reference manual: | cloneRate.pdf |
Vignettes: |
Analysis of human blood data Validating growth rate estimates via simulation |
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 |
Please use the canonical form https://CRAN.R-project.org/package=cloneRate to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.