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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 ORCID iD [cre, aut, cph], Yubo Shuai [aut, cph], Jason Schweinsberg ORCID iD [aut, cph], Kit Curtius ORCID iD [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:

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.