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
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

Linking:

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