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 [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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