Type: Package
Package: cloneRate
Title: Estimate Growth Rates from Phylogenetic Trees
Version: 0.2.3
Authors@R: c(
    person("Brian", "Johnson", email = "brian.d.johnson97@gmail.com", 
           role = c("cre", "aut", "cph"),
           comment = c(ORCID = "0000-0002-9477-4677")),
    person("Yubo", "Shuai", role = c("aut", "cph")),
    person("Jason", "Schweinsberg", role = c("aut", "cph"),
           comment = c(ORCID = "0000-0002-4152-0059")),
    person("Kit", "Curtius", role = c("aut", "cph"),
           comment = c(ORCID = "0000-0002-2678-0960"))
  )
Description: 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>.
License: MIT + file LICENSE
NeedsCompilation: yes
URL: https://github.com/bdj34/cloneRate,
        https://bdj34.github.io/cloneRate/
BugReports: https://github.com/bdj34/cloneRate/issues
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)
Suggests: car, covr, ggplot2, ggsurvfit, knitr, parallel, rmarkdown,
        survival, testthat (>= 3.0.0)
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)
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Biarch: true
SystemRequirements: GNU make
Packaged: 2023-09-21 17:39:04 UTC; apple
Author: Brian Johnson [cre, aut, cph] (<https://orcid.org/0000-0002-9477-4677>),
  Yubo Shuai [aut, cph],
  Jason Schweinsberg [aut, cph] (<https://orcid.org/0000-0002-4152-0059>),
  Kit Curtius [aut, cph] (<https://orcid.org/0000-0002-2678-0960>)
Maintainer: Brian Johnson <brian.d.johnson97@gmail.com>
Repository: CRAN
Date/Publication: 2023-09-22 15:40:02 UTC
Built: R 4.5.3; x86_64-w64-mingw32; 2026-06-22 05:59:46 UTC; windows
Archs: x64
