Type: Package
Package: cloneRate
Title: Estimate Growth Rates from Phylogenetic Trees
Version: 0.2.3.9000
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, phangorn,
        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
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Biarch: true
SystemRequirements: GNU make
Config/pak/sysreqs: cmake libgmp3-dev make libmpfr-dev
Repository: https://bdj34.r-universe.dev
Date/Publication: 2024-04-10 16:58:50 UTC
RemoteUrl: https://github.com/bdj34/clonerate
RemoteRef: HEAD
RemoteSha: f56cde173d9c0aefe57284884adf6eb64ea9525a
Packaged: 2026-09-22 08:52:59 UTC; root
Author: Brian Johnson [cre, aut, cph] (ORCID:
    <https://orcid.org/0000-0002-9477-4677>),
  Yubo Shuai [aut, cph],
  Jason Schweinsberg [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-4152-0059>),
  Kit Curtius [aut, cph] (ORCID: <https://orcid.org/0000-0002-2678-0960>)
Maintainer: Brian Johnson <brian.d.johnson97@gmail.com>