cloneRate

Estimate Growth Rates from Phylogenetic Trees

v0.2.3 · Sep 22, 2023 · MIT + file LICENSE

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>.

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CRAN Check Status

13 OK

Show all 13 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	568.7s
r-devel-linux-x86_64-debian-gcc	OK	401.4s
r-devel-linux-x86_64-fedora-clang	OK	868.8s
r-devel-linux-x86_64-fedora-gcc	OK	1033.2s
r-devel-windows-x86_64	OK	568s
r-oldrel-macos-arm64	OK
r-oldrel-macos-x86_64	OK	491s
r-oldrel-windows-x86_64	OK	781s
r-patched-linux-x86_64	OK	563.1s
r-release-linux-x86_64	OK
r-release-macos-arm64	OK	118s
r-release-macos-x86_64	OK	559s
r-release-windows-x86_64	OK	579s

Check History

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026

ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026

ERROR r-devel-linux-x86_64-debian-gcc

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘cloneRate-dataAnalysis.Rmd’ using rmarkdown

Quitting from cloneRate-dataAnalysis.Rmd:41-53 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlan
...[truncated]...
ysis.Rmd’

--- re-building ‘cloneRate-simulate.Rmd’ using rmarkdown
--- finished re-building ‘cloneRate-simulate.Rmd’

SUMMARY: processing the following file failed:
  ‘cloneRate-dataAnalysis.Rmd’

Error: Vignette re-building failed.
Execution halted

OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026

NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026

NOTE r-oldrel-macos-arm64

installed package size

installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is 39.3Mb
  sub-directories of 1Mb or more:
    libs  37.2Mb

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

ERROR 10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026

ERROR r-devel-windows-x86_64

whether package can be installed

Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.6/cloneRate.Rcheck/00install.out' for details.

NOTE r-oldrel-macos-arm64

installed package size

installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is 39.3Mb
  sub-directories of 1Mb or more:
    libs  37.2Mb

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-oldrel-macos-arm64

installed package size

installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is 39.3Mb
  sub-directories of 1Mb or more:
    libs  37.2Mb

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

Dependency Network

Version History

1 tracked

new 0.2.3 Mar 10, 2026

R Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Sep 22, 2023. Releases before tracking aren’t shown.