cloneRate

0.2.3

Estimate Growth Rates from Phylogenetic Trees

0packages depend

2.7Kdownloads / year

78.3%test coverage

12/13checks pass

Overview

About

Maintained by Brian JohnsonFirst published 2023-09-221 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("cloneRate", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("bdj34/cloneRate")

Development version from bdj34/cloneRate. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-clonerate

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-cloneRate

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-cloneRate

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 14.3 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.14

78.3%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-29
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-27
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 4 earlier snapshots

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 620 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 92%
Documented parameters: 100%
Return-value docs: 100%
References docs: 33%

Downloads

2.7K

CRAN downloads in the past year

Rank #12,019 · ~7/day · ~221/mo

Releases R versions

Daily download trend is not available in this view yet.

33730 days

83290 days

2.7K1 year

Compare downloads with other packages →

Also on431 r2u3 autocran

Repository

GitHub ↗ bdj34/clonerate

5Stars

1Forks

0Open issues

0Open PRs

1Releases

299Commits

2Contributors

299 commits · Last activity 2024-04-10 · 0% stars, 30d

Stars over time

2023-11-12 · 42026-07-07 · 5

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/bdj34/clonerate on 2026-08-02.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (6)

apemethodsRcpp Rmpfr rstan rstantools

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.18.0)

Suggests (9)

car covr ggplot2 ggsurvfit knitrparallelrmarkdownsurvivaltestthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Brian Johnson

Maintainer, Author, Copyright holder

Authors (4)

Brian Johnson

Maintainer, Author, Copyright holder

Kit Curtius

Author, Copyright holder

Jason Schweinsberg

Author, Copyright holder

Yubo Shuai

Author, Copyright holder

Brian Johnson

Maintainer, Author, Copyright holder

Kit Curtius

Author, Copyright holder

Jason Schweinsberg

Author, Copyright holder

Yubo Shuai

Author, Copyright holder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.2.3Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2023-09-22
Total releases: 1 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6.0
Bundled data: 336 KB / 4 files
Download size: 1.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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