R Observatory: Metrics for phylosamp version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phylosamp

1.0.1Package record

Sample Size Calculations for Molecular and Phylogenetic Studies

0packages depend

2.9Kdownloads / year

58.9%test coverage

13/13flavors OK

Overview

About

Maintained by Justin LesslerCRAN page ↗GitHub ↗Issues ↗

Implements novel tools for estimating sample sizes needed for phylogenetic studies, including studies focused on estimating the probability of true pathogen transmission between two cases given phylogenetic linkage and studies focused on tracking pathogen variants at a population level. Methods described in Wohl, Giles, and Lessler (2021) and in Wohl, Lee, DiPrete, and Lessler (2023).

Changes in 1.0.1

Added a NEWS.md file to track changes to the package.
Added relR_* functions to the package to allow for sample size and power calculations when estimating differential transmission between groups

From NEWS.md in the release

Install

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

install.packages("phylosamp", 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("HopkinsIDD/phylosamp")

Development version from HopkinsIDD/phylosamp. 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-phylosamp

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-phylosamp

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-phylosamp

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
NOTE12 OK, 1 NOTE2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 1,005 wordsVignettesYes · 10 · dynamicNEWSYes · 67% structured · mentions 1.0.1Citation fileYes · cites a publication

Help pages: 63 (1 internal)includes a package overview page
Examples that run: 100%54 run in a plain check
Exported functions with examples: 93%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (10)

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #17,735 · ~8/day · ~239/mo

Releases R versions

Daily download trend is not available in this view yet.

27230 days

73090 days

2.9K1 year

Compare downloads with other packages →

Also on70 r2u7 autocran

How downloads are counted

Repository

hopkinsidd/phylosamp ↗Organization: HopkinsIDD

14Stars

3Forks

0Open issues

0Open PRs

6Releases

165Commits

4Commit identities

rpackagephylogeneticssampling

165 commits · Last activity 2023-05-23 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: 6

Stars over time

2025-05-19 · 132026-07-14 · 14

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/hopkinsidd/phylosamp on 2026-10-22.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2023-05-23

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing phylosamp adds 3 packages (2 with compiled code, 1.5 MB of source tarballs). Heaviest: rlang 766 KB, cli 629 KB, lifecycle 105 KB.

Depends (2)

R >= 2.10stats

Imports (3)

cli lifecycle rlang

LinkingTo (0)

none

Suggests (8)

cowplot ggplot2 knitr purrr RColorBrewer reshape2 rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Justin Lessler

Author, Maintainer since 0.1.6 (2021)

Lucy D'Agostino McGowan

Author, Contributor · added in 1.0.1

John R Giles

Author, Contributor

Elizabeth C Lee

Author, Contributor · added in 1.0.1

Shirlee Wohl

Author, Contributor

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.1Latest
record
2023-05-24 · current release · diff ↗ ·
added 39 exports
gendist_distribution, gendist_roc_format, gendist_sensspec_cutoff, optim_roc_threshold, relR_power, relR_power_simulated, relR_samplesize, relR_samplesize_basic, relR_samplesize_ci, translink_expected_links_obs, translink_expected_links_obs_mtml, translink_expected_links_obs_mtsl, translink_expected_links_obs_stsl, translink_expected_links_true, translink_expected_links_true_mtml, translink_expected_links_true_mtsl, translink_expected_links_true_stsl, translink_fdr, translink_prob_transmit, translink_prob_transmit_mtml, translink_prob_transmit_mtsl, translink_prob_transmit_stsl, translink_samplesize, translink_tdr, varfreq_cdf_logistic, varfreq_expected_mbias, varfreq_freq_logistic, varfreq_obs_freq, vartrack_cod_ratio, vartrack_prob_detect and 9 more
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.6
record
2021-11-22
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-11-22
Total releases: 2 / 5 yrs
License: GPL-2 OSI
Minimum R: ≥ 2.10
Bundled data: 11 KB / 1 file
Download size: 2.3 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("phylosamp")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1371/journal.pcbi.1009182, 10.1016/j.xcrm.2023.101022, 10.48550/arxiv.2305.12184.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for phylosamp version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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