PoolTestR

0.2.0

Prevalence and Regression for Pool-Tested (Group-Tested) Data

0packages depend

3.2Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Angus McLureFirst published 2021-02-085 releasesCRAN page ↗GitHub ↗

An easy-to-use tool for working with presence/absence tests on 'pooled' or 'grouped' samples. The primary application is for estimating prevalence of a marker in a population based on the results of tests on pooled specimens. This sampling method is often employed in surveillance of rare conditions in humans or animals (e.g. molecular xenomonitoring). The package was initially conceived as an R-based alternative to the molecular xenomonitoring software, 'PoolScreen' https://sites.uab.edu/statgenetics/software/. However, it goes further, allowing for estimates of prevalence to be adjusted for hierarchical sampling frames, and perform flexible mixed-effect regression analyses (McLure et al. Environmental Modelling and Software. DOI:10.1016/j.envsoft.2021.105158). The package is currently in early stages, however more features are planned or in the works: e.g. adjustments for imperfect test specificity/sensitivity, functions for helping with optimal experimental design, and functions for spatial modelling.

Install

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

install.packages("PoolTestR", 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("AngusMcLure/PoolTestR")

Development version from AngusMcLure/PoolTestR. 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-pooltestr

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

# 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-PoolTestR

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

Health

CRAN checks

1ERROR12NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
ERROR r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 12.1 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

ERROR2026-07-16
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-07-08
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-07
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 3 earlier snapshots

NOTE2026-04-22
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
0 OK · 13 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 615 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 91%
Return-value docs: 100%
References docs: 20%

Downloads

3.2K

CRAN downloads in the past year

Rank #11,929 · ~9/day · ~269/mo

Releases R versions

Daily download trend is not available in this view yet.

33630 days

87390 days

3.2K1 year

Compare downloads with other packages →

Also on421 r2u25 autocran

Repository

GitHub ↗ angusmclure/pooltestr

7Stars

3Forks

13Open issues

0Open PRs

4Releases

272Commits

4Contributors

272 commits · Last activity 2025-11-25 · 0% stars, 30d

Stars over time

2025-05-02 · 62026-07-07 · 7

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/angusmclure/pooltestr on 2026-07-19.

Continuous integration (2)

GitHub ActionsTravis CI

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (13)

brms dplyr lme4methodsprogress Rcpp (>= 0.12.0)RcppParallel rlang rstan rstantoolsstatsstringr tibble

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.26.0)

Suggests (1)

covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Angus McLure

Author, Maintainer

Authors (1)

Angus McLure

Author, Maintainer

Contributors (1)

Caitlin Cherryh

Contributor · added in 0.2.0

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.2.0Latest
2024-12-05 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.1.3
2022-07-01 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.1.2
2022-01-19 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.1
2021-02-15 · diff ↗
0.1.0
2021-02-08
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-02-08
Total releases: 5 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.4.0
Bundled data: 18 KB / 3 files
Download size: 80 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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