R Observatory: Metrics for raretrans version 1.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

raretrans

1.0.5

Bayesian Priors for Matrix Population Models

0packages depend

1.5Kdownloads / year

96.6%test coverage

13/13checks pass

Overview

About

Maintained by Raymond TremblayFirst published 2026-04-222 releasesCRAN page ↗GitHub ↗

Provides functions to correct biased transition and fertility estimates in population projection matrices caused by small sample sizes. Small or short-term studies frequently produce structural zeros (biologically possible transitions never observed) and structural ones (transitions estimated at 100% survival, stasis, or mortality that are biologically implausible). Both distort matrix structure and bias estimates of population growth. Implements a multinomial-Dirichlet Bayesian prior for transition probabilities and a Gamma-Poisson prior for reproduction, allowing analysts to incorporate prior biological knowledge and regularise estimates from rare or unobserved events. Includes functions to compute marginal posterior credible intervals for all transition probabilities (transition_CrI()), visualise those intervals as point-range plots (plot_transition_CrI()), and display the full posterior beta density for each matrix entry (plot_transition_density()). Methods are described in Tremblay et al. (2021) doi:10.1016/j.ecolmodel.2021.109526.

Install

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

install.packages("raretrans", 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("atiretoo/raretrans")

Development version from atiretoo/raretrans. 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-raretrans

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-raretrans

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-raretrans

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

Health

CRAN checks

13OK

Slowest check: 7.3 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.80

96.6%

Coverage · measured lines

100%

Documentation · exports

3

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 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
OK2026-05-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-05-17
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
8 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 482 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 9%

Downloads

1.5K

CRAN downloads in the past year

Rank #10,615 · ~4/day · ~124/mo

Releases R versions

Daily download trend is not available in this view yet.

17830 days

90890 days

1.5K1 year

Compare downloads with other packages →

Also on39 r2u22 autocran

Repository

GitHub ↗ atiretoo/raretrans

0Stars

0Forks

4Open issues

0Open PRs

2Releases

266Commits

6Contributors

266 commits · Last activity 2026-05-15

Releases over time

2019-06-21 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/atiretoo/raretrans on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (3)

ggplot2 rlangstats

LinkingTo (0)

none

Suggests (15)

bslib dplyr formatR gridExtra huxtable knitr popdemo popbio purrr rmarkdown RColorBrewer shiny testthat tibble tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Raymond Tremblay

Author, Maintainer, Copyright holder

Authors (3)

Raymond Tremblay

Author, Maintainer, Copyright holder

Maria-Eglee Perez

Author

Andrew Tyre

Author, Copyright holder

Contributors (1)

Sasha Tenhumberg

Contributor

Copyright holders (2)

Raymond Tremblay

Author, Maintainer, Copyright holder

Andrew Tyre

Author, Copyright holder

Package Timeline

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

1.0.5Latest
2026-05-16 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.4
2026-04-22
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-22
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 12 KB / 1 file
Download size: 703 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("raretrans")

Format

Tremblay, R., Perez, M., Tenhumberg, S., & Tyre, A. (2026). raretrans: Bayesian Priors for Matrix Population Models (Version 1.0.5) [Computer software]. https://doi.org/10.32614/CRAN.package.raretrans

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 raretrans version 1.0.5 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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