R Observatory: Metrics for NeStage version 0.8.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

NeStage

0.8.0

Effective Population Size from Stage-Structured Populations

0packages depend

2.1Kdownloads / year

0.0%test coverage

13/13checks pass

Overview

About

Maintained by Raymond L. TremblayFirst published 2026-03-181 releasesCRAN page ↗GitHub ↗

Computes effective population size (Ne) and the Ne/N ratio for stage-structured populations using the matrix population model framework of Yonezawa (2000) doi:10.1111/j.0014-3820.2000.tb01244.x. Functions are provided for sexually reproducing, clonally reproducing, and mixed (sexual + clonal) populations. Includes sensitivity and elasticity analyses for Ne/N with respect to vital rates.

Install

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

install.packages("NeStage", 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("RaymondLTremblay/NeStage")

Development version from RaymondLTremblay/NeStage. 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-nestage

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-NeStage

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-NeStage

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

Health

CRAN checks

13OK

Slowest check: 1.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.02

0.0%

Coverage · measured lines

100%

Documentation · exports

1

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
OK2026-03-18
5 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 830 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 97%
Return-value docs: 100%
References docs: 33%

Downloads

2.1K

CRAN downloads in the past year

Rank #10,786 · ~6/day · ~177/mo

Releases R versions

Daily download trend is not available in this view yet.

17730 days

91590 days

2.1K1 year

Compare downloads with other packages →

Also on37 r2u26 autocran

Repository

GitHub ↗ raymondltremblay/nestage

0Stars

0Forks

0Open issues

0Open PRs

2Releases

33Commits

1Contributors

conservation-biologyeffective-population-sizeevolutiongenetic-driftpopulation-ecologypopulation-geneticsrr-package

License GPL-3.0 · 33 commits · Last activity 2026-03-23

Releases over time

2026-03-06 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/raymondltremblay/nestage on 2026-08-23.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Research and citation (1)

JOSS paper

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (1)

ggplot2

LinkingTo (0)

none

Suggests (10)

dplyr tidyr purrr expm gt knitr popbio popdemo rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Raymond L. Tremblay

Author, Maintainer

Authors (1)

Raymond L. Tremblay

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.8.0Latest
2026-03-18 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-03-18
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Download size: 648 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("NeStage")

The authors publish a JOSS paper, so they have said how they want this cited. Run citation() and use what it gives you.

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 NeStage version 0.8.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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