R Observatory: Metrics for NeStage version 0.8.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

NeStage

0.8.1Package record

Effective Population Size from Stage-Structured Populations

0packages depend

2.8Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Raymond L. TremblayCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 0.8.1

Bug fix: internally computed generation time L

When L = NULL, Ne_clonal_Y2000(), Ne_sexual_Y2000(), Ne_mixed_Y2000() and Ne_sensitivity_L() (reference line) computed L incorrectly. The term sum(F * T^x) already equals l_x * m_x, but it was multiplied by l_x a second time, and the cohort was started from the stable stage distribution instead of from newborns. The returned L was about one third of the correct value (4.728 instead of 13.399 for *Fritillaria camtschatcensis* Miz), so Ne/N was overestimated and minimum census size underestimated.
L is now the mean age of reproduction of a newborn cohort entering recruit_row, and reproduces Table 4 of Yonezawa et al. (2000) exactly (13.399 Miz, 8.353 Nan). Results obtained by supplying L directly are unchanged.

Show all changes in 0.8.1Hide the rest of the changes in 0.8.1

Ne_sensitivity_L() now calls the same internal function rather than a separate copy of the calculation.
New tests in tests/testthat/test-generation-time.R; the Yonezawa vignette replication check now compares the computed L with Table 4.

From NEWS.md in the release

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. 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-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). 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: 1.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK5 OK2026-03-18

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.8.1

READMEYes · 830 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 0.8.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9
Examples that run: 100%8 run in a plain check
Exported functions with examples: 89%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 33%

Vignettes (4)

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #13,108 · ~8/day · ~236/mo

Releases R versions

Daily download trend is not available in this view yet.

35630 days

87790 days

2.8K1 year

Compare downloads with other packages →

Also on42 r2u5 autocran

How downloads are counted

Repository

raymondltremblay/nestage ↗Account: RaymondLTremblay

0Stars

0Forks

0Open issues

0Open PRs

3Releases

36Commits

1Commit identities

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

License file reads as GPL-3.0 · 36 commits · Last activity 2026-10-07 · Default branch at 0.8.1.9000, ahead of CRAN 0.8.1 (checked 2026-10-22)

Responsiveness

not measured

Releases over time

2026-03-06 · 12026-10-08 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/raymondltremblay/nestage on 2026-10-22.

CRAN release process (1)

cran-comments.md

Research and citation (1)

JOSS paper

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing NeStage adds 17 packages (7 with compiled code, 14 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

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.

How these are counted

Code & Tests

People & History

People (1)

Raymond L. Tremblay

Author, Maintainer since 0.8.0 (2026)

Releases (2)

Pick two releases to compare their code metrics.

0.8.1Latest
record
2026-10-07 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.8.0
record
2026-03-17
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-03-17
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Download size: 362 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("NeStage")

Format

Tremblay, R. L. (2026). NeStage: Effective Population Size from Stage-Structured Populations (Version 0.8.1) [Computer software]. https://doi.org/10.32614/CRAN.package.NeStage

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 0.8.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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