R Observatory: Metrics for StAMPP version 1.6.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

StAMPP

1.6.3Package record

Statistical Analysis of Mixed Ploidy Populations

3packages depend

17.6Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by LW PembletonCRAN page ↗GitHub ↗

Allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. doi:10.1111/1755-0998.12129 for the appropriate citation and user manual. Thank you in advance.

Changes in 1.6.3

Other changes

updated maintainer email

From NEWS.md in the release

Install

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

install.packages("StAMPP", 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("lpembleton/StAMPP")

Development version from lpembleton/StAMPP. 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-stampp

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-StAMPP

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-StAMPP

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) stamppFst.Rd:20: Lost braces
    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
checkRd: (-1) stamppFst.Rd:21: Lost braces
    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
checkRd: (-1) stamppFst.Rd:22: Lost braces
    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘LW Pembleton <lwpembleton@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "LW",
                    family = "Pembleton",
                    role = c("aut", "cre"),
                    email = "lwpembleton@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 2.9 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTE2026-09-08
ERROR12 NOTE, 1 ERROR2026-09-07
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6.3

READMEYes · 195 wordsVignettesNoNEWSYes · 100% structured · mentions 1.6.3Citation fileYes · cites a publication

Help pages: 9
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 86%
Help pages citing references: 56%

How these are measured

Downloads

17.6K

CRAN downloads in the past year

Rank #3,196 · ~48/day · ~1.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

3.8K90 days

17.6K1 year

Compare downloads with other packages →

Also on349 r2u2 autocran1.4K conda_forge452 bioconda131 c2d4u

How downloads are counted

Repository

lpembleton/stampp ↗Account: lpembleton

6Stars

1Forks

0Open issues

0Open PRs

2Releases

12Commits

2Commit identities

12 commits · Last activity 2022-11-30 · 0% stars, 30d · Default branch at 1.6.3.9000, ahead of CRAN 1.6.3 (checked 2026-10-25)

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 180
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-06-26 · 42026-07-07 · 6

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/lpembleton/stampp on 2026-10-25.

Continuous integration (1)

GitHub Actions

Docs source (3)

pkgdown

GitHub Pages site last deployed 2022-11-30 · The repository has a site deploy workflow

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing StAMPP adds 67 packages (39 with compiled code, 73 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (2)

R >= 3.2.0pegas

Imports (6)

paralleldoParallel foreach adegenetmethodsutils

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

4indirect

Imports 3

Depends, Imports or LinkingTo, most downloaded first

dartR dartR.base dartR.spatial

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (1)

LW Pembleton

Maintainer since 1.0 (2013)

Releases (9)

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.6.3Latest
record
2021-08-08 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
1.6.2
record
2021-04-26 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.6.1
record
2020-03-20 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.5.1
record
2017-11-10 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.4
record
2015-07-06 · diff ↗

Show 7 earlier eventsHide 7 earlier events

R
R 3.2.0 released · 2015-04-16
1.3
record
2014-09-01 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.2
record
2014-03-11 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 7 exports
stamppConvert, stamppNeisD, stamppFst, stamppGmatrix, stamppPhylip, stamppAmova, stampp2genlight
1.1
record
2013-06-06 · diff ↗
1.0
record
2013-05-29
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-05-29
Total releases: 9 / 13 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.2.0
Bundled data: 2.4 KB / 2 files
Download size: 77 KB

Appears in task views

Missing Data

Cite

Cite this package

Run in R for the authors' entry:

citation("StAMPP")

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

It points to 10.1111/1755-0998.12129.

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 StAMPP version 1.6.3 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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