R Observatory: Metrics for polysat version 1.7-7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

polysat

1.7-7Package record

Tools for Polyploid Microsatellite Analysis

1packages depend

55.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Lindsay V. ClarkCRAN page ↗GitHub ↗

A collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes. It can import and export data in ABI 'GeneMapper', 'Structure', 'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi', 'POPDIST', 'STRand', and binary presence/absence formats. It can calculate pairwise distances between individuals using a stepwise mutation model or infinite alleles model, with or without taking ploidies and allele frequencies into account. These distances can be used for the calculation of clonal diversity statistics or used for further analysis in R. Allelic diversity statistics and Polymorphic Information Content are also available. polysat can assist the user in estimating the ploidy of samples, and it can estimate allele frequencies in populations, calculate pairwise or global differentiation statistics based on those frequencies, and export allele frequencies to 'SPAGeDi' and 'adegenet'. Functions are also included for assigning alleles to isoloci in cases where one pair of microsatellite primers amplifies alleles from two or more independently segregating isoloci. polysat is described by Clark and Jasieniuk (2011) doi:10.1111/j.1755-0998.2011.02985.x and Clark and Schreier (2017) doi:10.1111/1755-0998.12639.

Changes in 1.7-7

Maintainer email address updated.
NEWS file reformatted according to CRAN specifications.

From NEWS in the release

Install

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

install.packages("polysat", 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("lvclark/polysat")

Development version from lvclark/polysat. 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-polysat

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-polysat

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-polysat

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: 4.4 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.7-7

README· In the repository, left out of the releaseVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.7-7Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 58
Examples that run: 98%53 run in a plain check (2 of them under a condition) · 1 never run
Exported functions with examples: 100%
Documented parameters: 91%
Return-value docs: 100%
Help pages citing references: 57%

Vignettes (2)

How these are measured

Downloads

55.4K

CRAN downloads in the past year

Rank #1,785 · ~152/day · ~4.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

3K30 days

11.6K90 days

55.4K1 year

Compare downloads with other packages →

Also on654 r2u6 autocran6.6K conda_forge360 bioconda100 c2d4u

How downloads are counted

Repository

lvclark/polysat ↗Account: lvclark

12Stars

5Forks

0Open issues

0Open PRs

11Releases

142Commits

2Commit identities

142 commits · Last activity 2024-12-20 · Default branch at 1.7-8, ahead of CRAN 1.7-7 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-03-06 · 122026-07-07 · 12

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/lvclark/polysat on 2026-10-21.

Governance and community (1)

Code of conduct

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing polysat adds 1 package (1 with compiled code, 1.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB.

Depends (0)

none

Imports (6)

methodsstatsutilsgrDevicesgraphicsRcpp

LinkingTo (1)

Rcpp

Suggests (3)

ade4 adegenet ape

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

1indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

poppr

How these are counted

Code & Tests

Datasets

People & History

People (4)

Lindsay V. Clark

Author, Maintainer since 0.1 (2010)

Alistair J. Hall

Contributor · added in 1.7-4

Tyler William Smith

Contributor · added in 1.7-4

Handunnethi Nihal de Silva

Contributor · added in 1.7-3

Releases (21)

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
1.7-7Latest
record
2022-08-23 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
1.7-6
record
2021-12-08 · diff ↗
1.7-5
record
2021-05-28 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.7-4
record
2019-03-06 · diff ↗
1.7-3
record
2018-06-07 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.7-2
record
2017-08-17 · diff ↗
1.7-1
record
2017-07-23 · diff ↗

Show 24 earlier eventsHide 24 earlier events

1.7-0
record
2017-05-03 · diff ↗ ·
added 1 export
PIC
R
R 3.4.0 released · 2017-04-21
1.6-0
record
2016-11-05 · diff ↗
1.5-0
record
2016-07-18 · diff ↗ ·
added 4 exports
plotSSAllo, processDatasetAllo, plotParamHeatmap, calcPopDiff
R
R 3.3.0 released · 2016-05-03
1.4-1
record
2015-08-18 · diff ↗
1.4-0
record
2015-06-13 · diff ↗ ·
added 6 exports
simAllopoly, catalanAlleles, alleleCorrelations, testAlGroups, mergeAlleleAssignments, recodeAllopoly
R
R 3.2.0 released · 2015-04-16
1.3-3
record
2014-09-22 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.3-2
record
2013-09-06 · diff ↗ ·
added 1 export
Simpson.var
R
R 3.0.0 released · 2013-04-03
1.3-1
record
2012-10-16 · diff ↗ ·
added 11 exports
genotypeProbs, meandistance.matrix2, assignClones, Shannon, Simpson, genotypeDiversity, Bruvo2.distance, reformatPloidies, alleleDiversity, read.STRand, gendata.to.genind
R
R 2.15.0 released · 2012-03-30
1.2-1
record
2012-01-15 · diff ↗ ·
removed 5 exports
distance.matrix.1locus, estimate.ploidy, codominant.to.dominant, dominant.to.codominant, estimate.freq

added 15 exports
genambig.to.genbinary, genbinary.to.genambig, simpleFreq, deSilvaFreq, write.freq.SPAGeDi, read.POPDIST, write.POPDIST, freq.to.genpop, genotypeProbs, meandistance.matrix2, assignClones, Shannon, Simpson, genotypeDiversity, Bruvo2.distance
R
R 2.14.0 released · 2011-10-31
1.2-0
record
2011-05-01 · diff ↗ ·
added 34 exports
Bruvo.distance, meandistance.matrix, read.GeneMapper, write.Structure, read.ATetra, read.Tetrasat, genambig.to.genbinary, genbinary.to.genambig, read.GenoDive, write.GenoDive, write.ATetra, write.Tetrasat, read.Structure, write.GeneMapper, calcFst, simpleFreq, deSilvaFreq, find.missing.gen, meandist.from.array, find.na.dist, find.na.dist.not.missing, Lynch.distance, write.SPAGeDi, read.SPAGeDi, write.freq.SPAGeDi, read.POPDIST, write.POPDIST, freq.to.genpop, genotypeProbs, meandistance.matrix2 and 4 more
R
R 2.13.0 released · 2011-04-13
1.1-0
record
2010-12-07 · diff ↗ ·
added 3 exports
read.POPDIST, write.POPDIST, freq.to.genpop
1.0-1
record
2010-10-19 · diff ↗
R
R 2.12.0 released · 2010-10-15
1.0
record
2010-10-01 · diff ↗ ·
removed 10 exports
read.POPDIST, write.POPDIST, freq.to.genpop, genotypeProbs, meandistance.matrix2, assignClones, Shannon, Simpson, genotypeDiversity, Bruvo2.distance
0.1
record
2010-06-24
R
R 2.11.0 released · 2010-04-22

Package metadata

First published: 2010-06-24
Total releases: 21 / 16 yrs
License: GPL-2 OSI
Bundled data: 11 KB / 4 files
Download size: 1.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("polysat")

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

It points to 10.1111/j.1755-0998.2011.02985.x, 10.1111/1755-0998.12639.

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 polysat version 1.7-7 [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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