R Observatory: Metrics for mappoly version 0.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mappoly

0.4.2

Genetic Linkage Maps in Autopolyploids

2packages depend

7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Marcelo MollinariFirst published 2020-10-1010 releasesCRAN page ↗GitHub ↗

Constructs genetic linkage maps in autopolyploid full-sib populations. Uses pairwise recombination fraction estimation as the first source of information to sequentially position allelic variants in specific homologous chromosomes. For situations where pairwise analysis has limited power, the algorithm relies on the multilocus likelihood obtained through a hidden Markov model (HMM). Methods are described in Mollinari and Garcia (2019) doi:10.1534/g3.119.400378 and Mollinari et al. (2020) doi:10.1534/g3.119.400620.

Install

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

install.packages("mappoly", 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("mmollina/MAPpoly")

Development version from mmollina/MAPpoly. 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-mappoly

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-mappoly

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 9.7 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

19

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
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 793 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 63%
Documented parameters: 98%
Return-value docs: 73%
References docs: 28%

Downloads

7K

CRAN downloads in the past year

Rank #5,258 · ~19/day · ~585/mo

Releases R versions

Daily download trend is not available in this view yet.

32830 days

1.5K90 days

7K1 year

Compare downloads with other packages →

Also on471 r2u44 c2d4u

Repository

GitHub ↗ mmollina/mappoly

33Stars

10Forks

13Open issues

0Open PRs

8Releases

980Commits

8Contributors

polyploidpolyploidypolyploid-genetic-mapping

980 commits · Last activity 2026-01-12 · 0% stars, 30d

Stars over time

2025-04-14 · 292026-07-07 · 33

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/mmollina/mappoly on 2026-08-16.

Continuous integration (2)

GitHub ActionsAppVeyor

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (19)

Rcpp RcppParallel RCurl fields ggpubr ggsci rstudioapi dplyr crayon cli magrittr reshape2 ggplot2 smacof princurve dendextend vcfR zoo plotly

LinkingTo (2)

Rcpp RcppParallel

Suggests (9)

updog plot3D fitPoly polymapR AGHmatrix gatepoints knitr rmarkdown stringr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

polymapR polyqtlR

Code & Tests

People & History

People (13)

Maintainer (1)

Marcelo Mollinari

Author, Maintainer

Authors (4)

Marcelo Mollinari

Author, Maintainer

Gabriel Gesteira

Author

Jeekin Lau

Author · added in 0.4.0

Cristiane Taniguti

Author · added in 0.4.0

Contributors (5)

Augusto Garcia

Contributor

Guilherme Pereira

Contributor · added in 0.4.2

Katharine Preedy

Contributor, Copyright holder

Oscar Riera-Lizarazu

Contributor · added in 0.4.0

Zhao-Bang Zeng

Contributor

Copyright holders (5)

Katharine Preedy

Contributor, Copyright holder

R Core Team

Copyright holder · added in 0.4.2

R Foundation for Statistical Computing

Copyright holder · added in 0.4.2

Robert Gentleman

Copyright holder

Ross Ihaka

Copyright holder

Listed in earlier versions (3)

R Foundation

no longer listed · 0.2.0 to 0.4.1

R-core

no longer listed · 0.2.0 to 0.4.1

Guilhereme Pereira

no longer listed · 0.2.0 to 0.4.1

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.4.2Latest
2026-01-12 · current release · diff ↗
unarchivedReturned to CRAN
2026-01-12
archivedRemoved from CRAN
2025-12-08
email to the maintainer is undeliverable
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.4.1
2024-03-06 · diff ↗
unarchivedReturned to CRAN
2024-03-06
archivedRemoved from CRAN
2024-03-05
issues were not corrected in time
0.4.0
2024-02-18 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.3.3
2023-01-05 · diff ↗
0.3.2
2022-12-02 · diff ↗
0.3.1
2022-07-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.0
2022-01-11 · diff ↗

Show 7 earlier events

R
R 4.1.0 released · 2021-05-18
0.2.3
2021-04-20 · diff ↗
0.2.1
2020-11-23 · diff ↗
unarchivedReturned to CRAN
2020-11-23
archivedRemoved from CRAN
2020-11-16
check problems were not corrected in time
0.2.0
2020-10-10
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-10-10
Total releases: 10 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 1.9 MB / 2 files
Download size: 3.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mappoly")

Format

Mollinari, M., R Core Team, R Foundation for Statistical Computing, Garcia, A., Gentleman, R., Gesteira, G., Ihaka, R., Lau, J., Pereira, G., Preedy, K., Riera-Lizarazu, O., Taniguti, C., & Zeng, Z. (2026). mappoly: Genetic Linkage Maps in Autopolyploids (Version 0.4.2) [Computer software]. https://doi.org/10.32614/CRAN.package.mappoly

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 mappoly version 0.4.2 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →