R Observatory: Metrics for mappoly version 0.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mappoly

0.4.2Package record

Genetic Linkage Maps in Autopolyploids

0packages dependsuggested by 2

7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Marcelo MollinariCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 0.4.2

Package resubmitted to CRAN after archival due to maintainer contact update.

From NEWS.md in the release

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. 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-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

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 4 earlier changesHide 4 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.2

READMEYes · 793 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · mentions 0.4.2Citation fileYes · cites a publication

Help pages: 155 (77 internal)
Examples that run: 63%36 run in a plain check · 19 only when donttest examples are enabled (R CMD check --as-cran) · 2 never run
Exported functions with examples: 70%
Documented parameters: 98%
Return-value docs: 73%
Help pages citing references: 28%

Vignettes (1)

mappoly_intro HTML

How these are measured

Downloads

7K

CRAN downloads in the past year

Rank #5,095 · ~19/day · ~581/mo

Releases R versions

Daily download trend is not available in this view yet.

64830 days

1.6K90 days

7K1 year

Compare downloads with other packages →

Also on438 r2u133 c2d4u

How downloads are counted

Repository

mmollina/mappoly ↗Account: mmollina

33Stars

10Forks

13Open issues

0Open PRs

8Releases

980Commits

8Commit identities

polyploidpolyploidypolyploid-genetic-mapping

980 commits · Last activity 2026-01-12 · 0% stars, 30d · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 90%
Median days to close, 50 most recently updated closed issues: 27
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-13 · 312026-07-07 · 33

How these are measured

PracticesBeta

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

Checks run against github.com/mmollina/mappoly on 2026-10-11.

Continuous integration (3)

GitHub ActionsR CMD check workflowAppVeyor

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (1)

GitHub Pages site last deployed 2026-01-12

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Installing mappoly adds 157 packages (87 with compiled code, 138 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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

0direct

0indirect

Suggested by 2

Suggests, most downloaded first

polymapR polyqtlR

How these are counted

Code & Tests

Datasets

People & History

People (13)

Marcelo Mollinari

Author, Maintainer since 0.2.0 (2020)

Gabriel Gesteira

Author

Jeekin Lau

Author · added in 0.4.0

Cristiane Taniguti

Author · added in 0.4.0

Augusto Garcia

Contributor

Guilherme Pereira

Contributor · added in 0.4.2

Katharine Preedy

Contributor, Copyright holder

MDS ordering algorithm

Oscar Riera-Lizarazu

Contributor · added in 0.4.0

Zhao-Bang Zeng

Contributor

R Core Team

Copyright holder · added in 0.4.2

Portions of C/C++ code adapted from R sources; see src/pairwise_estimation.cpp

R Foundation for Statistical Computing

Copyright holder · added in 0.4.2

Portions of C/C++ code adapted from R sources; see src/pairwise_estimation.cpp

Robert Gentleman

Copyright holder

C code for MLE optimization in src/pairwise_estimation.cpp

Ross Ihaka

Copyright holder

C code for MLE optimization in src/pairwise_estimation.cpp

Listed in earlier versions (3)

Show 3 peopleHide 3 people

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

Releases (10)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-01-12
0.4.2Latest
record
2026-01-12 · current release · diff ↗ ·
removed 1 export
print_mrk
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
unarchivedReturned to CRAN
2024-03-06
0.4.1
record
2024-03-06 · diff ↗
archivedRemoved from CRAN
2024-03-05
issues were not corrected in time
0.4.0
record
2024-02-18 · diff ↗ ·
removed 31 exports
.mappoly_data_skeleton, .vcf_get_depth, .vcf_get_ploidy, .vcf_get_probabilities, .vcf_transform_dosage, aggregate_matrix, calc_genoprob_one_parent, check_if_rf_is_possible, create_map, est_rf_hmm_single, est_rf_hmm_single_one_parent, filter_non_conforming_classes, get_cache_two_pts_from_web, get_ols_map, get_rf_from_mat, get_states_and_emission_one_parent, get_w_m, gg_color_hue, imf_h, imf_k, imf_m, mf_h, mf_m, paralell_pairwise_discrete_rcpp, perm_pars, perm_tot, poly_cross_simulate, split_mappoly, table_to_mappoly, update_missing and 1 more

added 9 exports
calc_genoprob_single_parent, cross_simulate, detect_info_par, edit_order, filter_aneuploid, framework_map, plot_mappoly.map2, plot_progeny_dosage_change, update_framework_map
R
R 4.3.0 released · 2023-04-21
0.3.3
record
2023-01-05 · diff ↗
0.3.2
record
2022-12-02 · diff ↗ ·
added 7 exports
.mappoly_data_skeleton, find_blocks, mp_pallet1, mp_pallet2, mp_pallet3, parallel_block, split_mappoly
0.3.1
record
2022-07-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.0
record
2022-01-11 · diff ↗ ·
removed 1 export
calc_homoprob

added 14 exports
calc_genoprob_one_parent, calc_homologprob, check_if_rf_is_possible, compare_maps, create_map, est_pairwise_rf2, est_rf_hmm_single_one_parent, export_qtlpoly, filter_individuals, get_states_and_emission_one_parent, is.prob.data, paralell_pairwise_discrete_rcpp, table_to_mappoly, v_2_m

Show 7 earlier eventsHide 7 earlier events

R
R 4.1.0 released · 2021-05-18
0.2.3
record
2021-04-20 · diff ↗ ·
added 2 exports
.vcf_get_probabilities, plot_GIC
unarchivedReturned to CRAN
2020-11-23
0.2.1
record
2020-11-23 · diff ↗ ·
removed 1 export
paralell_pairwise

added 6 exports
aggregate_matrix, get_dosage_type, get_ols_map, paralell_pairwise_discrete, paralell_pairwise_probability, read_fitpoly
archivedRemoved from CRAN
2020-11-16
check problems were not corrected in time
0.2.0
record
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

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' entry:

citation("mappoly")

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

It points to 10.1534/g3.119.400378, 10.1534/g3.119.400620.

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 v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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