R Observatory: Metrics for gap version 1.15.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

gap

1.15.2Package record

Genetic Analysis Package

4packages dependsuggested by 1

333.3Kdownloads / year

–test coverage

8/13flavors OK

Overview

About

Maintained by Jing Hua ZhaoCRAN page ↗GitHub ↗Issues ↗

As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. doi:10.18637/jss.v023.i08], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

Install

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

install.packages("gap", 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("jinghuazhao/R")

Development version from jinghuazhao/R. 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-gap

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-gap

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-gap

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

5NOTE8OK

Check messages

NOTEdependencies in R coder-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-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

Base package in Suggests/Enhances imported in NAMESPACE:
  ‘grDevices’

r-devel-windows-x86_64

Base package in Suggests/Enhances imported in NAMESPACE:
  'grDevices'

Additional issues

OpenBLAS

CRAN check page ↗

Slowest check: 4.3 min · r-devel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-09-11
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-27
ERROR12 OK, 1 ERROR2026-06-23

Show 5 earlier changesHide 5 earlier changes

OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-31
WARNING12 OK, 1 WARNING2026-05-13
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.15.2

READMENoVignettesYes · 2 · dynamicNEWSNoCitation fileYes · cites a publication

Cites a JSS article

Help pages: 118 (1 internal)includes a package overview page
Examples that run: 19%18 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 76 never run
Exported functions with examples: 84%
Documented parameters: 100%
Return-value docs: 90%
Help pages citing references: 43% with a bibliography file

Also includes 1 demo script (run with demo())

Vignettes (2)

How these are measured

Downloads

333.3K

CRAN downloads in the past year

Rank #626 · ~913/day · ~27.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

29.4K30 days

93.2K90 days

333.3K1 year

Compare downloads with other packages →

Also on2.4K r2u198 autocran10.4K conda_forge430 bioconda273 c2d4u

How downloads are counted

Repository

jinghuazhao/r ↗Account: jinghuazhao

13Stars

4Forks

5Open issues

0Open PRs

0Releases

3,002Commits

4Commit identities

geneticslmmimputation

3,002 commits · Last activity 2026-09-29 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2024-03-15 · 122026-07-07 · 13

How these are measured

PracticesBeta

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

Checks run against github.com/jinghuazhao/r on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on macOS

Docs source (2)

GitHub Pages site last deployed 2026-09-29 · The repository has a site deploy workflow

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

Dependencies

Declared dependencies

36 external dependencies (excludes base and recommended)

Installing gap adds 67 packages (36 with compiled code, 67 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (2)

R >= 2.10gap.datasets

Imports (4)

dplyr ggplot2 plotly Rdpack

LinkingTo (0)

none

Suggests (38)

BradleyTerry2 DiagrammeRMASSMatrixMCMCglmm R2jags bdsmatrix bookdown calibrate circlize coda cowplot coxmeforeigngeneticsgrDeviceshaplo.stats htmltools htmlwidgets jsonlite kinship2 knitrlatticemagic matrixStats meta metafornlmepedigree pedigreemm plotrix readr reshape rmarkdown rms scalessurvivalvalr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

12indirect

Imports 4

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

DHARMa BayesianTools PopGenReport gaawr2

Suggests, most downloaded first

rehh

How these are counted

Code & Tests

Datasets

People & History

People (5)

Jing Hua Zhao

Author, Maintainer · added in 1.0-15

Kurt Hornik

Contributor · added in 1.2.3-6

Uwe Ligges

Contributor · added in 1.5-3

Brian Ripley

Contributor · added in 1.0-15

Achim Zeileis

Contributor · added in 1.3-1

Maintainer since 0.3 (2004)

Listed in earlier versions (6)

Show 6 peopleHide 6 people

Jing Hua Zhao in collaboration with other colleagues

no longer listed · 0.3 to 1.0-14

with help from Kurt Hornik of the R core development team

no longer listed · 0.3 to 0.4

with help from Kurt Hornik

no longer listed · 0.5 to 1.0-14

Brian Ripley of the R core development team

no longer listed · 0.5 to 1.0-14

colleagues with inputs from Kurt Hornik

no longer listed · 1.0-15 to 1.2.3-1

Uwe Liggs

no longer listed · 1.2.3-6 to 1.5-1

Releases (55)

Pick two releases to compare their code metrics.

1.15.2Latest
record
2026-05-28 · current release · diff ↗
1.15.1
record
2026-05-24 · diff ↗ ·
added 1 export
ACDE
R
R 4.6.0 released · 2026-04-24
1.14
record
2026-02-19 · diff ↗
1.9
record
2026-02-06 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.6
record
2024-08-27 · diff ↗ ·
added 1 export
qtlFinder
R
R 4.4.0 released · 2024-04-24
1.5-3
record
2023-08-26 · diff ↗ ·
added 2 exports
ci2ms, runshinygap
R
R 4.3.0 released · 2023-04-21
1.5-1
record
2023-01-22 · diff ↗ ·
added 8 exports
ReadGRM, ReadGRMBin, WriteGRM, WriteGRMBin, a2g, allele.recode, g2a, geno.recode
1.5
record
2023-01-13 · diff ↗
1.4-2
record
2023-01-09 · diff ↗ ·
removed 1 export
gsmr

added 4 exports
KCC, hap.control, makeped, mr
1.3-1
record
2022-10-21 · diff ↗ ·
removed 66 exports
allele.recode, allDuplicated, a2g, Cox.est, Cox.T, cov.invlogit, DevH0dominant, DevH0dominant.est, DevH0recessive, DevH0recessive.est, DevHaGdominant, DevHaGdominant.est, DevHaGrecessive, DevHaGrecessive.est, g2a, g2a.c, gc.control, gcode, geno.recode, getPTE, getb1star, grec2g, hap.control, htr, HapDesign, HapFreqSE, invlogit, KCC, k, lambda1000 and 36 more

added 9 exports
circos.mhtplot2, labelManhattan, miamiplot2, mr_forestplot, pedtodot_verbatim, qtl2dplot, qtl2dplotly, qtl3dplotly, qtlClassifier
1.2.3-6
record
2022-05-14 · diff ↗ ·
removed 3 exports
h2, mhtplot2d, mhtplot3d

added 14 exports
allDuplicated, get_b_se, get_pve_se, get_sdy, grid2d, h2_mzdz, ixy, pqtl2dplot, pqtl2dplotly, pqtl3dplotly, revStrand, runshinygap, textbox, xy
R
R 4.2.0 released · 2022-04-22

Show 71 earlier eventsHide 71 earlier events

R
R 4.1.0 released · 2021-05-18
1.2.3-1
record
2021-04-21 · diff ↗ ·
added 6 exports
gsmr, log10pvalue, mhtplot3d, mr.boot, pvalue, weighted.median
R
R 4.0.0 released · 2020-04-24
1.2.2
record
2020-02-02 · diff ↗ ·
added 8 exports
chr_pos_a1_a2, cs, inv_chr_pos_a1_a2, lambda1000, logp, makeRLEplot, mhtplot2d, snptest_sample
1.2.1
record
2019-06-05 · diff ↗ ·
added 14 exports
cis.vs.trans.classification, circos.cis.vs.trans.plot, circos.cnvplot, circos.mhtplot, cnvplot, gc.lambda, h2.jags, hwe.jags, invnormal, log10p, METAL_forestplot, mhtplot.trunc, miamiplot, sentinels
R
R 3.6.0 released · 2019-04-26
1.1-22
record
2018-06-08 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.1-21
record
2018-01-24 · diff ↗
1.1-20
record
2017-11-25 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.1-17
record
2017-04-19 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.1-16
record
2015-06-06 · diff ↗
1.1-14
record
2015-06-04 · diff ↗
1.1-13
record
2015-06-03 · diff ↗ ·
added 1 export
MCMCgrm
R
R 3.2.0 released · 2015-04-16
1.1-12
record
2014-08-18 · diff ↗ ·
added 7 exports
h2G, ReadGRM, ReadGRMPLINK, ReadGRMPCA, WriteGRM, WriteGRMBin, WriteGRMSAS
R
R 3.1.0 released · 2014-04-10
1.1-10
record
2013-09-30 · diff ↗ ·
added 4 exports
h2GE, h2l, ReadGRMBin, VR
1.1-9
record
2013-04-08 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.1-8
record
2013-02-26 · diff ↗ ·
removed 1 export
twinan90

added 4 exports
AE3, allele.recode, geno.recode, mhtplot2
R
R 2.15.0 released · 2012-03-30
1.1-6
record
2012-03-15 · diff ↗ ·
removed 10 exports
ci, Dev, Dev.est, DevHa.recessive, DevHa.recessive.est, ExpN.recessiveH0, ExpN.recessiveHa, geno.p, hw, twinan90

added 2 exports
allele.recode, geno.recode
1.1-3
record
2011-12-06 · diff ↗ ·
removed 9 exports
ci, Dev, Dev.est, DevHa.recessive, DevHa.recessive.est, ExpN.recessiveH0, ExpN.recessiveHa, geno.p, hw
R
R 2.14.0 released · 2011-10-31
1.1-2
record
2011-05-03 · diff ↗ ·
removed 2 exports
allele.recode, geno.recode

added 10 exports
ci, Dev, Dev.est, DevHa.recessive, DevHa.recessive.est, ExpN.recessiveH0, ExpN.recessiveHa, geno.p, hw, twinan90
R
R 2.13.0 released · 2011-04-13
1.1-1
record
2010-12-10 · diff ↗
1.1-0
record
2010-11-17 · diff ↗ ·
added 2 exports
hmht.control, mht.control
R
R 2.12.0 released · 2010-10-15
1.0-23
record
2010-06-25 · diff ↗ ·
removed 1 export
abc

added 35 exports
ab, Cox.est, Cox.T, ci, cov.invlogit, Dev, Dev.est, DevH0dominant, DevH0dominant.est, DevH0recessive, DevH0recessive.est, DevHaGdominant, DevHaGdominant.est, DevHaGrecessive, DevHaGrecessive.est, DevHa.recessive, DevHa.recessive.est, ExpN.recessiveH0, ExpN.recessiveHa, geno.p, getPTE, getb1star, h2, hw, hwe.cc, invlogit, k, klem, logit, masize and 5 more
R
R 2.11.0 released · 2010-04-22
1.0-22
record
2010-01-02 · diff ↗ ·
added 1 export
x2
1.0-21
record
2009-11-22 · diff ↗ ·
added 2 exports
abc, read.ms.output
R
R 2.10.0 released · 2009-10-26
1.0-20
record
2009-08-26 · diff ↗ ·
added 2 exports
b2r, mvmeta
R
R 2.9.0 released · 2009-04-17
1.0-17
record
2009-01-02 · diff ↗ ·
added 2 exports
HapDesign, HapFreqSE
R
R 2.8.0 released · 2008-10-20
R
R 2.7.0 released · 2008-04-22
1.0-15
record
2008-04-10 · diff ↗ ·
removed 2 exports
kbyl, tbyt

added 13 exports
asplot, ESplot, gcontrol2, LD22, LDkl, metap, metareg, mhtplot, PARn, qqfun, snp.ES, snp.HWE, snp.PAR
1.0-14
record
2008-03-02 · diff ↗ ·
added 2 exports
KCC, pbsize2
R
R 2.6.0 released · 2007-10-03
1.0-13
record
2007-10-02 · diff ↗
1.0-12
record
2007-07-31 · diff ↗ ·
removed 6 exports
Ginv, allele.recode, compositeLD, geno.recode, printBanner, print.compositeLD

added 3 exports
BFDP, FPRP, qqunif
1.0-11
record
2007-06-14 · diff ↗ ·
added 1 export
comp.score
R
R 2.5.0 released · 2007-04-24
1.0-10
record
2007-01-05 · diff ↗ ·
removed 1 export
mi.inference

added 1 export
micombine
R
R 2.4.0 released · 2006-10-03
1.0-9
record
2006-09-21 · diff ↗ ·
added 2 exports
mi.inference, tscc
R
R 2.3.0 released · 2006-04-24
1.0-8
record
2006-04-04 · diff ↗ ·
added 1 export
twinan90
1.0-6
record
2006-02-13 · diff ↗ ·
added 50 exports
Ginv, a2g, allele.recode, bt, ccsize, chow.test, compositeLD, fbsize, g2a, g2a.c, gc.control, gc.em, gcode, gcontrol, gcp, genecounting, geno.recode, gif, grec2g, hap, hap.control, hap.em, hap.score, htr, hwe, hwe.hardy, kbyl, kin.morgan, m2plem, makeped and 20 more
1.0-5
record
2006-01-17 · diff ↗ ·
added 50 exports
Ginv, a2g, allele.recode, bt, ccsize, chow.test, compositeLD, fbsize, g2a, g2a.c, gc.control, gc.em, gcode, gcontrol, gcp, genecounting, geno.recode, gif, grec2g, hap, hap.control, hap.em, hap.score, htr, hwe, hwe.hardy, kbyl, kin.morgan, m2plem, makeped and 20 more
R
R 2.2.0 released · 2005-10-06
1.0-3
record
2005-07-24 · diff ↗
R
R 2.1.0 released · 2005-04-18
1.0-2
record
2005-04-15 · diff ↗
1.0-1
record
2005-04-10 · diff ↗ ·
removed 50 exports
Ginv, a2g, allele.recode, bt, ccsize, chow.test, compositeLD, fbsize, g2a, g2a.c, gc.control, gc.em, gcode, gcontrol, gcp, genecounting, geno.recode, gif, grec2g, hap, hap.control, hap.em, hap.score, htr, hwe, hwe.hardy, kbyl, kin.morgan, m2plem, makeped and 20 more
0.8-3
record
2004-12-21 · diff ↗
R
R 2.0.0 released · 2004-10-04
0.8-2
record
2004-08-17 · diff ↗
R
R 1.9.0 released · 2004-04-12
0.8
record
2004-02-29 · diff ↗
0.7
record
2004-02-02 · diff ↗
0.5
record
2004-01-22 · diff ↗
0.4
record
2004-01-18 · diff ↗
0.3
record
2004-01-14
R
R 1.8.0 released · 2003-10-08

Package metadata

First published: 2004-01-14
Total releases: 55 / 22 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 0.6 KB / 4 files
Download size: 808 KB

Appears in task views

Meta-Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("gap")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 gap version 1.15.2 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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