R Observatory: Metrics for hapassoc version 1.2-9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hapassoc

1.2-9Package record

Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm

0packages depend

3.3Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by K. BurkettCRAN page ↗Website ↗

The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.

Install

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

install.packages("hapassoc", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-hapassoc

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-hapassoc

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-hapassoc

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

2NOTE11OK

Check messages

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

Maintainer: ‘K. Burkett <kburkett@uottawa.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "K.",
                      family = "Burkett",
                      role = c("aut", "cre"),
                      email = "kburkett@uottawa.ca"),
               person(given = "B.",
                      family = "McNeney",
                      role = "aut",
                      email = "mcneney@sfu.ca"),
               person(given = "J.",
                      family = "Graham",
                      role = "aut",
                      email = "jgraham@stat.sfu.ca"),
               person(given = c("with", "code", "for", "case-control", "data", "contributed", "by", "Zhijian"),
                      family = "Chen",
                      role = "aut",
                      email = "z11chen@math.uwaterloo.ca"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 2.4 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2-9

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsiteYes

Help pages: 7
Examples that run: 100%5 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 71%

Vignettes (1)

hapassoc PDF

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #9,839 · ~9/day · ~274/mo

Releases R versions

Daily download trend is not available in this view yet.

47830 days

1K90 days

3.3K1 year

Compare downloads with other packages →

Also on376 r2u8 autocran137 c2d4u

How downloads are counted

Repository

sfustatgen/research ↗

Responsiveness

not measured

How these are measured

PracticesBeta

Repository github.com/sfustatgen/research is linked, but repository-practices checks have not run for it yet.

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

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Installing hapassoc adds no packages beyond those that come with R.

Depends (2)

R >= 2.6.0stats

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (4)

· added in 1.2

with code for case-control data contributed by

Maintainer since 1.1 (2006), previously S. Blay (0.4 to 1.0-1) and M. Pratola (0.1 to 0.3)

Listed in earlier versions (1)

M. Pratola

no longer listed · 0.4 to 0.7

Releases (24)

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
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R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.2-9Latest
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2022-05-25 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
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
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R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.2-8
record
2015-05-11 · diff ↗ ·
removed 3 exports
summary.hapassoc, anova.hapassoc, logLik.hapassoc
R
R 3.2.0 released · 2015-04-16
1.2-7
record
2014-08-25 · diff ↗
R
R 3.1.0 released · 2014-04-10

Show 40 earlier eventsHide 40 earlier events

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R 3.0.0 released · 2013-04-03
1.2-6
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2012-09-22 · diff ↗
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2012-04-05 · diff ↗
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R 2.15.0 released · 2012-03-30
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R 2.14.0 released · 2011-10-31
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R 2.13.0 released · 2011-04-13
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R 2.12.0 released · 2010-10-15
1.2-4
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R 2.11.0 released · 2010-04-22
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R 2.10.0 released · 2009-10-26
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R 2.9.0 released · 2009-04-17
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R 2.8.0 released · 2008-10-20
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R 2.7.0 released · 2008-04-22
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R 2.6.0 released · 2007-10-03
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R 2.5.0 released · 2007-04-24
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R 2.4.0 released · 2006-10-03
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2006-04-29 · diff ↗
R
R 2.3.0 released · 2006-04-24
1.0
record
2006-04-13 · diff ↗ ·
added 5 exports
hapassoc, pre.hapassoc, summary.hapassoc, anova.hapassoc, logLik.hapassoc
R
R 2.2.0 released · 2005-10-06
0.7
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2005-07-01 · diff ↗
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2005-06-10 · diff ↗
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R 2.1.0 released · 2005-04-18
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2004-11-04 · diff ↗
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R 2.0.0 released · 2004-10-04
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0.3
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2004-04-14 · diff ↗
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R 1.9.0 released · 2004-04-12
0.2
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2004-03-26 · diff ↗
0.1
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2004-01-28
R
R 1.8.0 released · 2003-10-08

Package metadata

First published: 2004-01-28
Total releases: 24 / 22 yrs
License: GPL-2 OSI
Minimum R: ≥ 2.6.0
Bundled data: 2.7 KB / 2 files
Download size: 233 KB

Appears in task views

Missing Data

Cite

Cite this package

Run in R for the authors' entry:

citation("hapassoc")

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

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 hapassoc version 1.2-9 [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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