Haplin

7.3.2

Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes

0packages depend

4.2Kdownloads / year

36.0%test coverage

13/13checks pass

Overview

About

Maintained by Hakon K. GjessingFirst published 2009-05-2729 releasesCRAN page ↗

Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in "Gjessing HK and Lie RT. Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes. Annals of Human Genetics (2006) 70, pp. 382-396".

Install

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

install.packages("Haplin", 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-haplin

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-Haplin

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-Haplin

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 10.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.43

36.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 33%
Documented parameters: 97%
Return-value docs: 90%
References docs: 52%

Downloads

4.2K

CRAN downloads in the past year

Rank #10,212 · ~12/day · ~352/mo

Releases R versions

Daily download trend is not available in this view yet.

37730 days

1.1K90 days

4.2K1 year

Compare downloads with other packages →

Also on402 r2u32 autocran84 c2d4u

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (6)

toolsmgcvMASSff rlangmethods

LinkingTo (0)

none

Suggests (5)

knitr Rmpi ggplot2 testthat rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 17,017 (61%)Other 6,477 (23%)Rd 3,192 (11%)Vignettes 752 (3%)C++ 379 (1%)C 108 (0%)

Code characteristics

Object systems

S327

Cyclomatic complexity: 6.0 median / 58 max
Test cases: 122 / 0.43 per code line

Test coverage

Line coverage

36%

Expression

33.0%

Tests / Examples

36.0% / 42% ex

Functions

193 39 exported

Complexity

11.4 avg / 58 max

Call network

193 nodes / 278 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

193 functions

Function	Cyclo	Coverage
cbindFiles exp	12	0%
convertPed exp	18	0%
finishParallelRun exp	2	0%
gxe exp	24	0%
hapPower exp	13	0%
hapPowerAsymp exp	19	0%

People & History

People (4)

Maintainer (1)

Hakon K. Gjessing

Author, Maintainer

Authors (1)

Hakon K. Gjessing

Author, Maintainer

Contributors (3)

Miriam Gjerdevik

Contributor · added in 7.0.0

Julia Romanowska

Contributor · added in 7.0.0

Oivind Skare

Contributor · added in 7.0.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
7.3.2Latest
2024-08-20 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
7.3.1
2024-02-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
7.3.0
2022-05-20 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
7.2.3
2020-09-07 · diff ↗
R
R 4.0.0 released · 2020-04-24
7.2.2
2020-01-07 · diff ↗
R
R 3.6.0 released · 2019-04-26
7.1.0
2019-04-17 · diff ↗
7.0.0
2018-05-28 · diff ↗
unarchivedReturned to CRAN
2018-05-28

Show 36 earlier events

archivedRemoved from CRAN
2018-05-25
depends on archived packages 'DatABEL' and 'GenABEL'
R
R 3.5.0 released · 2018-04-23
6.2.1
2017-10-18 · diff ↗
R
R 3.4.0 released · 2017-04-21
6.2.0
2017-02-28 · diff ↗
6.0.1
2016-05-26 · diff ↗
6.0
2016-05-25 · diff ↗
R
R 3.3.0 released · 2016-05-03
5.5
2015-05-15 · diff ↗
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
5.3
2013-05-23 · diff ↗
5.2
2013-05-02 · diff ↗
R
R 3.0.0 released · 2013-04-03
3.0.0
2013-03-18 · diff ↗
5.0.2
2013-03-18 · diff ↗
5.0.1
2013-03-08 · diff ↗
5.0
2013-02-06 · diff ↗
2.15.3
2013-02-05 · diff ↗
R
R 2.15.0 released · 2012-03-30
4.1
2012-03-16 · diff ↗
2.15.0
2012-03-15 · diff ↗
4.0
2012-01-27 · diff ↗
2.14.2
2012-01-26 · diff ↗
R
R 2.14.0 released · 2011-10-31
R
R 2.13.0 released · 2011-04-13
R
R 2.12.0 released · 2010-10-15
3.5
2010-05-26 · diff ↗
2.11.1
2010-05-17 · diff ↗
R
R 2.11.0 released · 2010-04-22
3.0.2
2010-01-10 · diff ↗
2.11.0
2010-01-08 · diff ↗
R
R 2.10.0 released · 2009-10-26
3.0.1
2009-05-27 · diff ↗
2.10.0
2009-05-25
R
R 2.9.0 released · 2009-04-17

Package metadata

First published: 2009-05-27
Total releases: 29 / 17 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Download size: 2.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Missing Data

Report a problem with this page →