qch

2.1.3

Query Composite Hypotheses

0packages depend

3.3Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Tristan Mary-HuardFirst published 2021-05-075 releasesCRAN page ↗

Provides functions for the joint analysis of Q sets of p-values obtained for the same list of items. This joint analysis is performed by querying a composite hypothesis, i.e. an arbitrary complex combination of simple hypotheses, as described in Mary-Huard et al. (2021) doi:10.1093/bioinformatics/btab592 and De Walsche et al.(2025) <doi: 10.1093/nargab/lqaf118>. In this approach, the Q-uplet of p-values associated with each item is distributed as a multivariate mixture, where each of the 2^Q components corresponds to a specific combination of simple hypotheses. The dependence between the p-value series is considered using a Gaussian copula function. A p-value for the composite hypothesis test is derived from the posterior probabilities.

Install

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

install.packages("qch", 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-qch

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-qch

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-qch

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 3.4 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-06-07
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.3K

CRAN downloads in the past year

Rank #9,339 · ~9/day · ~278/mo

Releases R versions

Daily download trend is not available in this view yet.

28930 days

1.1K90 days

3.3K1 year

Compare downloads with other packages →

Also on396 r2u8 autocran

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (9)

copula dplyrgraphicsks purrr Rcppstatsstringrutils

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Tristan Mary-Huard

Author, Maintainer

Authors (2)

Tristan Mary-Huard

Author, Maintainer

Annaig De Walsche

Author · added in 2.0.0

Contributors (1)

Franck Gauthier

Contributor · added in 2.0.0

Package Timeline

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

2.1.3Latest
2026-05-27 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.1.2
2026-02-16 · diff ↗
2.1.0
2025-07-04 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.0.0
2024-03-29 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.0
2021-05-07
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-05-07
Total releases: 5 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 305 KB / 2 files
Download size: 333 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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