R Observatory: Metrics for CJAMP version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CJAMP

0.1.1Package record

Copula-Based Joint Analysis of Multiple Phenotypes

0packages depend

2.9Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Stefan KonigorskiCRAN page ↗

We provide a computationally efficient and robust implementation of the recently proposed C-JAMP (Copula-based Joint Analysis of Multiple Phenotypes) method (Konigorski et al., 2019, submitted). C-JAMP allows estimating and testing the association of one or multiple predictors on multiple outcomes in a joint model, and is implemented here with a focus on large-scale genome-wide association studies with two phenotypes. The use of copula functions allows modeling a wide range of multivariate dependencies between the phenotypes, and previous results are supporting that C-JAMP can increase the power of association studies to identify associated genetic variants in comparison to existing methods (Konigorski, Yilmaz, Pischon, 2016, DOI:10.1186/s12919-016-0045-6; Konigorski, Yilmaz, Bull, 2014, DOI:10.1186/1753-6561-8-S1-S72). In addition to the C-JAMP functions, functions are available to generate genetic and phenotypic data, to compute the minor allele frequency (MAF) of genetic markers, and to estimate the phenotypic variance explained by genetic markers.

Install

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

install.packages("CJAMP", 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-cjamp

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-CJAMP

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-CJAMP

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: ‘Stefan Konigorski <stefan.konigorski@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 2.9 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE10 OK, 2 NOTE2026-04-25
ERROR9 OK, 4 NOTE, 1 ERROR2026-03-30
NOTE9 OK, 5 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileYes · computed when R runs itWebsitenot declared in DESCRIPTION

Help pages: 10
Examples that run: 90%9 run in a plain check · 1 hold no code
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

C-JAMP: Copula-based Joint Analysis of Multiple Phenotypes PDF

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #12,344 · ~8/day · ~238/mo

Releases R versions

Daily download trend is not available in this view yet.

39430 days

90090 days

2.9K1 year

Compare downloads with other packages →

Also on81 r2u7 autocran

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing CJAMP adds 4 packages (1 with compiled code, 4.8 MB of source tarballs). Heaviest: optimx 2.2 MB, nloptr 2.1 MB, pracma 389 KB.

Depends (0)

none

Imports (2)

statsoptimx

LinkingTo (0)

none

Suggests (3)

MASSknitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Stefan Konigorski

Author, Maintainer since 0.1.0 (2018)

Yildiz E. Yilmaz

Contributor, Thesis advisor

Releases (2)

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
R
R 4.4.0 released · 2024-04-24
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
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.1.1Latest
record
2019-03-20 · current release · diff ↗
0.1.0
record
2018-04-24
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-04-24
Total releases: 2 / 8 yrs
License: GPL-2 OSI
Download size: 613 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CJAMP")

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 CJAMP version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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