R Observatory: Metrics for cit version 2.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

cit

2.3.2Package record

Causal Inference Test

0packages depend

3.9Kdownloads / year

20.4%test coverage

13/13flavors OK

Overview

About

Maintained by Joshua MillsteinCRAN page ↗GitHub ↗Issues ↗

A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. Described in Millstein, Chen, and Breton (2016), DOI:10.1093/bioinformatics/btw135, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.

Install

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

install.packages("cit", 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("USCbiostats/cit")

Development version from USCbiostats/cit. 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-cit

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-cit

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.5 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
WARNING12 OK, 1 WARNING2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.2

READMEYes · 5 wordsVignettesNoNEWSYes · 67% structured · does not mention 2.3.2Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 9includes a package overview page
Examples that run: 100%8 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 100%

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #9,980 · ~11/day · ~325/mo

Releases R versions

Daily download trend is not available in this view yet.

41930 days

1K90 days

3.9K1 year

Compare downloads with other packages →

Also on381 r2u69 c2d4u

How downloads are counted

Repository

uscbiostats/cit ↗Organization: USCbiostats

3Stars

1Forks

0Open issues

0Open PRs

0Releases

29Commits

4Commit identities

29 commits · Last activity 2024-06-27 · 0% stars, 30d · Default branch at 2.4.0, ahead of CRAN 2.3.2 (checked 2026-10-22)

Responsiveness

not measured

Stars over time

2024-07-19 · 22026-07-07 · 3

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/uscbiostats/cit on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Reproducibility and dev environment (1)

Makefile

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

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

Depends (1)

R >= 4.3.0

Imports (0)

none

LinkingTo (0)

none

Suggests (1)

tinytest

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Joshua Millstein

Author, Maintainer since 1.0 (2011)

Releases (17)

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
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R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-05-25
R
R 4.1.0 released · 2021-05-18
archivedRemoved from CRAN
2020-10-27
required archived package 'RefManageR'
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
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R 3.4.0 released · 2017-04-21
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R 3.3.0 released · 2016-05-03
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R 3.2.0 released · 2015-04-16
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R 3.1.0 released · 2014-04-10
3.0.3Latest
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2013-12-19 · current release · diff ↗

Show 20 earlier eventsHide 20 earlier events

R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
2.14.1
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2011-12-09 · diff ↗
R
R 2.14.0 released · 2011-10-31
2.13.2
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2011-07-19 · diff ↗ ·
added 2 exports
cit, plotcit
2.3.2
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2024-06-28 · diff ↗
2.3.1
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2021-05-25 · diff ↗
2.2
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2017-12-15 · diff ↗
2.1
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2016-11-15 · diff ↗ ·
added 2 exports
fdr.q.para, fdr.q.perm
2.0
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2016-03-07 · diff ↗
1.9
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2016-01-10 · diff ↗
1.8
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2016-01-09 · diff ↗
1.7
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2015-10-28 · diff ↗
1.5
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2015-10-25 · diff ↗ ·
removed 2 exports
cit, plotcit

added 6 exports
linreg, cit.cp, cit.bp, fdr.od, fdr.cit, iuq
1.4
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2015-03-10 · diff ↗
1.3
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2014-12-10 · diff ↗
1.2
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2013-12-20 · diff ↗
1.1
record
2011-12-10 · diff ↗
1.0
record
2011-09-07
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-07-19
Total releases: 17 / 15 yrs
License: Artistic-2.0 OSI
Minimum R: ≥ 4.3.0
Download size: 28 KB

Appears in task views

Causal Inference

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("cit")

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 cit version 2.3.2 [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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