R Observatory: Metrics for citcdf version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

citcdf

1.1.0Package record

Conditional Independence Testing with Cumulative Distribution Functions

0packages depend

680downloads / year

85.1%test coverage

13/13flavors OK

Overview

About

Maintained by Boris P. HejblumCRAN page ↗GitHub ↗Website ↗Issues ↗

Complex hypothesis testing through conditional cumulative distribution function estimation. Method is detailed in: Gauthier M, Agniel D, Thiébaut R & Hejblum BP (2021). "Distribution-free complex hypothesis testing for single-cell RNA-seq differential expression analysis", bioRxiv doi:10.1101/2021.05.21.445165.

Changes in 1.1.0

perm_cont():
now draws **without replacement**, so the conditional permutation

X_star is a genuine permutation of X (rather than a re-sample) and

preserves X's empirical marginal distribution.

Because this changes both the RNG stream and the null distribution, permutation

p-values from cit_perm(),cit_multi() and cit_gsa() will differ from

previous versions. Of note, previous scheme could be anti-conservative, and

some limiting cases were badly handled.

now uses QR decomposition through .lm.fit() to be robust to badly scaled

covariates (eg library sizes).

now weights draws with a **Gaussian kernel** on the fitted

values (bandwidth sd(fit) * n^(-1/3)) rather than previous

Show all changes in 1.1.0Hide the rest of the changes in 1.1.0

1/(difference in fitted values)^2 (each observation effectively drew

from its two nearest neighbours whatever the sample size, leading to bad

calibration of the test with too many false positives). This also changes

the null distribution.

space_y = TRUE now uses the same y-threshold grid across all tests:

cit_asymp(), and cit_gsa() adopt cit_perm()'s upper endpoint max(Y)

instead of the second-largest observation. Asymptotic results will be different

than previously with defaults, although calibration remains unchanged.

similarly, ccdf() now uses the same y-threshold grid as the tests when

space_y = TRUE (starting at the smallest non-zero observation rather than

the second smallest). CCDF values from ccdf(space_y = TRUE) therefore differ

from previous versions (the default space_y = FALSE is unaffected). It also

no longer errors when all Y are equal.

first CRAN release

From NEWS.md in the release

Install

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

install.packages("citcdf", 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("sistm/citcdf")

Development version from sistm/citcdf. 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-citcdf

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-citcdf

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-citcdf

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

13OK

CRAN check page ↗

Slowest check: 6.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OKNow
OK7 OK2026-08-22

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 184 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 1.1.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 11 (1 internal)includes a package overview page
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 89%
Return-value docs: 100%
Help pages citing references: 55%

Vignettes (1)

User guide to the citcdf R package HTML

How these are measured

Downloads

680

CRAN downloads in the past year

Rank #19,225 · ~2/day · ~57/mo

Releases R versions

Daily download trend is not available in this view yet.

28330 days

68090 days

6801 year

Compare downloads with other packages →

Also on17 r2u10 autocran

How downloads are counted

Repository

sistm/citcdf ↗Organization: sistmFork of Mgauth/ccdf

3Stars

1Forks

1Open issues

1Open PRs

1Releases

358Commits

4Commit identities

License file reads as GPL-3.0 · 358 commits · Last activity 2026-10-19 · 0% stars, 30d · Default branch at 1.2.1, ahead of CRAN 1.1.0 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-08-22 · 22026-09-05 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/sistm/citcdf on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-09 · The repository has a site deploy workflow

pkgdown site last built 2026-10-09

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing citcdf adds 28 packages (13 with compiled code, 25 MB of source tarballs). Heaviest: ggplot2 6.0 MB, patchwork 3.2 MB, survey 2.3 MB.

Depends (1)

R >= 4.1

Imports (7)

ggplot2 pbapplyparallelpatchwork RcppNumerical survey viridisLite

LinkingTo (0)

none

Suggests (10)

BiocSet bnlearn GSA knitr quarto reactable rmarkdown sessioninfo SeuratObject testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (6)

Author

Author

Author

Contributor

Contributor

Releases (1)

1.1.0Latest
record
2026-08-21 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-08-21
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1
Download size: 539 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("citcdf")

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

It points to 10.1101/2021.05.21.445165.

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 citcdf version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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