R Observatory: Metrics for CAFT version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CAFT

0.1.0Package record

Rank-Based Compositional Analysis using Log-Linear Models for Microbiome Data with Zero Cells

0packages depend

1.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Mo LiCRAN page ↗GitHub ↗Issues ↗

Provides rank-based compositional differential abundance analysis for microbiome count data with zero cells using the compositional accelerated failure time model of Satten, Li and Zhao (2025) "CAFT: A Compositional Log-Linear Model for Microbiome Data with Zero Cells" doi:10.1101/2025.11.26.690468. Zero counts are treated as censored observations below sample-specific detection limits, avoiding the use of pseudocounts. The package implements estimation and hypothesis testing procedures for assessing associations between microbial taxa and covariates while accounting for the compositional structure of sequencing count data. It supports taxon-level differential abundance analysis, estimation of regression effects under censoring induced by detection limits, and inference based on rank-based methods that remain applicable in the presence of excess zeros. Functions are provided for model fitting, significance testing, extraction of effect estimates, and summarization of results across taxa. The package also provides optional bootstrap calibration of taxon-level p-values for sensitivity analysis in small-taxon settings.

Install

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

install.packages("CAFT", 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("mli171/CAFT")

Development version from mli171/CAFT. 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-caft

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-CAFT

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-CAFT

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: 6.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-06-26

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 274 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 11%

Vignettes (1)

A brief guide to CAFT

How these are measured

Downloads

1.2K

CRAN downloads in the past year

Rank #13,475 · ~3/day · ~102/mo

Releases R versions

Daily download trend is not available in this view yet.

26130 days

86490 days

1.2K1 year

Compare downloads with other packages →

Also on32 r2u6 autocran

How downloads are counted

Repository

mli171/caft ↗Account: mli171

0Stars

0Forks

0Open issues

0Open PRs

1Releases

83Commits

1Commit identities

83 commits · Last activity 2026-06-24 · Default branch at 0.1.1, ahead of CRAN 0.1.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 26
Median days to close, 50 most recently updated closed PRs: not measured

Releases over time

2026-06-24 · 12026-07-07 · 1

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/mli171/caft on 2026-10-21.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing CAFT adds 47 packages (24 with compiled code, 37 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, survey 2.3 MB.

Depends (1)

R >= 4.3.0

Imports (9)

doParallel doRNG expm foreach ggplot2 ggtext ICSNPMASSstats

LinkingTo (0)

none

Suggests (4)

graphicsknitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Mo Li

Glen A. Satten

Author, Contributor, Copyright holder

Ni Zhao

Author, Contributor, Copyright holder

Releases (1)

0.1.0Latest
record
2026-06-25 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-25
Total releases: 1 / 1 yrs
License: LGPL (>= 2) OSI
Minimum R: ≥ 4.3.0
Bundled data: 316 KB / 2 files
Download size: 411 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CAFT")

Format

Li, M., Satten, G. A., & Zhao, N. (2026). CAFT: Rank-Based Compositional Analysis using Log-Linear Models for Microbiome Data with Zero Cells (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.CAFT

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 CAFT version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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