R Observatory: Metrics for CAFT version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CAFT

0.1.0

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

0packages depend

436downloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Mo LiFirst published 2026-06-251 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

13OK

Slowest check: 6.9 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

9

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-26
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 274 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 11%

Downloads

436

CRAN downloads in the past year

Rank #23,276 · ~1/day · ~36/mo

Releases R versions

Daily download trend is not available in this view yet.

14130 days

43690 days

4361 year

Compare downloads with other packages →

Also on16 r2u4 autocran

Repository

GitHub ↗ mli171/caft

0Stars

0Forks

0Open issues

0Open PRs

1Releases

83Commits

1Contributors

83 commits · Last activity 2026-06-24

Releases over time

2026-06-24 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/mli171/caft on 2026-08-09.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (3)

Maintainer (1)

Mo Li

Author, Contributor, Maintainer, Copyright holder

Authors (3)

Mo Li

Author, Contributor, Maintainer, Copyright holder

Glen A. Satten