R Observatory: Metrics for ALDEx3 version 1.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ALDEx3

1.4.0Package record

Linear Models for Sequence Count Data

0packages depend

3.7Kdownloads / year

91.3%test coverage

13/13flavors OK

Overview

About

Maintained by Justin SilvermanCRAN page ↗

Provides scalable generalized linear and mixed effects models tailored for sequence count data analysis (e.g., analysis of 16S or RNA-seq data). Uses Dirichlet-multinomial sampling to quantify uncertainty in relative abundance or relative expression conditioned on observed count data. Implements scale models as a generalization of normalizations which account for uncertainty in scale (e.g., total abundances) as described in Nixon et al. (2025) doi:10.1186/s13059-025-03609-3 and McGovern et al. (2025) doi:10.1101/2025.08.05.668734.

Changes in 1.4.0

Maintenance

Made BLMM reject invalid or ill-conditioned raw anchor Hessians instead of ridge-regularising and inverting them. Draw-specific Newton updates are now checked against their profiled REML objective, and rejected draws fall back selectively to exact lme4 rather than returning pathological uncertainty.

From NEWS.md in the release

Install

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

install.packages("ALDEx3", 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-aldex3

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-ALDEx3

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-ALDEx3

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: 10.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-30
ERROR10 OK, 3 ERROR2026-07-27
NOTE12 OK, 1 NOTE2026-07-16
OK14 OK2026-03-13
ERROR13 OK, 1 ERROR2026-03-12

Show 1 earlier changeHide 1 earlier change

OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.0

READMEYes · 960 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.4.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 21
Examples that run: 80%4 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 71%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 14%

Vignettes (2)

ALDEx3 Mixed-Effects Engines HTML
ALDEx3-Quickstart HTML

How these are measured

Downloads

3.7K

CRAN downloads in the past year

Rank #5,079 · ~10/day · ~309/mo

Releases R versions

Daily download trend is not available in this view yet.

60430 days

1.6K90 days

3.7K1 year

Compare downloads with other packages →

Also on160 r2u45 autocran

How downloads are counted

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing ALDEx3 adds 32 packages (17 with compiled code, 27 MB of source tarballs). Heaviest: ggplot2 6.0 MB, lme4 4.3 MB, nloptr 2.1 MB.

Depends (1)

R >= 3.5

Imports (12)

purrr lme4 lmerTest reformulasparallelMASSnlmeabind matrixStatsmethodsstatsTMB

LinkingTo (3)

TMB RcppEigenMatrix

Suggests (6)

rBeta2009 testthat lmtest sandwich knitr rmarkdown

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)

Justin Silverman

Author, Maintainer since 1.0.0 (2026)

Greg Gloor

Author

Kyle McGovern

Author, Contributor

Releases (6)

Pick two releases to compare their code metrics.

1.4.0Latest
record
2026-10-19 · current release · diff ↗
1.3.1
record
2026-08-26 · diff ↗
1.2.0
record
2026-07-15 · diff ↗ ·
added 2 exports
aldex.effect, aldex.plot
R
R 4.6.0 released · 2026-04-24
1.0.2
record
2026-02-05 · diff ↗
1.0.1
record
2026-02-03 · diff ↗
1.0.0
record
2026-01-31
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-01-31
Total releases: 6 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Bundled data: 25 KB / 2 files
Download size: 215 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ALDEx3")

Format

Silverman, J., Gloor, G., & McGovern, K. (2026). ALDEx3: Linear Models for Sequence Count Data (Version 1.4.0) [Computer software]. https://doi.org/10.32614/CRAN.package.ALDEx3

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 ALDEx3 version 1.4.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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