parafac4microbiome

1.3.2

Parallel Factor Analysis Modelling of Longitudinal Microbiome Data

1packages depend

2.7Kdownloads / year

89.1%test coverage

13/13checks pass

Overview

About

Maintained by Geert Roelof van der PloegFirst published 2024-09-175 releasesCRAN page ↗GitHub ↗

Creation and selection of PARAllel FACtor Analysis (PARAFAC) models of longitudinal microbiome data. You can import your own data with our import functions or use one of the example datasets to create your own PARAFAC models. Selection of the optimal number of components can be done using assessModelQuality() and assessModelStability(). The selected model can then be plotted using plotPARAFACmodel(). The Parallel Factor Analysis method was originally described by Caroll and Chang (1970) doi:10.1007/BF02310791 and Harshman (1970) https://www.psychology.uwo.ca/faculty/harshman/wpppfac0.pdf.

Install

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

install.packages("parafac4microbiome", 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("GRvanderPloeg/parafac4microbiome")

Development version from GRvanderPloeg/parafac4microbiome. 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-parafac4microbiome

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-parafac4microbiome

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-parafac4microbiome

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 9.9 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.62

89.1%

Coverage · measured lines

97%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 342 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

2.7K

CRAN downloads in the past year

Rank #12,708 · ~8/day · ~229/mo

Releases R versions

Daily download trend is not available in this view yet.

23030 days

84390 days

2.7K1 year

Compare downloads with other packages →

Also on141 r2u16 autocran

Repository

GitHub ↗ grvanderploeg/parafac4microbiome

9Stars

2Forks

1Open issues

0Open PRs

9Releases

162Commits

1Contributors

dimensionality-reductionmicrobiomemicrobiome-datamultiwaymultiway-algorithmsparallel-factor-analysis

162 commits · Last activity 2025-09-24 · 0% stars, 30d

Stars over time

2025-03-29 · 62026-07-07 · 9

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/grvanderploeg/parafac4microbiome on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (17)

compositions cowplot doParallel dplyr foreach ggplot2 ggpubr lifecycle magrittrmethodsmultiwayparallelpracma rlang rTensorstatstidyr

LinkingTo (0)

none

Suggests (8)

knitr phyloseq rmarkdown TreeSummarizedExperiment (>= 2.16.1)SummarizedExperiment testthat withr NPLStoolbox

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

NPLStoolbox

Code & Tests

Code Composition

R 3,079 (66%)Rd 1,164 (25%)Vignettes 445 (9%)

Code characteristics

Cyclomatic complexity: 5.5 median / 30 max
Test cases: 142 / 0.62 per code line

Test coverage

Line coverage

89%

Expression

89.0%

Tests / Examples

89.1% / 79% ex

Functions

30 29 exported

Complexity

6.7 avg / 30 max

Call network

30 nodes / 29 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

30 functions

Function	Cyclo	Coverage
importPhyloseq exp	8	0%
importTreeSummarizedExperiment exp	12	0%
ignore_unused_imports	1	0%
vect_to_fac exp	7	74%
processDataCube exp	5	86%
parafac_fun exp	4	92%

People & History

People (5)

Maintainer (1)

Geert Roelof van der Ploeg

Author, Maintainer

Authors (1)

Geert Roelof van der Ploeg

Author, Maintainer

Contributors (3)

Anna Heintz-Buschart

Contributor

Age Smilde

Contributor

Johan Westerhuis

Contributor

University of Amsterdam

Funders (1)

University of Amsterdam

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.3.2Latest
2025-07-31 · current release · diff ↗
1.2.1
2025-05-20 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.2
2025-03-22 · diff ↗
1.0.3
2024-09-24 · diff ↗
1.0.2
2024-09-17
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-17
Total releases: 5 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 1.5 MB / 3 files
Download size: 2.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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