R Observatory: Metrics for slfm version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

slfm

1.0.2Package record

Fitting a Bayesian Sparse Latent Factor Model in Gene Expression Analysis

0packages depend

2.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Vinicius MayrinkCRAN page ↗

Set of tools to find coherent patterns in gene expression (microarray) data using a Bayesian Sparse Latent Factor Model (SLFM) DOI:10.1007/978-3-319-12454-4_15. Considerable effort has been put to build a fast and memory efficient package, which makes this proposal an interesting and computationally convenient alternative to study patterns of gene expressions exhibited in matrices. The package contains the implementation of two versions of the model based on different mixture priors for the loadings: one relies on a degenerate component at zero and the other uses a small variance normal distribution for the spike part of the mixture.

Changes in 1.0.2

including package \alias as per "Documenting packages" in R-exts.

From NEWS in the release

Install

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

install.packages("slfm", 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-slfm

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-slfm

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-slfm

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: 3.2 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.2

READMENoVignettesNoNEWSYes · 33% structured · mentions 1.0.2Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites a JSS article

Help pages: 6includes a package overview page
Examples that run: 100%1 run in a plain check
Exported functions with examples: 25%
Documented parameters: 100%
Return-value docs: 25%
Help pages citing references: 17%

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #15,258 · ~7/day · ~220/mo

Releases R versions

Daily download trend is not available in this view yet.

27930 days

78590 days

2.6K1 year

Compare downloads with other packages →

Also on347 r2u5 autocran56 c2d4u

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing slfm adds 3 packages (2 with compiled code, 2.9 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppArmadillo 1.0 MB, coda 73 KB.

Depends (1)

R >= 3.1.0

Imports (3)

Rcpp codalattice

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Vinicius Mayrink

Author, Maintainer since 1.0.1 (2020)

Joao Duarte

Author

Previously maintained by Joao Duarte (0.1 to 1.0.0).

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.2Latest
record
2023-11-28 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
unarchivedReturned to CRAN
2020-03-15
1.0.1
record
2020-03-15 · diff ↗
archivedRemoved from CRAN
2020-03-03
check problems were not corrected despite reminders
1.0.0
record
2019-07-28 · diff ↗
0.2.3
record
2019-05-27 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21

Show 7 earlier eventsHide 7 earlier events

R
R 3.3.0 released · 2016-05-03
0.2.2
record
2015-08-10 · diff ↗
0.2.1
record
2015-08-08 · diff ↗
0.2.0
record
2015-07-29 · diff ↗ ·
added 1 export
plot_matrix
R
R 3.2.0 released · 2015-04-16
0.1
record
2014-05-08
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-05-08
Total releases: 8 / 12 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.1.0
Download size: 11 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("slfm")

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

It points to 10.18637/jss.v090.i09.

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 slfm version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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