R Observatory: Metrics for SIMMS version 1.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SIMMS

1.3.2Package record

Subnetwork Integration for Multi-Modal Signatures

0packages depend

3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Syed HaiderCRAN page ↗

Algorithms to create prognostic biomarkers using biological genesets or networks.

Install

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

install.packages("SIMMS", 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-simms

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-SIMMS

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-SIMMS

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: 2.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-25
ERROR12 OK, 1 ERROR2026-10-24
OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05

Show 4 earlier changesHide 4 earlier changes

NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.2

READMENoVignettesYes · 1 · dynamicNEWSYes · 100% structuredCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 24includes a package overview page
Examples that run: 76%16 run in a plain check · 5 hold no code
Exported functions with examples: 87%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

SIMMS HTML

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #15,383 · ~8/day · ~254/mo

Releases R versions

Daily download trend is not available in this view yet.

29130 days

80090 days

3K1 year

Compare downloads with other packages →

Also on79 r2u4 autocran54 c2d4u

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing SIMMS adds 70 packages (35 with compiled code, 60 MB of source tarballs). Heaviest: stringi 11 MB, bslib 5.6 MB, igraph 4.8 MB.

Depends (6)

R >= 3.2.0survivalMASSglmnet doParallel foreach

Imports (1)

randomForestSRC

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown xtable

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Syed Haider

Author, Maintainer since 0.0.1 (2013)

Paul C. Boutros

Author

Michal Grzadkowski

Contributor

Releases (11)

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
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-04-24
1.3.2Latest
record
2022-04-24 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2022-02-23
requires archived package 'randomForestSRC'
R
R 4.1.0 released · 2021-05-18
1.3.1
record
2021-01-07 · diff ↗
unarchivedReturned to CRAN
2020-06-06
1.3.0
record
2020-06-06 · diff ↗
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-03-29
check problems were not corrected in time
1.2.0
record
2019-05-05 · diff ↗ ·
added 1 export
centre.scale.dataset
R
R 3.6.0 released · 2019-04-26

Show 13 earlier eventsHide 13 earlier events

1.1.2
record
2019-03-07 · diff ↗ ·
added 22 exports
calculate.meta.survival, calculate.network.coefficients, calculate.sensitivity.stats, create.KM.plot, create.classifier.multivariate, create.classifier.univariate, create.sensitivity.plot, create.survivalplots, create.survobj, derive.network.features, dichotomize.dataset, dichotomize.meta.dataset, fit.coxmodel, fit.interaction.model, fit.survivalmodel, get.adjacency.matrix, get.chisq.stats, get.program.defaults, load.cancer.datasets, make.matrix, pred.survivalmodel, prepare.training.validation.datasets
R
R 3.5.0 released · 2018-04-23
1.1.1
record
2017-10-11 · diff ↗
1.1.0
record
2017-09-06 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.0.2
record
2015-09-21 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+
R
R 3.2.0 released · 2015-04-16
1.0.1
record
2015-02-22 · diff ↗
1.0.0
record
2015-02-16 · diff ↗ ·
removed 20 exports
derive.network.features, prepare.training.validation.datasets, fit.survivalmodel, pred.survivalmodel, create.survivalplots, get.program.defaults, calculate.meta.survival, calculate.network.coefficients, get.adjacency.matrix, get.chisq.stats, make.matrix, create.survobj, load.cancer.datasets, dichotomize.dataset, dichotomize.meta.dataset, fit.coxmodel, fit.interaction.model, create.KM.plot, create.sensitivity.plot, calculate.sensitivity.stats

added 1 export
pattern:^[[:alpha:]]+
R
R 3.1.0 released · 2014-04-10
0.0.1
record
2013-06-11
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-06-11
Total releases: 11 / 13 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.2.0
Download size: 362 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SIMMS")

Format

Haider, S., C. Boutros, P., & Grzadkowski, M. (2022). SIMMS: Subnetwork Integration for Multi-Modal Signatures (Version 1.3.2) [Computer software]. https://doi.org/10.32614/CRAN.package.SIMMS

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 SIMMS version 1.3.2 [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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