R Observatory: Metrics for sharp version 1.4.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

sharp

1.4.8Package record

Stability-enHanced Approaches using Resampling Procedures

1packages depend

4.7Kdownloads / year

23.1%test coverage

13/13flavors OK

Overview

About

Maintained by Barbara BodinierCRAN page ↗GitHub ↗Issues ↗

In stability selection (N Meinshausen, P Bühlmann (2010) doi:10.1111/j.1467-9868.2010.00740.x) and consensus clustering (S Monti et al (2003) doi:10.1023/A:1023949509487), resampling techniques are used to enhance the reliability of the results. In this package (B Bodinier et al (2025) doi:10.18637/jss.v112.i05), hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2023a) doi:10.1093/jrsssc/qlad058 and B Bodinier et al (2023b) doi:10.1093/bioinformatics/btad635). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.

Changes in 1.4.8

Update glmnet

From NEWS.md in the release

Install

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

install.packages("sharp", 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("barbarabodinier/sharp")

Development version from barbarabodinier/sharp. 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-sharp

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-sharp

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-sharp

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-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK, 1 FAILURE2026-06-08
WARNING12 OK, 1 WARNING2026-06-07
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.8

READMEYes · 548 wordsVignettesNoNEWSYes · 100% structured · mentions 1.4.8Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites a JSS article

Help pages: 85 (22 internal)includes a package overview page
Examples that run: 56%31 run in a plain check (8 of them under a condition) · 24 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 91%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 27% with a bibliography file

How these are measured

Downloads

4.7K

CRAN downloads in the past year

Rank #7,838 · ~13/day · ~392/mo

Releases R versions

Daily download trend is not available in this view yet.

50630 days

1.1K90 days

4.7K1 year

Compare downloads with other packages →

Also on81 r2u6 autocran

How downloads are counted

Repository

barbarabodinier/sharp ↗Account: barbarabodinier

18Stars

1Forks

6Open issues

0Open PRs

14Releases

455Commits

6Commit identities

License file reads as GPL-3.0 · 455 commits · Last activity 2025-07-23 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 81
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-06-19 · 142026-07-07 · 18

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/barbarabodinier/sharp on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (1)

README.Rmd

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Installing sharp adds 32 packages (16 with compiled code, 24 MB of source tarballs). Heaviest: igraph 4.8 MB, glmnet 2.7 MB, mclust 2.7 MB.

Depends (2)

R >= 3.5fake

Imports (13)

abind beepr future future.apply glassoFast glmnetgrDevicesigraph mclust nloptr plotrix Rdpack withr

LinkingTo (0)

none

Suggests (18)

clustercorpcor dbscan elasticnet gglasso mixOmicsnnetOpenMx RCy3 randomcoloR rCOSA rmarkdownrpartsgPLS sparclsurvivaltestthat visNetwork

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

LSAMBA

How these are counted

Code & Tests

People & History

People (1)

Barbara Bodinier

Author, Maintainer since 1.1.0 (2022)

Releases (13)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.4.8Latest
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2025-07-23 · current release · diff ↗
1.4.7
record
2025-04-11 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.4.6
record
2024-02-03 · diff ↗
1.4.5
record
2024-01-22 · diff ↗
1.4.4
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2023-10-22 · diff ↗
1.4.3
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2023-08-28 · diff ↗
1.4.2
record
2023-06-09 · diff ↗ ·
removed 3 exports
LavaanMatrix, LavaanModel, PenalisedSEM
1.4.1
record
2023-05-31 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.4.0
record
2023-04-18 · diff ↗ ·
added 10 exports
CART, LavaanMatrix, LavaanModel, LinearSystemMatrix, OpenMxMatrix, OpenMxModel, PenalisedLinearSystem, PenalisedOpenMx, PenalisedSEM, StructuralModel
1.3.0
record
2023-01-17 · diff ↗ ·
added 14 exports
Clustering, ClusteringAlgo, ClusteringPerformance, Clusters, CoMembership, ConsensusMatrix, ConsensusScore, DBSCANClustering, GMMClustering, HierarchicalClustering, KMeansClustering, PAMClustering, Stable, WeightBoxplot
1.2.1
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2022-12-10 · diff ↗ ·
removed 2 exports
PlotROC, ROC

added 1 export
IncrementalPlot
1.2.0
record
2022-08-15 · diff ↗ ·
removed 12 exports
BlockDiagonal, BlockMatrix, BlockStructure, Contrast, Heatmap, MakePositiveDefinite, MatchingArguments, SimulateAdjacency, SimulateComponents, SimulateGraphical, SimulatePrecision, SimulateRegression

added 3 exports
Ensemble, EnsemblePredictions, Refit

Show 2 earlier eventsHide 2 earlier events

1.1.0
record
2022-06-17
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-06-17
Total releases: 13 / 4 yrs
License: GPL (>= 3) OSI
Additional repositories: barbarabodinier.github.io
Minimum R: ≥ 3.5
Download size: 1.2 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("sharp")

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

It points to 10.18637/jss.v112.i05.

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 sharp version 1.4.8 [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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