R Observatory: Metrics for jackstraw version 1.3.21

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

jackstraw

1.3.21Package record

Statistical Inference for Unsupervised Learning

0packages depend

5.5Kdownloads / year

64.1%test coverage

13/13flavors OK

Overview

About

Maintained by Neo Christopher ChungCRAN page ↗

Test for association between the observed data and their estimated latent variables. The jackstraw package provides a resampling strategy and testing scheme to estimate statistical significance of association between the observed data and their latent variables. Depending on the data type and the analysis aim, the latent variables may be estimated by principal component analysis (PCA), factor analysis (FA), K-means clustering, and related unsupervised learning algorithms. The jackstraw methods learn over-fitting characteristics inherent in this circular analysis, where the observed data are used to estimate the latent variables and used again to test against that estimated latent variables. When latent variables are estimated by PCA, the jackstraw enables statistical testing for association between observed variables and latent variables, as estimated by low-dimensional principal components (PCs). This essentially leads to identifying variables that are significantly associated with PCs. Similarly, unsupervised clustering, such as K-means clustering, partition around medoids (PAM), and others, finds coherent groups in high-dimensional data. The jackstraw estimates statistical significance of cluster membership, by testing association between data and cluster centers. Clustering membership can be improved by using the resulting jackstraw p-values and posterior inclusion probabilities (PIPs), with an application to unsupervised evaluation of cell identities in single cell RNA-seq (scRNA-seq).

Changes in 1.3.21

Commented out unimportant tests that fail on CRAN

From NEWS.md in the release

Install

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

install.packages("jackstraw", 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-jackstraw

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

# 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-jackstraw

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: 1.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-04
ERROR12 OK, 1 ERROR2026-09-02
OK13 OK2026-08-05
ERROR11 OK, 2 ERROR2026-07-11
OK10 OK2026-04-25

Show 4 earlier changesHide 4 earlier changes

NOTE12 OK, 2 NOTE2026-03-29
ERROR11 OK, 2 NOTE, 1 ERROR2026-03-22
NOTE12 OK, 2 NOTE2026-03-15
ERROR11 OK, 2 NOTE, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.21

READMEYes · 766 wordsVignettesNoNEWSYes · 67% structured · mentions 1.3.21Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 20 (2 internal)includes a package overview page
Examples that run: 42%5 run in a plain check · 7 never run
Exported functions with examples: 75%
Documented parameters: 99%
Return-value docs: 94%
Help pages citing references: 75%

How these are measured

Downloads

5.5K

CRAN downloads in the past year

Rank #5,885 · ~15/day · ~462/mo

Releases R versions

Daily download trend is not available in this view yet.

55130 days

1.4K90 days

5.5K1 year

Compare downloads with other packages →

Also on104 r2u4 autocran1.6K bioconda

How downloads are counted

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing jackstraw adds 45 packages (24 with compiled code, 26 MB of source tarballs). Heaviest: ggplot2 6.0 MB, rsvd 3.3 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.0.0

Imports (10)

methodsstatsstats4corpcor irlba rsvd ClusterRclusterBEDMatrix genio

LinkingTo (0)

none

Suggests (4)

qvalue lfa gcatest testthat

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 (4)

Neo Christopher Chung

Author, Maintainer since 1.0 (2014)

Wei Hao

Author · added in 1.1

Alejandro Ochoa

Author · added in 1.3.8

John D. Storey

Author · added in 1.1

Listed in earlier versions (2)

Chung

no longer listed · 1.3.15 to 1.3.21

Storey

no longer listed · 1.3.15 to 1.3.21

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-04-22
archivedRemoved from CRAN
2026-04-09
issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2024-02-07
archivedRemoved from CRAN
2024-01-11
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-11-25
archivedRemoved from CRAN
2022-05-23
check issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-06-11
archivedRemoved from CRAN
2021-05-27
check problems were not corrected in time
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26

Show 19 earlier eventsHide 19 earlier events

R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
2.15.3Latest
record
2013-01-28 · current release · diff ↗ ·
added 2 exports
jackstraw, permutationPA
1.3.21
record
2026-04-22 · diff ↗ ·
added 2 exports
ncp_est, pvals_nc_chisq
1.3.17
record
2024-09-16 · diff ↗
1.3.15
record
2024-08-30 · diff ↗ ·
added 2 exports
jackstraw_alstructure, jackstraw_lfa
1.3.9
record
2024-02-07 · diff ↗
1.3.8
record
2022-11-25 · diff ↗ ·
removed 2 exports
jackstraw_lfa, lfa.corpcor
1.3.1
record
2021-06-11 · diff ↗
1.3
record
2018-12-03 · diff ↗ ·
added 2 exports
jackstraw_irlba, jackstraw_rpca
1.2
record
2018-08-07 · diff ↗ ·
removed 5 exports
jackstraw, jackstraw.FUN, jackstraw.LFA, jackstraw.PCA, jackstraw.parametric

added 10 exports
find_k, jackstraw_MiniBatchKmeans, jackstraw_cluster, jackstraw_kmeans, jackstraw_kmeanspp, jackstraw_lfa, jackstraw_pam, jackstraw_pca, jackstraw_subspace, pip
1.1.1
record
2017-09-04 · diff ↗
1.1
record
2015-12-29 · diff ↗ ·
added 5 exports
jackstraw.FUN, jackstraw.LFA, jackstraw.PCA, jackstraw.parametric, lfa.corpcor
1.0
record
2014-01-31
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2013-01-28
Total releases: 12 / 13 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.0.0
Bundled data: 264 KB / 1 file
Download size: 314 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("jackstraw")

Format

Chung, N. C., Hao, W., Ochoa, A., & Storey, J. D. (2026). jackstraw: Statistical Inference for Unsupervised Learning (Version 1.3.21) [Computer software]. https://doi.org/10.32614/CRAN.package.jackstraw

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 jackstraw version 1.3.21 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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