R Observatory: Metrics for slideimp version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

slideimp

1.2.0Package record

Numeric Matrices K-NN and PCA Imputation

0packages depend

4Kdownloads / year

77.3%test coverage

13/13flavors OK

Overview

About

Maintained by Hung PhamCRAN page ↗GitHub ↗Website ↗Issues ↗

Fast k-nearest neighbors (K-NN) and principal component analysis (PCA) imputation algorithms for missing values in epigenetic data or other high-dimensional numeric matrices. For PCA, a locally optimal block preconditioned conjugate gradient (LOBPCG) eigensolver with warm starts of both the eigenblock and search direction is also supported. Two complementary imputation strategies are available. Group-wise imputation (e.g., by chromosome) is recommended for Illumina DNA methylation microarrays (e.g., 450K, EPIC) and other matrices with groupable columns. A sliding window approach for K-NN or PCA imputation is recommended only for whole-genome methylation data such as whole-genome bisulfite sequencing (WGBS) or Enzymatic Methyl-seq (EM-seq). The package also supports hyperparameter tuning via repeated cross-validation. The K-NN algorithm is described in: Hastie, T., Tibshirani, R., Sherlock, G., Eisen, M., Brown, P. and Botstein, D. (1999) "Imputing Missing Data for Gene Expression Arrays". The PCA imputation is an optimized reimplementation of the imputePCA() function from the 'missMDA' package described in: Josse, J. and Husson, F. (2016) doi:10.18637/jss.v070.i01 "missMDA: A Package for Handling Missing Values in Multivariate Data Analysis".

Changes in 1.2.0

Breaking changes

knn_imp() no longer supports Ball Tree-based imputation due to lower

accuracy compared to brute-force K-NN.

New features

pca_imp() gained a .progress argument to display imputation progress.

Minor improvements and fixes

Fixed pca_imp() tests that broke due to upstream changes in

missMDA::imputePCA() and FactoMineR::svd.triplet().

Implemented an internal .crate() function, a minimal version of

carrier::crate().

DESCRIPTION now describes the LOBPCG eigensolver and its warm-start

behavior across EM iterations in pca_imp().

Show all changes in 1.2.0Hide the rest of the changes in 1.2.0

Minor wording improvements.
Added citation information.

From NEWS.md in the release

Install

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

install.packages("slideimp", 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("hhp94/slideimp")

Development version from hhp94/slideimp. 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-slideimp

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-slideimp

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-slideimp

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: 9.4 min · r-oldrel-macos-arm64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-21
ERROR11 OK, 2 ERROR2026-06-12
OK12 OK2026-04-25

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 2 NOTE, 1 ERROR2026-04-17
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.0

READMEYes · 958 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.2.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

The repository also keeps web-only articles.

Description cites a JSS article

Help pages: 18 (1 internal)includes a package overview page
Examples that run: 100%17 run in a plain check (2 of them under a condition)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 11%

Vignettes (1)

slideimp HTML

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #18,736 · ~11/day · ~333/mo

Releases R versions

Daily download trend is not available in this view yet.

25830 days

68590 days

4K1 year

Compare downloads with other packages →

Also on295 r2u12 autocran

How downloads are counted

Repository

hhp94/slideimp ↗Account: hhp94

0Stars

0Forks

0Open issues

0Open PRs

6Releases

214Commits

1Commit identities

License file reads as GPL-2.0 · 214 commits · Last activity 2026-09-28 · Default branch at 1.2.0.11, ahead of CRAN 1.2.0 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 91%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 0

Releases over time

2025-12-23 · 12026-07-07 · 6

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/hhp94/slideimp on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-08-12 · The repository has a site deploy workflow

pkgdown site last built 2026-08-12

Lint, format, editor (1)

Air

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-04-22
Seen in the repository: CLAUDE.md
Named in .Rbuildignore: .claude, CLAUDE.md

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing slideimp adds 13 packages (10 with compiled code, 21 MB of source tarballs). Heaviest: BH 14 MB, Rcpp 1.8 MB, collapse 1.4 MB.

Depends (1)

R >= 4.3.0

Imports (8)

bigmemory checkmate cli collapse mirai Rcppstatsutils

LinkingTo (3)

Rcpp RcppArmadillo RcppThread

Suggests (6)

knitr missMDA RhpcBLASctl rmarkdown testthat withr

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)

Hung Pham

Posit Software, PBC

Copyright holder · added in 1.2.0

Copyright holder of code adapted from the 'carrier' package, MIT licensed

Releases (4)

Pick two releases to compare their code metrics.

1.2.0Latest
record
2026-06-16 · current release · diff ↗
1.1.0
record
2026-05-01 · diff ↗ ·
removed 1 export
register_group_resolver

added 3 exports
lobpcg_control, mat_miss, slideimp_resolve_group
R
R 4.6.0 released · 2026-04-24
1.0.0
record
2026-04-16 · diff ↗ ·
removed 1 export
group_features

added 3 exports
prep_groups, register_group_resolver, sample_na_loc
0.5.4
record
2026-01-07
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-01-07
Total releases: 4 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.3.0
Download size: 132 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("slideimp")

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

It points to 10.1093/bioinformatics/btag318.

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 slideimp version 1.2.0 [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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