R Observatory: Metrics for pensim version 1.3.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pensim

1.3.6Package record

Simulation of High-Dimensional Data and Parallelized Repeated Penalized Regression

0packages depend

3.2Kdownloads / year

50.4%test coverage

11/13flavors OK

Overview

About

Maintained by Levi WaldronCRAN page ↗GitHub ↗Website ↗Issues ↗

Simulation of continuous, correlated high-dimensional data with time to event or binary response, and parallelized functions for Lasso, Ridge, and Elastic Net penalized regression with repeated starts and two-dimensional tuning of the Elastic Net.

Install

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

install.packages("pensim", 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("waldronlab/pensim")

Development version from waldronlab/pensim. 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-pensim

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-pensim

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-pensim

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Levi Waldron <lwaldron.research@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Levi",
                    family = "Waldron",
                    role = c("aut", "cre"),
                    email = "lwaldron.research@gmail.com")
as necessary.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 2.7 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.6

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 9includes a package overview page
Examples that run: 100%9 run in a plain check
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 89%

Vignettes (1)

pensim package user guide

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #14,047 · ~9/day · ~267/mo

Releases R versions

Daily download trend is not available in this view yet.

33730 days

83790 days

3.2K1 year

Compare downloads with other packages →

Also on71 r2u2 autocran

How downloads are counted

Repository

waldronlab/pensim ↗Organization: waldronlab

0Stars

1Forks

0Open issues

0Open PRs

0Releases

40Commits

1Commit identities

40 commits · Last activity 2022-12-06

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 125
Median days to close, 50 most recently updated closed PRs: not measured

How these are measured

PracticesBeta

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

Checks run against github.com/waldronlab/pensim on 2026-10-22.

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 (3)

pkgdown

GitHub Pages site last deployed 2022-12-06 · The repository has a site deploy workflow

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing pensim adds 3 packages (3 with compiled code, 3.2 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppArmadillo 1.0 MB, penalized 374 KB.

Depends (1)

R >= 2.10.0

Imports (4)

methodsparallelpenalizedMASS

LinkingTo (0)

none

Suggests (4)

survivalROCsurvivalrmarkdown knitr

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 (from the free-text Author field) (1)

Levi Waldron

Maintainer since 1.0.1 (2011)

Listed in earlier versions (6)

Show 6 peopleHide 6 people

C. Huttenhower*

no longer listed · 1.0.2 to 1.2.9

I. Jurisica*

no longer listed · 1.0.2 to 1.2.9

M. Pintilie

no longer listed · 1.0.2 to 1.2.9

L. Waldron

no longer listed · 1.0.2 to 1.2.9

F. A. Shepherd

no longer listed · 1.0.3 to 1.2.9

M.-S. Tsao

no longer listed · 1.0.3 to 1.2.9

Releases (13)

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
1.3.6Latest
record
2022-12-09 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.3.3
record
2021-05-11 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.3.2
record
2020-04-20 · diff ↗
1.3.1
record
2020-03-28 · 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
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16

Show 15 earlier eventsHide 15 earlier events

R
R 3.1.0 released · 2014-04-10
1.2.9
record
2014-03-14 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.2.6
record
2013-01-15 · diff ↗
R
R 2.15.0 released · 2012-03-30
1.2.4
record
2012-02-23 · diff ↗ ·
removed 1 export
pattern:.

added 6 exports
opt1D, opt2D, opt.nested.crossval, create.data, opt.splitval, scan.l1l2
1.2.1
record
2012-01-23 · diff ↗
1.1.4
record
2012-01-22 · diff ↗ ·
added 1 export
pattern:.
R
R 2.14.0 released · 2011-10-31
1.1.3
record
2011-07-23 · diff ↗
1.0.3
record
2011-06-30 · diff ↗
R
R 2.13.0 released · 2011-04-13
1.0.2
record
2011-02-03 · diff ↗
1.0.1
record
2011-01-25
R
R 2.12.0 released · 2010-10-15

Package metadata

First published: 2011-01-25
Total releases: 13 / 15 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10.0
Bundled data: 2.0 MB / 3 files
Download size: 2.3 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("pensim")

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

It points to 10.1093/bioinformatics/btr591.

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 pensim version 1.3.6 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →