R Observatory: Metrics for penAFT version 0.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

penAFT

0.3.2Package record

Fit the Semiparametric Accelerated Failure Time Model with Elastic Net and Sparse Group Lasso Penalties

1packages depend

3.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Aaron J. MolstadCRAN page ↗GitHub ↗Website ↗Issues ↗

The semiparametric accelerated failure time (AFT) model is an attractive alternative to the Cox proportional hazards model. This package provides a suite of functions for fitting one popular rank-based estimator of the semiparametric AFT model, the regularized Gehan estimator. Specifically, we provide functions for cross-validation, prediction, coefficient extraction, and visualizing both trace plots and cross-validation curves. For further details, please see Suder, P. M. and Molstad, A. J., (2022) Scalable algorithms for semiparametric accelerated failure time models in high dimensions, Statistics in Medicine doi:10.1002/sim.9264.

Install

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

install.packages("penAFT", 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("ajmolstad/penAFT")

Development version from ajmolstad/penAFT. 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-penaft

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-penAFT

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-penAFT

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: 4.1 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.2

READMENoVignettesNoNEWSNoCitation fileNoWebsiteYes

Help pages: 8includes a package overview page
Examples that run: 86%6 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #12,822 · ~9/day · ~286/mo

Releases R versions

Daily download trend is not available in this view yet.

41730 days

86890 days

3.4K1 year

Compare downloads with other packages →

Also on342 r2u6 autocran

How downloads are counted

Repository

ajmolstad/penaft ↗Account: ajmolstad

1Stars

1Forks

0Open issues

0Open PRs

0Releases

96Commits

3Commit identities

survival-analysisvariable-selection

96 commits · Last activity 2024-12-03

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

Checks run against github.com/ajmolstad/penaft on 2026-10-11.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing penAFT adds 20 packages (10 with compiled code, 17 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, isoband 1.5 MB.

Depends (0)

none

Imports (4)

RcppMatrixggplot2 irlba

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

SMAHP

How these are counted

Code & Tests

People & History

People (2)

Aaron J. Molstad

Author, Maintainer since 0.2.0 (2022)

Piotr M. Suder

Author

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.3.2Latest
record
2025-06-16 · current release · diff ↗
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
0.3.0
record
2023-04-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.2.0
record
2022-01-25
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-25
Total releases: 3 / 4 yrs
License: GPL (>= 2) OSI
Download size: 19 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("penAFT")

Format

Molstad, A. J., & Suder, P. M. (2025). penAFT: Fit the Semiparametric Accelerated Failure Time Model with Elastic Net and Sparse Group Lasso Penalties (Version 0.3.2) [Computer software]. https://doi.org/10.32614/CRAN.package.penAFT

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 penAFT version 0.3.2 [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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