penAFT

0.3.2

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

1packages depend

3.5Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Aaron J. MolstadFirst published 2022-01-253 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 86%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.5K

CRAN downloads in the past year

Rank #14,695 · ~9/day · ~288/mo

Releases R versions

Daily download trend is not available in this view yet.

16330 days

70290 days

3.5K1 year

Compare downloads with other packages →

Also on405 r2u7 autocran

Repository

GitHub ↗ ajmolstad/penaft

1Stars

1Forks

0Open issues

0Open PRs

0Releases

96Commits

3Contributors

survival-analysisvariable-selection

96 commits · Last activity 2024-12-03

Repository practices

Upstream repositoryBeta

Checks run against github.com/ajmolstad/penaft on 2026-08-02.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

RcppMatrixggplot2 irlba

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

SMAHP

Code & Tests

People & History

People (2)

Maintainer (1)

Aaron J. Molstad

Author, Maintainer

Authors (2)

Aaron J. Molstad

Author, Maintainer

Piotr M. Suder

Author

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.3.2Latest
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
2023-04-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.2.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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