R Observatory: Metrics for survPen version 2.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

survPen

Multidimensional Penalized Splines for (Excess) Hazard Models, Relative Mortality Ratio Models and Marginal Intensity Models

1packages dependsuggested by 2

30.3Kdownloads / year

83.7%test coverage

13/13flavors OK

Overview

About

Maintained by Mathieu FauvernierCRAN page ↗GitHub ↗Issues ↗

Fits (excess) hazard, relative mortality ratio or marginal intensity models with multidimensional penalized splines allowing for time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (thanks to explicit calculation of the derivatives of the likelihood) and offers a unified framework for multidimensional penalized hazard and excess hazard models. Later versions (>2.0.0) include penalized models for relative mortality ratio, and marginal intensity in recurrent event setting. survPen may be of interest to those who 1) analyse any kind of time-to-event data: mortality, disease relapse, machinery breakdown, unemployment, etc 2) wish to describe the associated hazard and to understand which predictors impact its dynamics, 3) wish to model the relative mortality ratio between a cohort and a reference population, 4) wish to describe the marginal intensity for recurrent event data. See Fauvernier et al. (2019a) doi:10.21105/joss.01434 for an overview of the package and Fauvernier et al. (2019b) doi:10.1111/rssc.12368 for the method.

Changes in 2.0.5

Changes:

The multiplicative model used as an illustration in the vignette had an incorrect specification. The t0 argument was lacking and therefore the start-stop nature of the data was not taken into account
Description of the output dataset of splitmult function added in the vignette
Description of the dataset HeartFailure added in the vignette

From NEWS in the release

Install

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

install.packages("survPen", 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("fauvernierma/survPen")

Development version from fauvernierma/survPen. 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-survpen

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-survPen

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-survPen

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: 8.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
NOTE12 OK, 1 NOTE2026-06-07

Show 4 earlier changesHide 4 earlier changes

OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.5

READMENoVignettesYes · 1 · dynamicNEWSYes · 33% structured · mentions 2.0.5Citation fileYes · cites a publication

Cites a JOSS paper

Help pages: 45
Examples that run: 96%23 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 65%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 13%

Vignettes (1)

Survival analysis with survPen

How these are measured

Downloads

30.3K

CRAN downloads in the past year

Rank #2,820 · ~83/day · ~2.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.9K30 days

5.3K90 days

30.3K1 year

Compare downloads with other packages →

Also on434 r2u2 autocran

How downloads are counted

Repository

fauvernierma/survpen ↗Account: fauvernierma

12Stars

1Forks

0Open issues

0Open PRs

5Releases

244Commits

3Commit identities

License file reads as GPL-3.0 · 244 commits · Last activity 2026-03-25 · The default branch showed an older version (2.0.3) than CRAN on 2026-10-21

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 48
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-09-05 · 122026-07-07 · 12

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/fauvernierma/survpen on 2026-10-21.

Continuous integration (2)

Travis CI (config file)AppVeyor

Governance and community (3)

Code of conductContributing guideSupport guide

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2026-03-25

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing survPen adds 3 packages (3 with compiled code, 3.6 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, statmod 91 KB.

Depends (1)

R >= 4.0.0

Imports (3)

statmodstatsRcpp

LinkingTo (2)

Rcpp RcppEigen

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

truncAIPW

Suggests, most downloaded first

rstpm2 SuperSurv

How these are counted

Code & Tests

Datasets

People & History

People (6)

Mathieu Fauvernier

Author, Maintainer since 1.0.0 (2019)

Laurent Remontet

Author · added in 1.1.0

Laurent Roche

Author · added in 1.1.0

Nadine Bossard

Contributor · added in 1.1.0

Elsa Coz

Contributor · added in 2.0.0

Zoe Uhry

Contributor · added in 1.1.0

Releases (15)

Pick two releases to compare their code metrics.

2.0.5Latest
record
2026-06-09 · current release · diff ↗
2.0.4
record
2026-05-09 · diff ↗
R
R 4.6.0 released · 2026-04-24
2.0.3
record
2026-03-20 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.0.2
record
2025-03-08 · diff ↗
2.0.1
record
2025-01-21 · diff ↗
2.0.0
record
2024-12-02 · diff ↗ ·
added 7 exports
CumulHazard, DerivCumulHazard, HazGL, Hess_rho_mult, grad_rho_mult, predSNS, splitmult
R
R 4.4.0 released · 2024-04-24
1.6.0
record
2023-09-14 · diff ↗ ·
added 1 export
pwcst
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.5.2
record
2021-09-11 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.5.1
record
2020-09-25 · diff ↗
1.5.0
record
2020-05-25 · diff ↗ ·
added 5 exports
%cross%, Hess_rho, colSums2, deriv_R, grad_rho

Show 8 earlier eventsHide 8 earlier events

R
R 4.0.0 released · 2020-04-24
1.3.0
record
2020-02-03 · diff ↗ ·
added 2 exports
%mult%, %vec%
1.2.0
record
2019-08-29 · diff ↗ ·
removed 2 exports
cor.var, inv.repam
1.1.0
record
2019-05-02 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0.1
record
2019-03-01 · diff ↗
1.0.0
record
2019-02-27
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-02-27
Total releases: 15 / 7 yrs
License: GPL-3 | file LICENSE OSI
Minimum R: ≥ 4.0.0
Bundled data: 148 KB / 4 files
Download size: 1.1 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("survPen")

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

It points to 10.21105/joss.01434.

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 survPen version 2.0.5 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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