R Observatory: Metrics for rstpm2 version 1.7.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rstpm2

1.7.1Package record

Smooth Survival Models, Including Generalized Survival Models

10packages dependsuggested by 10

173.3Kdownloads / year

31.7%test coverage

13/13flavors OK

Overview

About

Maintained by Mark ClementsCRAN page ↗GitHub ↗Issues ↗

R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth doi:10.1177/0962280216664760. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects doi:10.1002/sim.7451, and copulas. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0(t)=exp(-exp(eta_0(t))) is modelled for natural splines for eta_0, and the time-dependent cumulative acceleration factor eta(t,x)=\int_0^t exp(eta_1(u,x)) du for log acceleration factor eta_1(u,x). The Markov multi-state models allow for a range of models with smooth transitions to predict transition probabilities, length of stay, utilities and costs, with differences, ratios and standardisation.

Install

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

install.packages("rstpm2", 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("mclements/rstpm2")

Development version from mclements/rstpm2. 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-rstpm2

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-rstpm2

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-rstpm2

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

Additional issues

rcnst

CRAN check page ↗

Slowest check: 9.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.7.1

READMEYes · 323 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · does not mention 1.7.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 35
Examples that run: 91%21 run in a plain check · 2 never run
Exported functions with examples: 75%
Documented parameters: 90%
Return-value docs: 100%
Help pages citing references: 80%

Vignettes (4)

How these are measured

Downloads

173.3K

CRAN downloads in the past year

Rank #904 · ~475/day · ~14.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

23.1K30 days

46.7K90 days

173.3K1 year

Compare downloads with other packages →

Also on2.7K r2u13 autocran7.5K conda_forge232 c2d4u

How downloads are counted

Repository

mclements/rstpm2 ↗Account: mclements

31Stars

12Forks

8Open issues

1Open PRs

6Releases

812Commits

13Commit identities

812 commits · Last activity 2025-08-27 · The default branch showed an older version (1.7.0) than CRAN on 2026-10-11

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 147
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/mclements/rstpm2 on 2026-10-11.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing rstpm2 adds 8 packages (6 with compiled code, 4.5 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppArmadillo 1.0 MB, mvtnorm 1.0 MB.

Depends (4)

R >= 3.0.2methodssurvivalsplines

Imports (11)

graphicsRcppstatsmgcvbbmle fastGHQuadutilsparallelmvtnorm numDeriv lsoda

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (10)

eha testthat ggplot2latticereadstata13 mstate scales survPen flexsurv timereg

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

10direct

49indirect

Depends 1 · Imports 9

Suggested by 10

Show all 20 packagesHide all 20 packages

Depends, Imports or LinkingTo, most downloaded first

flexsurv eventPred JointFPM expertsurv afthd EventPredInCure fmx cuRe survalis TukeyGH77

Suggests, most downloaded first

insight marginaleffects tram multinma simsurv biostat3 rsimsum fastml mexhaz rpsurv

How these are counted

Code & Tests

Datasets

People & History

People (10)

Mark Clements

Author, Maintainer since 1.2.2 (2015)

Benjamin Christoffersen

Author · added in 1.5.2

Xing-Rong Liu

Author

Alessandro Gasparini

Contributor · added in 1.4.4

Lasse Hjort Jakobsen

Contributor · added in 1.4.4

Paul Lambert

Contributor

Patrick Alken

Copyright holder · added in 1.4.4

Gordon Smyth

Copyright holder · added in 1.4.4

Rhys Ulerich

Copyright holder · added in 1.4.4

Simon Wood

Copyright holder · added in 1.4.4

Releases (28)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.7.1Latest
record
2025-11-13 · current release · diff ↗
1.7.0
record
2025-08-27 · diff ↗
1.6.9
record
2025-07-25 · diff ↗
1.6.7
record
2025-05-11 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.6.6.1
record
2024-12-21 · diff ↗
1.6.6
record
2024-10-29 · diff ↗
1.6.5
record
2024-08-20 · diff ↗
1.6.4
record
2024-08-19 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.6.3
record
2023-12-05 · diff ↗ ·
removed 2 exports
aft_mixture, aft_integrated

added 2 exports
voptimize, voptimise
R
R 4.3.0 released · 2023-04-21
1.6.2
record
2023-03-08 · diff ↗
1.6.1
record
2023-02-28 · diff ↗ ·
added 2 exports
aft_mixture, aft_integrated
1.5.9
record
2023-01-07 · diff ↗

Show 24 earlier eventsHide 24 earlier events

1.5.8
record
2022-10-17 · diff ↗ ·
added 1 export
gsm_design
1.5.7
record
2022-07-14 · diff ↗ ·
added 1 export
smoothpwc
1.5.6
record
2022-05-10 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.5.5
record
2022-04-19 · diff ↗ ·
added 2 exports
markov_sde, bhazard
R
R 4.1.0 released · 2021-05-18
1.5.2
record
2021-03-03 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.5.1
record
2019-11-06 · diff ↗
1.5.0
record
2019-10-15 · diff ↗ ·
added 10 exports
gsm, markov_msm, ratio_markov_msm, zeroModel, hrModel, aftModel, addModel, hazFun, splineFun, standardise
R
R 3.6.0 released · 2019-04-26
1.4.5
record
2019-01-17 · diff ↗
1.4.4
record
2018-11-01 · diff ↗ ·
added 1 export
vuniroot
1.4.2
record
2018-05-29 · diff ↗ ·
added 5 exports
eform, coef, confint, predictnl.default, confint.predictnl
R
R 3.5.0 released · 2018-04-23
1.4.1
record
2017-09-20 · diff ↗
1.4.0
record
2017-08-31 · diff ↗ ·
added 2 exports
aft, nsxD
R
R 3.4.0 released · 2017-04-21
1.3.4
record
2016-10-09 · diff ↗ ·
added 1 export
cox.tvc
R
R 3.3.0 released · 2016-05-03
1.3.2
record
2016-04-13 · diff ↗
1.3.1
record
2016-02-24 · diff ↗
1.2.2
record
2015-07-26
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-07-26
Total releases: 28 / 11 yrs
License: GPL-2 | GPL-3 OSI
Minimum R: ≥ 3.0.2
Bundled data: 119 KB / 4 files
Download size: 1.1 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("rstpm2")

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

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 rstpm2 version 1.7.1 [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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