rstpm2

1.7.1

Smooth Survival Models, Including Generalized Survival Models

19packages depend

175.9Kdownloads / year

31.7%test coverage

13/13checks pass

Overview

About

Maintained by Mark ClementsFirst published 2015-07-2628 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

13OK

Slowest check: 9.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.11

31.7%

Coverage · measured lines

94%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 323 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 94%
Documented parameters: 90%
Return-value docs: 100%
References docs: 80%

Downloads

175.9K

CRAN downloads in the past year

Rank #1,073 · ~482/day · ~14.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

10.7K30 days

38.4K90 days

175.9K1 year

Compare downloads with other packages →

Also on4.7K r2u29 autocran7.8K conda_forge118 c2d4u

Repository

GitHub ↗ mclements/rstpm2

31Stars

12Forks

8Open issues

1Open PRs

6Releases

812Commits

13Contributors

812 commits · Last activity 2025-08-27

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/mclements/rstpm2 on 2026-07-26.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

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

19direct

46indirect

cuRe EventPredInCure JointFPM TukeyGH77 afthd eventPred expertsurv flexsurv fmx survalis biostat3 fastml insight marginaleffects mexhaz multinma rsimsum simsurv tram

Code & Tests

Datasets

People & History

People (10)

Maintainer (1)

Mark Clements

Author, Maintainer

Authors (3)

Mark Clements

Author, Maintainer

Benjamin Christoffersen

Author · added in 1.5.2

Xing-Rong Liu

Author

Contributors (3)

Alessandro Gasparini

Contributor · added in 1.4.4

Lasse Hjort Jakobsen

Contributor · added in 1.4.4

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.7.1Latest
2025-11-13 · current release · diff ↗
1.7.0
2025-08-27 · diff ↗
1.6.9
2025-07-25 · diff ↗
1.6.7
2025-05-11 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.6.6.1
2024-12-21 · diff ↗
1.6.6
2024-10-29 · diff ↗
1.6.5
2024-08-20 · diff ↗
1.6.4
2024-08-19 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.6.3
2023-12-05 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.6.2
2023-03-08 · diff ↗
1.6.1
2023-02-28 · diff ↗
1.5.9
2023-01-07 · diff ↗

Show 24 earlier events

1.5.8
2022-10-17 · diff ↗
1.5.7
2022-07-14 · diff ↗
1.5.6
2022-05-10 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.5.5
2022-04-19 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.5.2
2021-03-03 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.5.1
2019-11-06 · diff ↗
1.5.0
2019-10-15 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.4.5
2019-01-17 · diff ↗
1.4.4
2018-11-01 · diff ↗
1.4.2
2018-05-29 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.4.1
2017-09-20 · diff ↗
1.4.0
2017-08-31 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.3.4
2016-10-09 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.3.2
2016-04-13 · diff ↗
1.3.1
2016-02-24 · diff ↗
1.2.2
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
Installed size: not tracked yet
With dependencies: not tracked yet

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