R Observatory: Metrics for mstate version 0.3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mstate

0.3.3Package record

Data Preparation, Estimation and Prediction in Multi-State Models

13packages dependsuggested by 14

171.6Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Hein PutterCRAN page ↗GitHub ↗Issues ↗

Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models, see Putter, Fiocco, Geskus (2007) doi:10.1002/sim.2712.

Changes in 0.3.3

Fixed issue with msprep() that occurred with very long vectors/mismatch between numeric id columns and integer id levels - thanks to @fumi-github for fixing #26
Fixed issue #16 inside msfit (dimension of hlp) - thanks to @MetzgerSK
Fixed issue #27 with msfit() and vartype=="aalen", similar to an issue in previous version - thanks to @MetzgerSK
Other fixes: #31 (dimensions preserved when transitions made by only one individual), #30 (two-state model with vartype=="aalen" now works), #13 (proper output returned for mssample() when output='data'),a minor issue with vis.mirror.pt(), Cuminc() update (coerces data to data.frame, and removes defunct failcode argument)

From NEWS.md in the release

Install

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

install.packages("mstate", 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("hputter/mstate")

Development version from hputter/mstate. 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-mstate

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-mstate

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-mstate

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

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘transhelp.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 4.4 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.3

READMEYes · 32 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.3.3Citation fileYes · cites a publication

Cites a JSS article

Help pages: 49includes a package overview page
Examples that run: 79%27 run in a plain check · 7 never run
Exported functions with examples: 79%
Documented parameters: 98%
Return-value docs: 90%
Help pages citing references: 43%

Vignettes (2)

How these are measured

Downloads

171.6K

CRAN downloads in the past year

Rank #872 · ~470/day · ~14.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

23.7K30 days

49.3K90 days

171.6K1 year

Compare downloads with other packages →

Also on2.8K r2u261 autocran3.4K conda_forge187 c2d4u

How downloads are counted

Repository

hputter/mstate ↗Account: hputter

16Stars

11Forks

9Open issues

0Open PRs

0Releases

136Commits

10Commit identities

136 commits · Last activity 2026-03-11 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 98
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-05-26 · 152026-07-07 · 16

How these are measured

PracticesBeta

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

Checks run against github.com/hputter/mstate on 2026-10-11.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-03-11

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing mstate adds 4 packages (2 with compiled code, 7.7 MB of source tarballs). Heaviest: data.table 5.7 MB, viridisLite 1.2 MB, rlang 766 KB.

Depends (1)

survival

Imports (5)

rlang data.tablelatticeRColorBrewer viridisLite

LinkingTo (0)

none

Suggests (5)

cmprsk ggplot2 knitr rmarkdown relsurv

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

13direct

53indirect

Depends 1 · Imports 12

Suggested by 14

Show all 27 packagesHide all 27 packages

Depends, Imports or LinkingTo, most downloaded first

flexsurv randomizeR Landmarking calibmsm ebmstate markovMSM maxcombo simIDM flassomsm icmstate dscoreMSM OptimalTiming presmoothedTP

Suggests, most downloaded first

rstpm2 msm riskRegression Epi pammtools popEpi hesim cohorttools PScr clusteredMSM survCurve mccount GFDrmtl survivalVignettes

How these are counted

Code & Tests

Datasets

People & History

People (6)

Hein Putter

Author, Maintainer since 0.2.1 (2009)

Edouard F. Bonneville

Author · added in 0.3.1

Marta Fiocco

Author

Liesbeth C. de Wreede

Author · added in 0.3.1

Ronald B. Geskus

Contributor · added in 0.3.1

Damjan Manevski

Contributor · added in 0.3.1

Listed in earlier versions (2)

Liesbeth de Wreede

no longer listed · 2.9.2 to 0.2.12

Ronald Geskus

no longer listed · 0.2.8 to 0.2.12

Releases (21)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
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R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31

Show 26 earlier eventsHide 26 earlier events

R
R 2.13.0 released · 2011-04-13
2.12.2Latest
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2011-01-06 · current release · diff ↗
R
R 2.12.0 released · 2010-10-15
2.12.0
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2010-10-12 · diff ↗
2.11.1
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2010-05-12 · diff ↗
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R 2.11.0 released · 2010-04-22
2.10.1
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2009-11-07 · diff ↗
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R 2.10.0 released · 2009-10-26
2.10.0
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2009-09-15 · diff ↗
2.9.2
record
2009-07-10 · diff ↗ ·
added 12 exports
msprep, events, paths, expand.covs, msfit, mssample, msboot, probtrans, Cuminc, redrank, trans.comprisk, trans.illdeath
0.3.3
record
2024-07-11 · diff ↗
0.3.2
record
2021-11-08 · diff ↗ ·
added 6 exports
haz_function, modify_transMat, msboot.relsurv, msboot.relsurv.boot, msfit.relsurv, varHaz.fixed
0.3.1
record
2020-12-17 · diff ↗ ·
added 13 exports
MarkovTest, absorbing, etm2msdata, is.circular, msdata2etm, optimal_weights_matrix, optimal_weights_multiple, to.trans2, tra2trans, trans2Q, trans2tra, vis.mirror.pt, vis.multiple.pt
0.2.12
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2019-12-11 · diff ↗
0.2.11
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2018-04-09 · diff ↗
0.2.10
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2016-12-04 · diff ↗
0.2.9
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2016-02-29 · diff ↗ ·
added 1 export
LMAJ
0.2.8
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2015-12-06 · diff ↗
0.2.7
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2014-05-30 · diff ↗ ·
added 3 exports
ELOS, xsect, cutLMms
0.2.6
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2011-01-06 · diff ↗ ·
added 1 export
crprep
0.2.5
record
2010-10-12 · diff ↗
0.2.4
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2010-06-02 · diff ↗
0.2.3
record
2009-11-06 · diff ↗ ·
added 1 export
transMat
0.2.2
record
2009-09-24 · diff ↗
0.2.1
record
2009-07-21
R
R 2.9.0 released · 2009-04-17

Package metadata

First published: 2009-07-10
Total releases: 21 / 17 yrs
License: GPL (>= 2) OSI
Bundled data: 166 KB / 8 files
Download size: 900 KB

Appears in task views

Epidemiology Survival Analysis

Cite

Cite this package

Run in R for the authors' entry:

citation("mstate")

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

It points to 10.18637/jss.v038.i07.

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 mstate version 0.3.3 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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