R Observatory: Metrics for pammtools version 0.8.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pammtools

0.8.1Package record

Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis

4packages dependsuggested by 3

62.7Kdownloads / year

90.9%test coverage

13/13flavors OK

Overview

About

Maintained by Andreas BenderCRAN page ↗GitHub ↗Website ↗Issues ↗

The Piece-wise exponential (Additive Mixed) Model (PAMM; Bender and others (2018) <doi: 10.1177/1471082X17748083>) is a powerful model class for the analysis of survival (or time-to-event) data, based on Generalized Additive (Mixed) Models (GA(M)Ms). It offers intuitive specification and robust estimation of complex survival models with stratified baseline hazards, random effects, time-varying effects, time-dependent covariates and cumulative effects (Bender and others (2019)), as well as support for left-truncated data as well as competing risks, recurrent events and multi-state settings. pammtools provides tidy workflow for survival analysis with PAMMs, including data simulation, transformation and other functions for data preprocessing and model post-processing as well as visualization.

Changes in 0.8.1

Enhancements

The cumulative post-processing functions (add_cumu_hazard(), add_surv_prob(), add_cif() -- for both their default and pamm_ic methods -- and add_trans_prob()) now **error** when newdata is not grouped so that the time variable is unique within each group (typically a forgotten group_by()), instead of silently accumulating cumulative quantities across distinct covariate profiles / causes / transitions and returning wrong curves. This generalises the guard already used for the interval-censoring pooling path (and mirrors the stopifnot() guard in the RMST example). All of these functions accept check_grouping = FALSE to opt out (e.g. for advanced workflows that intentionally accumulate over rows with varying covariates). The guard detects mis-grouping via repeated time values within a group: grids built with make_newdata() are always caught, but hand-built grids stacking profiles with *disjoint* time grids are indistinguishable from a single profile with time-varying covariates and pass undetected.

Show all changes in 0.8.1Hide the rest of the changes in 0.8.1

Documentation

Standardized the headings and subheadings in the package vignettes to sentence-style capitalization for consistency and readability.
Fixed function help page titles to follow sentence-style capitalization (as_ped, dplyr_verbs, geom_hazard, geom_stepribbon, gg_laglead, gg_state_occupation, pammtools). Also corrected typos in get_event_types (Exctract → Extract) and has_tdc (timd → time).
Updated pammtools.R help page to include all available vignettes: Bayesian, cumulative effects, interval-censored, model evaluation, multi-state, recurrent events, shape constraints, simulations, and xgboost backend.
Updated website configuration (_pkgdown.yml) to align navbar and reference section titles with vignette headlines and apply consistent sentence-style capitalization throughout the documentation site.

From NEWS.md in the release

Install

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

install.packages("pammtools", 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("adibender/pammtools")

Development version from adibender/pammtools. 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-pammtools

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-pammtools

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-pammtools

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: 6.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.8.1

READMEYes · 110 wordsVignettes· In the repository, left out of the releaseNEWSYes · 67% structured · mentions 0.8.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 104 (63 internal)includes a package overview page
Examples that run: 89%25 run in a plain check (1 of them under a condition) · 2 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 58%
Documented parameters: 95%
Return-value docs: 27%
Help pages citing references: 1%

How these are measured

Downloads

62.7K

CRAN downloads in the past year

Rank #1,716 · ~172/day · ~5.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

3.8K30 days

12.4K90 days

62.7K1 year

Compare downloads with other packages →

Also on2.1K r2u4 autocran102 c2d4u

How downloads are counted

Repository

adibender/pammtools ↗Account: adibender

51Stars

13Forks

12Open issues

2Open PRs

21Releases

1,373Commits

11Commit identities

rrstatssurvival-analysisadditive-modelspiece-wise-exponentialpammpammtools

1,373 commits · Last activity 2026-08-13 · 0% stars, 30d · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 87%
Median days to close, 50 most recently updated closed issues: 40
Median days to close, 50 most recently updated closed PRs: 5

Stars over time

2025-10-17 · 502026-07-07 · 51

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/adibender/pammtools on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-08-13 · The repository has a site deploy workflow

pkgdown site last built 2026-08-13, before release 0.8.1 (2026-08-25)

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Git structural (1)

.gitattributes

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-02-16
Named in .Rbuildignore: .claude
Named in .gitignore: .claude
Pull request it wrote: opened by a project member
Commits: 28 by its own account · at least 12 crediting it in the message
Codexfirst seen 2026-06-17
Named in .Rbuildignore: .codex

From outside contributors

Claude Code
Pull requests: 6 from outside contributors, first on 2026-06-02, 6 from forks

Models named in its commits

Claude Opus 4.88 commits · Jun to Jul 2026
Claude Opus 4.63 commits · Feb 2026
Claude Fable 51 commit · Jun 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing pammtools adds 99 packages (52 with compiled code, 88 MB of source tarballs). Heaviest: stringi 11 MB, TH.data 8.2 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1.0

Imports (16)

mgcvsurvivalcheckmate magrittr rlang tidyr ggplot2 dplyr purrr (>= 0.2.3)tibble lazyeval Formula mvtnorm pec vctrs (>= 0.3.0)scam

LinkingTo (0)

none

Suggests (5)

testthat mstate broom etm xgboost

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

6indirect

Imports 4

Suggested by 3

Depends, Imports or LinkingTo, most downloaded first

relsurv autoReg KMunicate robber

Suggests, most downloaded first

adjustedCurves contsurvplot weightedsurv

How these are counted

Code & Tests

Datasets

People & History

People (5)

Andreas Bender

Author, Maintainer since 0.1.7 (2018)

Philipp Kopper

Author · added in 0.5.4

Johannes Piller

Author · added in 0.7.3

Fabian Scheipl

Author

Lukas Burk

Contributor · added in 0.5.8

Releases (20)

Pick two releases to compare their code metrics.

0.8.1Latest
record
2026-06-22 · current release · diff ↗
0.8.0
record
2026-06-22 · diff ↗ ·
added 4 exports
add_inspections, gg_state_occupation, pamm_ic, pamm_ic_cr
R
R 4.6.0 released · 2026-04-24
0.7.4
record
2026-02-16 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.7.3
record
2025-03-24 · diff ↗ ·
added 2 exports
add_counterfactual_transitions, add_trans_prob
R
R 4.4.0 released · 2024-04-24
0.5.93
record
2024-02-25 · diff ↗
0.5.92
record
2023-07-13 · diff ↗ ·
removed 1 export
as_ped_recurrent

added 1 export
as_ped_multistate
R
R 4.3.0 released · 2023-04-21
0.5.91
record
2023-03-24 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.5.8
record
2022-01-09 · diff ↗ ·
removed 1 export
fill

added 1 export
distinct
0.5.7
record
2021-06-21 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.5.6
record
2021-03-29 · diff ↗

Show 13 earlier eventsHide 13 earlier events

0.5.4
record
2020-12-18 · diff ↗ ·
added 2 exports
add_cif, as_ped_recurrent
0.2.4
record
2020-06-06 · diff ↗
0.2.3
record
2020-05-27 · diff ↗ ·
removed 1 export
riskset_info
R
R 4.0.0 released · 2020-04-24
0.2.2
record
2020-03-12 · diff ↗
0.2.1
record
2020-02-09 · diff ↗ ·
added 2 exports
is.pamm, pamm
0.1.14
record
2019-09-08 · diff ↗ ·
removed 3 exports
add_term2, group_by_, split_tdc
R
R 3.6.0 released · 2019-04-26
0.1.11
record
2019-04-18 · diff ↗ ·
removed 3 exports
distinct_, rename_, select_

added 1 export
add_term2
0.1.9
record
2019-03-14 · diff ↗
0.1.8
record
2019-01-02 · diff ↗
0.1.7
record
2018-11-16
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-11-16
Total releases: 20 / 8 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 219 KB / 6 files
Download size: 487 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("pammtools")

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

It points to 10.1177/1471082x17748083.

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 pammtools version 0.8.1 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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