R Observatory: Metrics for casebase version 0.10.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

casebase

0.10.7Package record

Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression

0packages dependsuggested by 1

35.3Kdownloads / year

65.7%test coverage

13/13flavors OK

Overview

About

Maintained by Sahir BhatnagarCRAN page ↗GitHub ↗Website ↗Issues ↗

Fit flexible and fully parametric hazard regression models to survival data with single event type or multiple competing causes via logistic and multinomial regression. Our formulation allows for arbitrary functional forms of time and its interactions with other predictors for time-dependent hazards and hazard ratios. From the fitted hazard model, we provide functions to readily calculate and plot cumulative incidence and survival curves for a given covariate profile. This approach accommodates any log-linear hazard function of prognostic time, treatment, and covariates, and readily allows for non-proportionality. We also provide a plot method for visualizing incidence density via population time plots. Based on the case-base sampling approach of Hanley and Miettinen (2009) DOI:10.2202/1557-4679.1125, Saarela and Arjas (2015) DOI:10.1111/sjos.12125, and Saarela (2015) DOI:10.1007/s10985-015-9352-x.

Changes in 0.10.7

Fix CRAN check errors caused by visreg 3.0's breaking argument rename: print.cond is now print_cond in plot.singleEventCB(type = "hazard").
visreg is now required to be >= 3.0.0 in Suggests.
Updated the "Plot Hazards and Hazard Ratios" vignette to drop the now-removed gg argument (visreg 3.0 always returns a ggplot object) and to remove the obsolete visreg2d perspective/image plot example.

From NEWS.md in the release

Install

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

install.packages("casebase", 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("sahirbhatnagar/casebase")

Development version from sahirbhatnagar/casebase. 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-casebase

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-casebase

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-casebase

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 OK2026-09-10
ERROR11 OK, 2 ERROR2026-07-29
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.10.7

READMEYes · 638 wordsVignettesYes · 7 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 0.10.7Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 15
Examples that run: 100%11 run in a plain check (3 of them under a condition)
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 47%

Vignettes (7)

How these are measured

Downloads

35.3K

CRAN downloads in the past year

Rank #2,262 · ~97/day · ~2.9K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.4K30 days

7.5K90 days

35.3K1 year

Compare downloads with other packages →

Also on201 r2u24 autocran189 c2d4u

How downloads are counted

Repository

sahirbhatnagar/casebase ↗Account: sahirbhatnagar

8Stars

5Forks

14Open issues

0Open PRs

5Releases

526Commits

4Commit identities

survival-analysiscox-regressioncompeting-risksrregression-models

526 commits · Last activity 2026-09-03

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 7
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-25 · 82026-07-07 · 8

How these are measured

PracticesBeta

14 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/sahirbhatnagar/casebase on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (1)

Code of conduct

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-09-03 · The repository has a site deploy workflow

pkgdown site last built 2026-09-03

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Lint, format, editor (2)

lintrRStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-09-03
Pull request it wrote: opened by a project member
Commits: at least 6 crediting it in the message

Models named in its commits

Claude Sonnet 56 commits · Sep 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

14 external dependencies (excludes base and recommended)

Installing casebase adds 19 packages (9 with compiled code, 21 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, VGAM 1.7 MB.

Depends (1)

R >= 3.5.0

Imports (7)

data.table ggplot2methodsmgcvstatssurvivalVGAM

LinkingTo (0)

none

Suggests (12)

colorspace covr dplyr eha glmnet knitr lubridate progress rmarkdownsplinestestthat visreg (>= 3.0.0)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

riskRegression

How these are counted

Code & Tests

Datasets

People & History

People (5)

Sahir Bhatnagar

Author, Maintainer since 0.1.0 (2017)

https://sahirbhatnagar.com/

James Hanley

Author

https://jhanley.biostat.mcgill.ca/

Jesse Islam

Author · added in 0.9.0

https://www.jesseislam.com/

Olli Saarela

Author

https://www.dlsph.utoronto.ca/faculty-profile/saarela-olli/

Maxime Turgeon

Author

https://www.maxturgeon.ca/

Releases (9)

Pick two releases to compare their code metrics.

0.10.7Latest
record
2026-09-03 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.10.6
record
2024-08-18 · diff ↗
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2024-04-10
0.10.5
record
2024-04-10 · diff ↗
archivedRemoved from CRAN
2024-04-04
issues were not corrected in time
0.10.4
record
2024-02-02 · diff ↗
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-11-16
0.10.3
record
2022-11-16 · diff ↗
archivedRemoved from CRAN
2022-11-11
issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
0.10.1
record
2021-10-20 · diff ↗
R
R 4.1.0 released · 2021-05-18

Show 7 earlier eventsHide 7 earlier events

0.9.1
record
2021-02-07 · diff ↗
0.9.0
record
2020-07-04 · diff ↗ ·
added 4 exports
absoluteRisk.CompRisk, fitSmoothHazard.fit, hazardPlot, prepareX
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
0.1.0
record
2017-04-29
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-04-29
Total releases: 9 / 9 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 293 KB / 6 files
Download size: 3.5 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("casebase")

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 casebase version 0.10.7 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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