R Observatory: Metrics for survextrap version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

survextrap

1.0.1Package record

Bayesian Flexible Parametric Survival Modelling and Extrapolation

0packages depend

6.3Kdownloads / year

86.9%test coverage

13/13flavors OK

Overview

About

Maintained by Christopher JacksonCRAN page ↗GitHub ↗Website ↗Issues ↗

Survival analysis using a flexible Bayesian model for individual-level right-censored data, optionally combined with aggregate data on counts of survivors in different periods of time. An M-spline is used to describe the hazard function, with a prior on the coefficients that controls over-fitting. Proportional hazards or flexible non-proportional hazards models can be used to relate survival to predictors. Additive hazards (relative survival) models, waning treatment effects, and mixture cure models are also supported. Priors can be customised and calibrated to substantive beliefs. Posterior distributions are estimated using 'Stan', and outputs are arranged in a tidy format. See Jackson (2023) doi:10.1186/s12874-023-02094-1.

Changes in 1.0.1

Minor changes to links in vignettes to satisfy CRAN check.

From NEWS.md in the release

Install

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

install.packages("survextrap", 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("chjackson/survextrap")

Development version from chjackson/survextrap. 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-survextrap

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-survextrap

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 19.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
ERROR12 OK, 1 ERROR2026-07-27
OK13 OK2026-06-09

Show 5 earlier changesHide 5 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 786 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 1.0.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 43 (1 internal)includes a package overview page
Examples that run: 100%3 run in a plain check
Exported functions with examples: 6%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 16%

Vignettes (3)

How these are measured

Downloads

6.3K

CRAN downloads in the past year

Rank #8,306 · ~17/day · ~527/mo

Releases R versions

Daily download trend is not available in this view yet.

42130 days

1.1K90 days

6.3K1 year

Compare downloads with other packages →

Also on368 r2u

How downloads are counted

Repository

chjackson/survextrap ↗Account: chjackson

13Stars

7Forks

3Open issues

0Open PRs

4Releases

202Commits

2Commit identities

License file reads as GPL-3.0 · 202 commits · Last activity 2026-03-10 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 16
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-29 · 112026-08-21 · 13

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/chjackson/survextrap 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 2026-03-10 · The repository has a site deploy workflow

pkgdown site last built 2022-06-30, before release 1.0.1 (2026-01-13)

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

29 external dependencies (excludes base and recommended)

Installing survextrap adds 49 packages (24 with compiled code, 45 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, loo 2.7 MB.

Depends (2)

R >= 3.5.0survival

Imports (9)

ggplot2 gridExtra loomethodsposterior Rcpp rstan splines2 tibble

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.26.0)

Suggests (16)

rstantools knitr rmarkdown testthat SHELF flexsurv flexsurvcuresplinesdplyr viridis forcats fs purrr tidyr stringr survminer

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Christopher Jackson

Michael Sweeting

Contributor

Iain Timmins

Contributor

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.1Latest
record
2026-01-13 · current release · diff ↗ ·
added 1 export
prior_sample
1.0
record
2025-06-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-06-10
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 8.8 KB / 5 files
Download size: 2.1 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("survextrap")

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

It points to 10.1186/s12874-023-02094-1.

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 survextrap version 1.0.1 [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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