R Observatory: Metrics for survex version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

survex

1.2.0Package record

Explainable Machine Learning in Survival Analysis

1packages dependsuggested by 1

5.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Mikołaj SpytekCRAN page ↗GitHub ↗Website ↗Issues ↗

Survival analysis models are commonly used in medicine and other areas. Many of them are too complex to be interpreted by human. Exploration and explanation is needed, but standard methods do not give a broad enough picture. 'survex' provides easy-to-apply methods for explaining survival models, both complex black-boxes and simpler statistical models. They include methods specific to survival analysis such as SurvSHAP(t) introduced in Krzyzinski et al., (2023) doi:10.1016/j.knosys.2022.110234, SurvLIME described in Kovalev et al., (2020) doi:10.1016/j.knosys.2020.106164 as well as extensions of existing ones described in Biecek et al., (2021) doi:10.1201/9780429027192.

Changes in 1.2.0

added new calculation_method for surv_shap() called "treeshap" that uses the treeshap package (#75)
enable to calculate SurvSHAP(t) explanations based on subsample of the explainer's data
changed default kernel width in SurvLIME from sqrt(p * 0.75) to sqrt(p) * 0.75
fixed error in SurvLIME when non-factor categorical_variables were provided

From NEWS.md in the release

Install

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

install.packages("survex", 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("ModelOriented/survex")

Development version from ModelOriented/survex. 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-survex

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-survex

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-survex

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: 3.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
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 1.2.0

READMEYes · 753 wordsVignettesNoNEWSYes · 100% structured · mentions 1.2.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 46 (6 internal)
Examples that run: 34%13 run in a plain check · 25 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 96%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

5.2K

CRAN downloads in the past year

Rank #6,453 · ~14/day · ~432/mo

Releases R versions

Daily download trend is not available in this view yet.

48130 days

1.3K90 days

5.2K1 year

Compare downloads with other packages →

Also on117 r2u6 autocran73 c2d4u

How downloads are counted

Repository

modeloriented/survex ↗Organization: ModelOriented

118Stars

10Forks

12Open issues

0Open PRs

3Releases

480Commits

6Commit identities

brier-scorescox-regressionexplainable-aiexplainable-machine-learningexplainable-mlexplanatory-model-analysisinterpretable-machine-learninginterpretable-ml

License file reads as GPL-3.0 · 480 commits · Last activity 2024-06-15 · 0% stars, 30d · Default branch at 1.2.0.9001, ahead of CRAN 1.2.0 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 26
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-06 · 1152026-09-04 · 118

How these are measured

PracticesBeta

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

Checks run against github.com/modeloriented/survex 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 (3)

pkgdown

GitHub Pages site last deployed 2024-06-15 · The repository has a site deploy workflow

pkgdown site last built 2024-06-15

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Installing survex adds 94 packages (44 with compiled code, 92 MB of source tarballs). Heaviest: stringi 11 MB, TH.data 8.2 MB, ggplot2 6.0 MB.

Depends (1)

R >= 3.5.0

Imports (6)

DALEX ggplot2 kernelshap pecsurvivalpatchwork

LinkingTo (0)

none

Suggests (20)

censored covr flexsurv gbm generics glmnet ingredients knitr mboost parsnip progressr randomForestSRC ranger reticulate rmarkdown rms testthat treeshap withr xgboost

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

highMLR

Suggests, most downloaded first

SuperSurv

How these are counted

Code & Tests

People & History

People (6)

Mikołaj Spytek

Author, Maintainer since 0.1.1 (2022)

Author

Author

Author

Author · added in 1.1.3

Lorenz A. Kapsner

Contributor · added in 1.2.0

Releases (5)

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
1.2.0Latest
record
2023-10-24 · current release · diff ↗
1.1.3
record
2023-09-06 · diff ↗ ·
added 4 exports
extract_predict_survshap, model_diagnostics, model_profile_2d, model_survshap
R
R 4.3.0 released · 2023-04-21
1.0.0
record
2023-03-20 · diff ↗ ·
added 3 exports
set_theme_survex, theme_default_survex, theme_vertical_default_survex
0.2.2
record
2022-12-01 · diff ↗ ·
added 2 exports
loss_adapt_mlr3proba, loss_integrate
0.1.1
record
2022-09-05
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-09-05
Total releases: 5 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Download size: 810 KB

Appears in task views

Survival Analysis

Cite

Cite this package

Run in R for the authors' entry:

citation("survex")

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 survex version 1.2.0 [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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