savvyr

0.1.2

Survival Analysis for AdVerse Events with VarYing Follow-Up Times

0packages depend

6.3Kdownloads / year

100.0%test coverage

13/13checks pass

Overview

About

Maintained by Thomas KuenzelFirst published 2024-02-203 releasesCRAN page ↗GitHub ↗

The SAVVY (Survival Analysis for AdVerse Events with VarYing Follow-Up Times) project is a consortium of academic and pharmaceutical industry partners that aims to improve the analyses of adverse event (AE) data in clinical trials through the use of survival techniques appropriately dealing with varying follow-up times and competing events, see Stegherr, Schmoor, Beyersmann, et al. (2021) doi:10.1186/s13063-021-05354-x. Although statistical methodologies have advanced, in AE analyses often the incidence proportion, the incidence density or a non-parametric Kaplan-Meier estimator are used, which either ignore censoring or competing events. This package contains functions to easily conduct the proposed improved AE analyses.

Install

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

install.packages("savvyr", 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("openpharma/savvyr")

Development version from openpharma/savvyr. 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-savvyr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-savvyr

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-savvyr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.3 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.46

100.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-06-08
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 50%

Downloads

6.3K

CRAN downloads in the past year

Rank #7,294 · ~17/day · ~524/mo

Releases R versions

Daily download trend is not available in this view yet.

30730 days

1.4K90 days

6.3K1 year

Compare downloads with other packages →

Also on92 r2u28 autocran

Repository

GitHub ↗ openpharma/savvyr

6Stars

1Forks

0Open issues

0Open PRs

1Releases

19Commits

5Contributors

19 commits · Last activity 2025-05-07 · 0% stars, 30d

Stars over time

2025-05-07 · 52026-07-07 · 6

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/openpharma/savvyr on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

Automation and maintenance (1)

pre-commit

Show all practices

Lint, format, editor (2)

lintrRStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (3)

checkmate etm Rdpack

LinkingTo (0)

none

Suggests (4)

kableExtra knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 665 (62%)Rd 290 (27%)Vignettes 116 (11%)

Code characteristics

Cyclomatic complexity: 1.0 median / 9 max
Test cases: 13 / 0.46 per code line

Test coverage

Line coverage

100%

Expression

100.0%

Tests / Examples

100.0% / 89% ex

Functions

7 6 exported

Complexity

2.3 avg / 9 max

Call network

7 nodes / 5 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

7 functions

Function	Cyclo	Coverage
aalen_johansen exp	9	100%
generate_data exp	1	100%
inc_prop exp	1	100%
one_minus_kaplan_meier exp	2	100%
prop_trans_inc_dens exp	1	100%
prop_trans_inc_dens_ce exp	1	100%

People & History

People (6)

Maintainer (1)

Thomas Kuenzel

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

F. Hoffmann-La Roche AG

Universität Ulm

Funders (2)

F. Hoffmann-La Roche AG

Universität Ulm

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.2Latest
2025-05-08 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.1
2024-06-10 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.0
2024-02-20
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-02-20
Total releases: 3 / 2 yrs
License: Apache License 2.0 OSI
Minimum R: ≥ 4.0
Download size: 635 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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