AdverseEvents

0.0.5

'shiny' Application for Adverse Event Analysis of 'OnCore' Data

0packages depend

5.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Z ThompsonFirst published 2024-11-045 releasesCRAN page ↗GitHub ↗

An application for analysis of Adverse Events, as described in Chen, et al., (2023) doi:10.3390/cancers15092521. The required data for the application includes demographics, follow up, adverse event, drug administration and optional tumor measurement data. The app can produce swimmers plots of adverse events, Kaplan-Meier plots and Cox Proportional Hazards model results for the association of adverse event biomarkers and overall survival and progression free survival. The adverse event biomarkers include occurrence of grade 3, low grade (1-2), and treatment related adverse events. Plots and tables of results are downloadable.

Install

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

install.packages("AdverseEvents", 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("dungtsa/AdverseEvents")

Development version from dungtsa/AdverseEvents. 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-adverseevents

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-AdverseEvents

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-AdverseEvents

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

Health

CRAN checks

13OK

Slowest check: 3.4 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,277 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 65%
Return-value docs: 100%
References docs: 0%

Downloads

5.5K

CRAN downloads in the past year

Rank #13,527 · ~15/day · ~460/mo

Releases R versions

Daily download trend is not available in this view yet.

26330 days

80290 days

5.5K1 year

Compare downloads with other packages →

Also on256 r2u56 autocran

Repository

GitHub ↗ dungtsa/adverseevents

1Stars

1Forks

0Open issues

0Open PRs

0Releases

18Commits

2Contributors

18 commits · Last activity 2025-08-18

Stars over time

2024-11-06 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

Checks run against github.com/dungtsa/adverseevents on 2026-07-19.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (16)

shiny shinycssloaders shinyjs tidyverse rio janitor DT skimr ggpubr ggnewscalesurvivalsurvminer ggplot2 shinythemes ggrepel lubridate

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

Vignettes 208 (60%)R 83 (24%)Rd 57 (16%)

Code characteristics

Cyclomatic complexity: 3.5 median / 5 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

2 2 exported

Complexity

3.5 avg / 5 max

Call network

2 nodes / 0 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (3)

Maintainer (1)

Z Thompson

Author, Maintainer

Authors (3)

Z Thompson

Author, Maintainer

DT Chen

Author

A Obermayer

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.0.5Latest
2026-02-03 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.0.4
2024-11-20 · diff ↗
removedRemoved from CRAN
2024-11-06
requested by the maintainer for legal reasons
0.0.3
2024-11-04 · diff ↗
0.0.2
2024-10-28 · diff ↗
0.0.1
2024-10-11
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-11-04
Total releases: 5 / 2 yrs
License: GPL-3 OSI
Download size: 4.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →