secuTrialR

1.3.3

Handling of Data from the Clinical Data Management System 'secuTrial'

0packages depend

7.5Kdownloads / year

95.1%test coverage

13/13checks pass

Overview

About

Maintained by Alan G. HaynesFirst published 2020-04-246 releasesCRAN page ↗GitHub ↗

Seamless and standardized interaction with data exported from the clinical data management system (CDMS) 'secuTrial'https://www.secutrial.com. The primary data export the package works with is a standard non-rectangular export.

Install

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

install.packages("secuTrialR", 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("SwissClinicalTrialOrganisation/secuTrialR")

Development version from SwissClinicalTrialOrganisation/secuTrialR. 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-secutrialr

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-secuTrialR

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-secuTrialR

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

Health

CRAN checks

13OK

Slowest check: 3.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.87

95.1%

Coverage · measured lines

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-30
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 2,584 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 96%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

7.5K

CRAN downloads in the past year

Rank #5,659 · ~21/day · ~627/mo

Releases R versions

Daily download trend is not available in this view yet.

39130 days

1.7K90 days

7.5K1 year

Compare downloads with other packages →

Also on109 r2u30 autocran2.2K conda_forge

Repository

GitHub ↗ swissclinicaltrialorganisation/secutrialr

10Stars

12Forks

21Open issues

1Open PRs

10Releases

1,409Commits

16Contributors

1,409 commits · Last activity 2025-04-07 · 0% stars, 30d

Stars over time

2025-03-17 · 92026-07-07 · 10

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/swissclinicaltrialorganisation/secutrialr on 2026-07-19.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (11)

haven readr readxl stringr tibble magrittr purrr tidyr dplyr rlang lubridate

LinkingTo (0)

none

Suggests (7)

knitr lintr rmarkdown testthat tuftetcltkigraph

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 6,232 (75%)Rd 1,210 (15%)Vignettes 864 (10%)

Code characteristics

Object systems

S329

Cyclomatic complexity: 3.0 median / 26 max
Test cases: 213 / 0.87 per code line

Test coverage

Line coverage

95%

Expression

94.8%

Tests / Examples

95.1% / 75% ex

Functions

79 28 exported

Complexity

4.5 avg / 26 max

Call network

79 nodes / 75 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

79 functions

Function	Cyclo	Coverage
export_date exp	2	0%
export_datetime exp	2	0%
datetimes_secuTrial.integer	3	0%
factorize_secuTrial.character	3	0%
factorize_secuTrial.logical	3	60%
mnppid2centre	2	60%

People & History

People (9)

Maintainer (1)

Alan G. Haynes

Maintainer, Author, Copyright holder

Authors (3)

Alan G. Haynes

Maintainer, Author, Copyright holder

Milica Markovic

Author, Copyright holder

Patrick R. Wright

Author, Copyright holder

Contributors (5)

Gilles Dutilh

Contributor

Silvia Grieder

Contributor · added in 1.1.1

Armando Lenz

Contributor

Pia Neuschwander

Contributor · added in 1.1.1

Constantin Sluka

Contributor · added in 1.1.1

Alan G. Haynes

Maintainer, Author, Copyright holder

Milica Markovic

Author, Copyright holder

Patrick R. Wright

Author, Copyright holder

Other (1)

Pascal Benkert

Compiler

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.3.3Latest
2024-05-30 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.1.1
2023-03-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.9
2021-03-11 · diff ↗
1.0.8
2020-12-07 · diff ↗
1.0.6
2020-10-26 · diff ↗
1.0.3
2020-04-24
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-04-24
Total releases: 6 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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