psHarmonize

0.3.6

Creates a Harmonized Dataset Based on a Set of Instructions

0packages depend

2.1Kdownloads / year

68.8%test coverage

12/13checks pass

Overview

About

Maintained by John StephenFirst published 2025-01-152 releasesCRAN page ↗GitHub ↗

Functions which facilitate harmonization of data from multiple different datasets. Data harmonization involves taking data sources with differing values, creating coding instructions to create a harmonized set of values, then making those data modifications. 'psHarmonize' will assist with data modification once the harmonization instructions are written. Coding instructions are written by the user to create a "harmonization sheet". This sheet catalogs variable names, domains (e.g. clinical, behavioral, outcomes), provides R code instructions for mapping or conversion of data, specifies the variable name in the harmonized data set, and tracks notes. The package will then harmonize the source datasets according to the harmonization sheet to create a harmonized dataset. Once harmonization is finished, the package also has functions that will create descriptive statistics using 'RMarkdown'. Data Harmonization guidelines have been described by Fortier I, Raina P, Van den Heuvel ER, et al. (2017) doi:10.1093/ije/dyw075. Additional details of our R package have been described by Stephen JJ, Carolan P, Krefman AE, et al. (2024) doi:10.1016/j.patter.2024.101003.

Install

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

install.packages("psHarmonize", 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("NUDACC/psHarmonize")

Development version from NUDACC/psHarmonize. 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-psharmonize

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-psHarmonize

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-psHarmonize

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.3 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.14

68.8%

Coverage · measured lines

93%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
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: 0%

Downloads

2.1K

CRAN downloads in the past year

Rank #20,941 · ~6/day · ~175/mo

Releases R versions

Daily download trend is not available in this view yet.

17230 days

52790 days

2.1K1 year

Compare downloads with other packages →

Also on113 r2u2 autocran

Repository

GitHub ↗ nudacc/psharmonize

2Stars

1Forks

3Open issues

1Open PRs

7Releases

101Commits

2Contributors

101 commits · Last activity 2025-10-16 · 0% stars, 30d

Stars over time

2025-03-09 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/nudacc/psharmonize on 2026-08-02.

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (9)

dplyr glue magrittr purrr RColorBrewer rlang rmarkdown stringr tidyr

LinkingTo (0)

none

Suggests (2)

testthat knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

John Stephen

Author, Maintainer

Authors (1)

John Stephen

Author, Maintainer

Contributors (1)

Maxwell Mansolf

Contributor · added in 0.3.6

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.3.6Latest
2025-10-16 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.3.5
2025-01-15
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-15
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 610 KB / 5 files
Download size: 721 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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