Package: Rmonize 2.0.0

Guillaume Fabre

Rmonize: Tools for Data Harmonization

Integrated tools to support rigorous and well documented data harmonization based on Maelstrom Research guidelines. The package includes functions to assess and prepare input elements, apply specified processing rules to generate harmonized datasets, validate data processing and identify processing errors, and document and summarize harmonized outputs. The harmonization process is defined and structured by two key user-generated documents: the DataSchema (specifying the list of harmonized variables to generate across datasets) and the Data Processing Elements (specifying the input elements and processing algorithms to generate harmonized variables in DataSchema formats). The package was developed to address key challenges of retrospective data harmonization in epidemiology (as described in Fortier I and al. (2017) <doi:10.1093/ije/dyw075>) but can be used for any data harmonization initiative.

Authors:Guillaume Fabre [aut, cre], Maelstrom Research [aut, fnd, cph]

Rmonize_2.0.0.tar.gz
Rmonize_2.0.0.zip(r-4.7)Rmonize_2.0.0.zip(r-4.6)Rmonize_2.0.0.zip(r-4.5)
Rmonize_2.0.0.tgz(r-4.6-any)Rmonize_2.0.0.tgz(r-4.5-any)
Rmonize_2.0.0.tar.gz(r-4.6-any)Rmonize_2.0.0.tar.gz(r-4.5-any)
Rmonize_2.0.0.tgz(r-4.5-emscripten)
Rmonize.pdf |Rmonize.html✨
Rmonize/json (API)
NEWS

# Install 'Rmonize' in R:
install.packages('Rmonize', repos = c('https://maelstrom-research.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/maelstrom-research/rmonize/issues

Datasets:

On CRAN:

Conda:

6.18 score 8 stars 76 scripts 255 downloads 30 exports 97 dependencies

Last updated from:a6a7c5a212. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK187
source / vignettesOK241
linux-release-x86_64OK180
macos-release-arm64OK202
macos-oldrel-arm64OK154
windows-develOK127
windows-releaseOK168
windows-oldrelOK177
wasm-releaseOK162

Exports:as_data_dictas_data_proc_elemas_dataschemaas_dataschema_mlstras_datasetas_dossieras_harmonized_dossierbookdown_opendata_dict_applydata_dict_evaluatedata_dict_extractdataschema_evaluatedataschema_extractdataset_evaluatedataset_summarizedataset_visualizedossier_createdossier_evaluatedossier_summarizeharmo_processharmonized_dossier_evaluateharmonized_dossier_summarizeharmonized_dossier_visualizeis_data_proc_elemis_dataschemais_dataschema_mlstrpooled_harmonized_dataset_createRmonize_templatesRmonize_websiteshow_harmo_error

Dependencies:askpassbase64encbitbit64bookdownbslibcachemcellrangerclicliprcpp11crayoncredentialscrosstalkcurldescdigestdplyrDTevaluatefabRfarverfastmapfontawesomeforcatsfsgenericsgertggplot2ghgitcredsgluegtablehavenhighrhmshtmltoolshtmlwidgetshttr2iniisobandjanitorjquerylibjsonliteknitrlabelinglaterlazyevallifecyclelubridatemadshapRmagrittrmemoisemimeopensslotelpillarpkgconfigprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrreadxlrematchrlangrmarkdownrprojrootrstudioapiS7sassscalessnakecasestringistringrsystibbletidyrtidyselecttimechangetinytextzdbusethisutf8vctrsviridisLitevroomwhiskerwithrwritexlxfunyamlzip

Explore and prepare input datasets and data dictionaries

Rendered fromc-explore-and-prepare-input-datasets-and-data-dictionaries.Rmdusingknitr::rmarkdownon Apr 02 2026.

Last update: 2025-07-25
Started: 2025-07-25

Install your working environment

Rendered froma-install-your-working-environment.Rmdusingknitr::rmarkdownon Apr 02 2026.

Last update: 2025-07-25
Started: 2025-07-25

Process inputs and generate harmonized outputs

Rendered fromd-process-inputs-and-generate-harmonized-outputs.Rmdusingknitr::rmarkdownon Apr 02 2026.

Last update: 2025-07-25
Started: 2025-07-25

Simple example of data processing with Rmonize

Rendered fromb-simple-example-of-data-processing-with-Rmonize.Rmdusingknitr::rmarkdownon Apr 02 2026.

Last update: 2025-07-25
Started: 2025-07-25

Summarize and secure harmonized outputs

Rendered frome-summarize-and-secure-harmonized-outputs.Rmdusingknitr::rmarkdownon Apr 02 2026.

Last update: 2025-07-25
Started: 2025-07-25

Readme and manuals

Help Manual

Help pageTopics
Objects exported from other packagesas_data_dict
Validate and coerce as a Data Processing Elements objectas_data_proc_elem
Validate and coerce as a DataSchema objectas_dataschema
Validate and coerce as a DataSchema object with specific format restrictionsas_dataschema_mlstr
Objects exported from other packagesas_dataset
Objects exported from other packagesas_dossier
Validate and coerce as a harmonized dossier objectas_harmonized_dossier
Objects exported from other packagesbookdown_open
Objects exported from other packagesdata_dict_apply
Objects exported from other packagesdata_dict_evaluate
Objects exported from other packagesdata_dict_extract
Generate an assessment report for Data Processing Elementsdata_proc_elem_evaluate
Generate an assessment report for a DataSchemadataschema_evaluate
Generate a DataSchema based on Data Processing Elementsdataschema_extract
Objects exported from other packagesdataset_evaluate
Objects exported from other packagesdataset_summarize
Objects exported from other packagesdataset_visualize
Objects exported from other packagesdossier_create
Objects exported from other packagesdossier_evaluate
Objects exported from other packagesdossier_summarize
Generate harmonized dataset(s) and associated metadataharmo_process
Generate an assessment report for a harmonized dossierharmonized_dossier_evaluate
Generate an assessment report and summary of a harmonized dossierharmonized_dossier_summarize
Generate a web-based visual report for a harmonized dossierharmonized_dossier_visualize
Test for a valid Data Processing Elements objectis_data_proc_elem
Test for a valid DataSchema objectis_dataschema
Test for a valid DataSchema object with specific format restrictionsis_dataschema_mlstr
Generate a pooled harmonized dataset from a harmonized dossierpooled_harmonized_dataset_create
Example objects to provide an illustrative use caseRmonize_examples
Call to online documentation to download templatesRmonize_templates
Call to package websiteRmonize_website
Print a summary of data processing in the consoleshow_harmo_error