Package: Rmonize 1.0.1

Guillaume Fabre

Rmonize: Support Retrospective Harmonization of Data

Functions to support rigorous retrospective data harmonization processing, evaluation, and documentation across datasets from different studies based on Maelstrom Research guidelines. The package includes the core functions to evaluate and format the main inputs that define the harmonization process, apply specified processing rules to generate harmonized data, diagnose processing errors, and summarize and evaluate harmonized outputs. The main inputs that define the processing are a DataSchema (list and definitions of harmonized variables to be generated) and Data Processing Elements (processing rules to be applied to generate harmonized variables from study-specific variables). The main outputs of processing are harmonized datasets, associated metadata, and tabular and visual summary reports. As described in Maelstrom Research guidelines for rigorous retrospective data harmonization (Fortier I and al. (2017) <doi:10.1093/ije/dyw075>).

Authors:Guillaume Fabre [aut, cre], Maelstrom-research group [fnd]

Rmonize_1.0.1.tar.gz
Rmonize_1.0.1.zip(r-4.5)Rmonize_1.0.1.zip(r-4.4)Rmonize_1.0.1.zip(r-4.3)
Rmonize_1.0.1.tgz(r-4.4-any)Rmonize_1.0.1.tgz(r-4.3-any)
Rmonize_1.0.1.tar.gz(r-4.5-noble)Rmonize_1.0.1.tar.gz(r-4.4-noble)
Rmonize_1.0.1.tgz(r-4.4-emscripten)Rmonize_1.0.1.tgz(r-4.3-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'))

Peer review:

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

Datasets:
  • Rmonize_DEMO - Demo objects to provide illustrative examples

On CRAN:

4.73 score 3 stars 12 scripts 169 downloads 30 exports 108 dependencies

Last updated 8 months agofrom:4c26ee785c. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 11 2024
R-4.5-winNOTENov 11 2024
R-4.5-linuxNOTENov 11 2024
R-4.4-winNOTENov 11 2024
R-4.4-macNOTENov 11 2024
R-4.3-winNOTENov 11 2024
R-4.3-macNOTENov 11 2024

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_helpRmonize_templatesshow_harmo_error

Dependencies:askpassbase64encbitbit64bookdownbslibcachemcellrangerclicliprcolorspacecpp11crayoncredentialscrosstalkcurldescdigestdplyrDTevaluatefabRfansifarverfastmapfontawesomeforcatsfsgenericsgertggplot2ghgitcredsgluegtablehavenhighrhmshtmltoolshtmlwidgetshttpuvhttr2iniisobandjaneaustenrjanitorjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelubridatemadshapRmagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrreadxlrematchrlangrmarkdownrprojrootrstudioapisassscalessnakecaseSnowballCstringistringrsystibbletidyrtidyselecttidytexttimechangetinytextokenizerstzdbusethisutf8vctrsviridisLitevroomwhiskerwithrwritexlxfunyamlzip

Data Processing Elements

Rendered fromb-Data-processing-elements.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-03-20
Started: 2024-03-20

Example with Rmonize_DEMO

Rendered fromc-Example-with-Rmonize_DEMO.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-03-20
Started: 2024-03-20

Glossary and templates

Rendered froma-Glossary-and-templates.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-03-20
Started: 2023-09-16

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 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
Demo objects to provide illustrative examplesRmonize_DEMO
Call to online documentationRmonize_help
Call to online documentation to download templatesRmonize_templates
Print a summary of data processing in the consoleshow_harmo_error