Rmonize 1.1.0 (release : 2024-05-01)

Bug fixes and improvements

• To process the data during testing, the DataSchema and/or the Data Processing Elements and/or input datasets might not be available. To be able to perform testings on harmonization, an additional parameter .debug has been added https://github.com/maelstrom-research/Rmonize/issues/56

• The report function can now work when the code is indented in the Data Processing Elements. https://github.com/maelstrom-research/Rmonize/issues/54

• The function show_harmo_error() now allows the user to avoid showing warnings https://github.com/maelstrom-research/Rmonize/issues/52

deprecated functions

To avoid confusion with help(function), the function Rmonize_help() has been renamed Rmonize_website().

Dependency changes

• set a minimum dplyr dependence to avoid bugs

Rmonize 1.0.1

Bug corrections and enhancements after testing with real data.

Bug fixes and improvements

Improvement in handling pooled data

The functions harmo_process(), pool_harmonized_dataset_create(), harmonized_dossier_create(), harmonized_dossier_evaluate(), harmonized_dossier_summarize(), harmonized_dossier_visualize() share the same parameter “harmonized_col_dataset” which is (if exists) the name of the column referring the input dataset names. If this column exists and is declared by the user, this will be used across the pipeline as a grouping/separating variable. By default, the name of each dataset will be used instead.

rename DEMO_file_harmo into Rmonize_DEMO and update examples

suppress the parameter overwrite = TRUE in the functions xxx_visualize()

• https://github.com/maelstrom-research/Rmonize/issues/38

in visual reports, void confusing changes in color scheme in visual reports.

• https://github.com/maelstrom-research/Rmonize/issues/37

Histograms for date variables display valid ranges.

• https://github.com/maelstrom-research/Rmonize/issues/31

in reports, change % NA as proportion in reports.

• https://github.com/maelstrom-research/Rmonize/issues/29

harmonized_dossier_visualize() report shows variable labels in the same language.

• https://github.com/maelstrom-research/Rmonize/issues/28

put id_creation in script and in rule in dpe (as in direct_mapping)

• https://github.com/maelstrom-research/Rmonize/issues/27

Allow special characters in names of datasets and data_dicts

• https://github.com/maelstrom-research/Rmonize/issues/23

In visual reports, the bar plot only appears when there are multiple missing value types, otherwise only the pie chart is shown.

• https://github.com/maelstrom-research/Rmonize/issues/22

enhance harmonized_dossier_visualize() output

• https://github.com/maelstrom-research/Rmonize/issues/17

enhance show_harmo_error() output

• https://github.com/maelstrom-research/Rmonize/issues/5

in reports, all of the percentages are now included under “Other values (non categorical)”, which gives a single value.

• https://github.com/maelstrom-research/Rmonize/issues/4

Function recode with special character is possible now

Rmonize 1.0.0

Functions to support rigorous retrospective data harmonization processing, evaluation, and documentation across datasets in a dossier 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.

This is still a work in progress, so please let us know if you used a function before and is not working any longer.

Helper functions and objects

• Rmonize_help() Call the help center for full documentation
• dowload_templates() Call the help center to the download template page
• Rmonize_DEMO Built-in material allowing the user to test the package with demo data

Assess and manipulate input files

• as_data_proc_elem() Validate and coerce any object as a Data Processing Elements
• as_dataschema(), as_dataschema_mlstr() Validate and coerce any object as the DataSchema
• as_harmonized_dossier() Validate and coerce any object as an harmonized dossier
• dataschema_extract() Extract and create the DataSchema from a data processing elements

Data processing

• harmo_process() Generate harmonized dataset(s) and annotated Data Processing Elements. This function internally runs other functions, which are :

• harmo_parse_process_rule(), harmo_process_add_variable(),harmo_process_case_when(), harmo_process_direct_mapping(),harmo_process_id_creation(), harmo_process_impossible(),harmo_process_merge_variable(), harmo_process_operation(),harmo_process_other(), harmo_process_paste(),harmo_process_recode(), harmo_process_rename(),harmo_process_undetermined()

• pooled_harmonized_dataset_create() Generate the pooled dataset from harmonized datasets in a dossier

Evaluation of the harmonization process

• show_harmo_error() Generate a summary of the annotated Data Processing Elements
• data_proc_elem_evaluate(),dataschema_evaluate(), harmonized_dossier_evaluate(),harmonized_dossier_summarize(), harmonized_dossier_visualize() Generate a quality assessment reports and summary statistics of inputs and outputs.

import from madshapR package:

• Shape and prepare input (datasets and data dictionaries) :

as_data_dict(),is_data_dict(), as_data_dict_mlstr(),is_data_dict_mlstr(), as_dataset(),is_dataset(), as_dossier(),is_dossier(), as_taxonomy()

• Extract and manipulate information from input :

data_extract(),data_dict_extract(), data_dict_apply(),dataset_zap_data_dict(),dossier_create() valueType_adjust()

• Assess input data :

dataset_evaluate(), data_dict_evaluate(),dossier_evaluate(), dataset_summarize(),dossier_summarize()

• Visualize input data :

bookdown_template(),bookdown_render(),bookdown_open(), dataset_visualize()