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
To avoid confusion with help(function), the function Rmonize_help() has been renamed Rmonize_website().
Bug corrections and enhancements after testing with real 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()
in visual reports, void confusing changes in color scheme in visual reports.
Histograms for date variables display valid ranges.
in reports, change % NA as proportion in reports.
harmonized_dossier_visualize() report shows variable labels in the same language.
put id_creation in script and in rule in dpe (as in direct_mapping)
Allow special characters in names of datasets and data_dicts
In visual reports, the bar plot only appears when there are multiple missing value types, otherwise only the pie chart is shown.
enhance harmonized_dossier_visualize() output
enhance show_harmo_error() output
in reports, all of the percentages are now included under “Other values (non categorical)”, which gives a single value.
Function recode with special character is possible now
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.
Rmonize_help() Call the help center for full documentationdowload_templates() Call the help center to the download template pageRmonize_DEMO Built-in material allowing the user to test the package with demo dataas_data_proc_elem() Validate and coerce any object as a Data Processing Elementsas_dataschema(), as_dataschema_mlstr() Validate and coerce any object as the DataSchemaas_harmonized_dossier() Validate and coerce any object as an harmonized dossierdataschema_extract() Extract and create the DataSchema from a data processing elementsharmo_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
show_harmo_error() Generate a summary of the annotated Data Processing Elementsdata_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.as_data_dict(),is_data_dict(), as_data_dict_mlstr(),is_data_dict_mlstr(), as_dataset(),is_dataset(), as_dossier(),is_dossier(), as_taxonomy()
data_extract(),data_dict_extract(), data_dict_apply(),dataset_zap_data_dict(),dossier_create() valueType_adjust()
dataset_evaluate(), data_dict_evaluate(),dossier_evaluate(), dataset_summarize(),dossier_summarize()
bookdown_template(),bookdown_render(),bookdown_open(), dataset_visualize()