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()