Changelog

Source: NEWS.md

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()

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

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

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

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()