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Changelog

Rgemini 2.0.0

  • Addition of RxNorm functions:
    • rxnorm_query() to identify drugs of interest from pharmacy table
    • prepare_pharm_for_validation() to standardize RxNorm mapping validation
    • normalize_text() utility function to standardize medication names
    • Rxnorm vignette with step-by-step instructions for pharmacy mapping workflow
      • Changes for internal GEMINI staff: Compared to the previous GEMINIpkg version of RxNorm, the following changes have been made
        • improved documentation
        • rxnorm_query(): Changes to input arguments and improved query speed
        • prepare_pharm_for_validation():
          • DB connection to drm_cleandb_v4_1_1 required to query lookup_pharmacy_mapping table with previously validated mappings
          • Pharmacy mapping DB no longer queried, but can be provided as custom_lookup input
  • Other new functions:
    • covid_surge_index() function that calculates the COVID surge index by hospital-month
    • cci_group() to derive grouping of intervention codes into CCI sections and subsections
    • cci_search() to identify CCI codes for interventions of interest
  • Testing improvements:
    • Unit tests are now also run in Python via rpy2 to ensure cross-language compatibility
  • Bug fixes
  • Miscellaneous:
    • Removed age exclusion in episodes_of_care() to accommodate paeds cohort
    • Updated readmission vignette to clarify use of restricted cohort (all-Med & ICU) in derived readmission flags
    • Refactored disability() and frailty_score() to remove dependency on fuzzyjoin package
    • Added hex sticker
    • Integration of issues with Jira

Rgemini 1.1.0

  • New functions:
    • data_coverage() function to facilitate data coverage checks
    • cohort_creation() to generate cohort and show number (%) of entries at each inclusion/exclusion step
    • neighbourhood_ses() deriving neighbourhood-level variables from the Statistics Canada Census & Ontario Marginalization Index
    • Utility functions:
      • quiet() to run any functions without warning/error/print messages
      • compare_sets() to find the number of unique and common elements in two sets
      • create_ntiles() to bin numeric variables into user-specified quantiles
  • Function enhancements:
    • Added option to return readmission genc_id in readmission() function
    • Aligned n_routine_bloodwork() with DRM by only returning lab tests with valid numeric results
    • Removed redundant check for acute-care transfers in episodes_of_care() (only use mapped institution types from lookup_transfer)
    • Enabled custom line color without specifying color grouping variable in plot_over_time()
  • Documentation updates:
    • Added pre-commit hooks: Run styler and check for browser() statements & large files
    • Improved documentation in readmission() vignette
    • Updated all links referencing the data dictionary
    • Improved organization of figures for vignettes

Rgemini 1.0.2

Rgemini 1.0.1

Rgemini 1.0.0

  • New function homelessness() to derive encounter-level homelessness flag based on ICD-10-CA diagnosis codes
  • Enhanced cell_suppression.R renderers for table1 to support simultaneous display of both mean and median
  • Small fix in episodes_of_care() for compatibility with future DB versions due to change in lookup_transfer table
  • Tested on GEMINI Data Repository v3

Rgemini 0.5.1

  • Improved query efficiency in mlaps() and other functions for clinical derived variables
  • Removed duplicated code in icu_entry()

Rgemini 0.5.0

  • New functions:

  • Function enhancements:

    • n_imaging, n_routine_bloodwork() and n_rbc_transfusion() refactored and updated to be able to exclude clinical records in ED
    • n_imaging, n_routine_bloodwork and n_rbc_transfusion refactored and updated to be able to exclude clinical records in ED
    • Inclusion of all routine blood tests (regardless of result value) in n_routine_bloodwork()
    • Option to derive ICU entries as a clinical outcome with customizable time windows in icu_entry()
    • For functions with date-time inputs: Allow for character and POSIXct inputs
    • Improved efficiency in mlaps() hospital query

  • Minor bug fixes & updated unit tests:

    • frailty_score(): Return frailty score 0
    • daily_census(): Limit time period by discharge date
    • disability(): Only return encounters in cohort input
    • Table 1 render functions: Enable prettyNum formatting
    • Rgemini:::check_input(): Return error for odbc connections

  • Small documentation updates & clean-up of pkdgown reference file

Rgemini 0.4.2

  • Small bug fix in Rgemini:::find_db_tablename()

Rgemini 0.4.1

  • Small bug fix in Rgemini:::check_input()

Rgemini 0.4.0

  • Adds n_missing() function to check number of missingness
  • Switch function frailty_score() to calculate the CIHI Hospital Frailty Risk Score for each encounter
  • Deprecates function frailty_score() that calculates the UK Hospital Frailty Risk Score
  • New utility function checking user inputs
  • Adds core mlaps() function and wrapper function to run over multiple sites and years
  • Adds er_los() function to calculate emergency room length-of-stay
  • New function dummy_ipadmdad() to simulate “ipadmdad” data with random hospital-level intercepts
  • Enhanced daily_census() function to allow exclusion of days with 0 counts
  • Additional input argument in covid_flag() for inclusion of ER diagnoses
  • New function disability() that derives disability flag for each encounter
  • Adds function to calculate Elixhauser comorbidity scores elixhauser_comorbidity_index()
  • Adds utility function to generate warning about mapped values
  • Standardizes citation format in function references section

Rgemini 0.3.1

  • Allows the user to specify the number of digits to round percentages to in cell suppression of categorical variables, without forcing rounding to integer
  • Allows user to render only one level for binary variables in table1
  • Fixes singularity due to missing levels in table1
  • Fixes find_db_tablename() and readmission() for DBs with foreign data wrappers

Rgemini 0.3.0

  • Exports n_rbc_transfusion() function
  • Adds installation instructions for GEMINI HPC
  • Tested on GEMINI Data Repository v2.1.2

Rgemini 0.2.0

  • Small bug fixes in n_imaging() and n_rbc_transfusion()
  • Standardized argument names for DB and cohort inputs
  • Standardized function names for count functions
  • Improved documentation

Rgemini 0.1.0

  • This is the initial release of Rgemini, which includes variety of functions to do data analysis with the GEMINI dataset