Changelog

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

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

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

New functions:
- Plotting functions & vignette for data exploration: plot_summary() and plot_over_time()
- Plotting functions & vignette for plot aesthetics: plot_theme() and gemini_colors()
- hospitalizations_last_n_days() to calculate the number of previous hospitalizations in a given window
- convert_dt() to handle date-time variables and show missing/invalid entries
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

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

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

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