Package index • Rgemini

Derived Variables

These functions derive variables from existing data.

charlson_comorbidity_index(): Compute Charlson comorbidity index (CCI) score

comorbidity_index(): Compute Comorbidity Index

covid_flag(): COVID Flag

daily_census(): Compute daily census

day_time_of_admission(): Compute day & time of hospital admissions

disability(): Identify encounters with disability

elixhauser_comorbidity_index(): Compute Elixhauser comorbidity score

episodes_of_care(): Identify episodes of care

er_los(): Compute Length of Stay in Emergency Room

frailty_score(): Compute CIHI Hospital Frailty Risk Score

homelessness(): Homelessness flag

hospital_fiscal_year(): Get hospital fiscal year

hospitalizations_last_n_days(): Compute number of previous hospitalizations for an encounter in a given window.

icu_entry(): Compute entry to Intensive Care Unit

icu_los(): Compute Length of Stay in Intensive Care Unit

in_hospital_mortality(): Compute in-hospital mortality using CIHI DAD

laps_assign_test(): Assign score to LAPS component

length_of_stay(): Compute hospital Length of Stay (LoS)

loop_mlaps(): Loop mLAPS

mlaps(): mLAPS

n_imaging(): Compute the number of radiology tests per encounter

n_missing() mi2(): Number of missingness

n_rbc_transfusions(): Count the number Red Blood Cell (RBC) Transfusions per encounter

n_routine_bloodwork(): Compute the number of routine bloodwork tests per encounter

neighbourhood_ses() neighborhood_ses(): Obtain commonly used neighbourhood-level socioeconomic status (SES) variables

readmission(): Compute readmission and episodes of care.

season(): Get Season

stat_holidays_ON(): Flag statutory holidays in Ontario

Data Transformation

These functions aid in querying the data, either by applying filters or mapping values.

diagnoses_at_admission(): Determine Diagnoses at Admission

icd_to_ccsr(): Identify CCSR categories for ICD-10-CA diagnosis codes

max_result_value(): Calculates maxima when input vector is not empty, else returns NA.

min_result_value(): Calculates minima when input vector is not empty, else returns NA.

Cohort Creation & Data Checks

These functions help with cohort generation and commonly performed data checks

cohort_creation(): Cohort creation

data_coverage(): Check data coverage

Cell Suppression

This includes all helper functions associated with producing a Table 1.

max_pairwise_smd(): Maximum Pairwise Standardized Mean Difference

render_cell_suppression.categorical(): Render Cell Suppression (Categorical)

render_cell_suppression.continuous(): Render Cell Suppression (Continuous)

render_cell_suppression.default(): Render Cell Suppression (Default)

render_cell_suppression.discrete(): Render Cell Suppression (Discrete)

render_cell_suppression.missing(): Render Cell Suppression (Missing)

render_cell_suppression.strat(): Render Cell Suppression (Strata)

render_default.discrete(): Render Default (Discrete)

render_mean.continuous(): Render Mean (Continuous)

render_median.continuous(): Render Median (Continuous)

render_strict_cell_suppression.categorical(): Render Strict Cell Suppression (Categorical)

Dummy Data

Helper functions designed to produce sample data.

dummy_admdad(): Generated simulated administrative data

dummy_diag(): Generate Simulated Diagnosis Data Table

dummy_ipadmdad(): Simulate ipadmdad data

dummy_lab(): Generated simulated lab data

sample_icd(): Simulate ICD-10 Diagnosis Codes

Plotting Functions

Functions for common plotting needs.

gemini_colors(): GEMINI colors

plot_color_palettes(): Plot GEMINI color palettes

plot_over_time(): Plot variable over time

plot_summary(): Plot descriptive summary statistics of multiple variables

plot_theme(): Plot theme for ggplots

scale_color_gemini(): Wrapper function for ggplot2::scale_color_manual() that applies GEMINI color palettes to ggplot objects.

scale_fill_gemini(): Wrapper function for ggplot2::scale_fill_manual() that applies GEMINI color palettes to ggplot objects.

Mapping files

Files containing variable mappings.

mapping_cihi_frailty: Mapping data for frailty_score function

mapping_disability: Mapping data for disability function

Utility Functions

check_input(): Check user inputs

coerce_to_datatable(): Coerce to data.table

compare_sets(): Compare two sets to get the number of unique and common elements in each set

coverage_message(): Coverage Message

convert_dt(): Convert date-time variables into POSIXct/POSIXt format.

create_ntiles(): Create N-tiles

find_db_tablename(): Find DB table/view name in database.

fix_var_str(): Fix variable strings

lunique(): Returns number of unique values

mapping_message(): Mapping Message

gemini_colors(): GEMINI colors

`%ni%`: Not In

scale_color_gemini(): Wrapper function for ggplot2::scale_color_manual() that applies GEMINI color palettes to ggplot objects.

scale_fill_gemini(): Wrapper function for ggplot2::scale_fill_manual() that applies GEMINI color palettes to ggplot objects.

return_hospital_field(): Return Hospital Field

quiet(): Suppress errors/messages/warnings