itcares: an Interactive Tool for Case-crossover Analyses of electronic...

In jomuller/ITCARES: an Interactive Tool for Case-crossover Analyses of electronic medical REcords for patient Safety

Description

The ITCARES package provides an interactive tool for use by clinical epidemiologists to systematically design case-crossover analysis of large EMR database. This tool embedded in a Shiny app can be accessed with its main function runShinyITCARES. The Shiny app is based on a set of 3 main functions:

1. first_case selects the earliest record containing one or more of the diagnostic codes

2. age_study_period_restrictions applies the age and study period restrictions

3. case_crossover performs the case-crossover analysis

Advanced users and developers may conduct and customize a step-by-step case-crossover analysis directly from the R console by calling the latter functions.

Details

runShinyITCARES() user interface

The user interface is divided into three columns. The left and right columns are dedicated to user inputs, whereas the middle column is dedicated to displaying the IT-CARES output. More specifically, the criteria for case selection and the criteria for exposure selection are provided in the left-hand and right-hand columns, respectively. The middle column is divided into three panels, i.e. the update button for generating new estimates (top), the graphical output (middle) and the tabular output (bottom).

Data model

The input dataset had to comply with a denormalized format containing at least the following eight columns:

1. patient ID;

2. episode ID;

3. diagnoses;

4. procedures;

5. age;

6. admission day;

7. year of the episode;

8. length of stay.

A simulated dataset, data(ep), has been formatted as described and is provided with the package. Simulation process is provided in the simulate_ep_data function.

Note

For bugreports, features request, use the github issue tracking at https://github.com/jomuller/ITCARES/issues.

Author(s)

Alexandre Caron, Gregoire Ficheur, Joris Muller

Examples

data(ep)
obj0 <- ep

obj1 <- first_case(
  data = obj0,
  diagnoses_case =  'PE',
  diagnoses_exclusion = 'EXCLUSION',
  exclude_in_case_stay = FALSE,
  n_of_stays_max = 20
)

obj1 

obj2 <- age_study_period_restrictions(
  data = obj0,
  cases = obj1,
  starting_year = 2007,
  final_year = 2013,
  age_min = 0,
  age_max = 120
)

obj2

obj3 <- case_crossover(
  case_stay = obj2,
  data = obj0,
  exposure_diagnoses = '',
  exposure_procedures = 'THR',
  screening_index_stay = FALSE,
  unique_exposure = TRUE,
  interval_length = 42,
  number_of_interval = 8,
  wash_out = 365,
  los_max = 42
)
obj3 
obj3$graph

jomuller/ITCARES documentation built on May 19, 2019, 7:26 p.m.