R/itcares.R

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

# -*- encoding:ASCII -*-

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# Package documentation for roxygen2
# Created the 2016-07-18 
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#' @title an Interactive Tool for Case-crossover Analyses of electronic medical REcords for patient Safety

#' 
#' @description The \pkg{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:
#' \enumerate{
#' \item \code{\link{first_case}} selects the earliest record containing one or more of the diagnostic codes
#' \item \code{\link{age_study_period_restrictions}} applies the age and study period restrictions
#' \item \code{\link{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
#' \subsection{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).

#' }
#' 
#' \subsection{Data model}{
#' The input dataset had to comply with a denormalized format containing at least the following eight columns:
#' \enumerate{
#'  \item patient ID;
#'  \item episode ID;
#'  \item diagnoses;
#'  \item procedures;
#'  \item age;
#'  \item admission day;
#'  \item year of the episode;
#'  \item length of stay.
#' }
#' A simulated dataset, \code{data(ep)}, has been formatted as described and is provided with the package. Simulation process is provided in the \code{\link{simulate_ep_data}} function.


#' 
#' }
#' 
#' @author Alexandre Caron, Gregoire Ficheur, Joris Muller
#' @note
#' For bugreports, features request, use the github issue tracking at \url{https://github.com/jomuller/ITCARES/issues}.
#' @docType package
#' @keywords main
#' @name itcares
#' @aliases ITCARES
#' @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

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