R/Backwards.R

In OhdsiReportGenerator: Observational Health Data Sciences and Informatics Report Generator

#' generatePresentationMultiple
#'
#' @description
#' Generates a presentation from a Strategus result
#'
#' @details
#' Specify the connection details to the result database and the schema name
#' to generate a presentation.
#' 
#' @param server The server containing the result database
#' @param username The username for an account that can access the result database
#' @param password The password for an account that can access the result database
#' @param dbms The dbms used to access the result database
#' @param resultsSchema The result database schema
#' @param targetId The cohort definition id for the target cohort
#' @param targetName A friendly name for the target cohort
#' @param cmSubsetId Optional a subset ID for the cohort method/prediction results
#' @param sccsSubsetId Optional a subset ID for the SCCS and characterization results 
#' @param indicationName A name for the indication if used or NULL
#' @param outcomeIds The cohort definition id for the outcome
#' @param outcomeNames Friendly names for the outcomes
#' @param comparatorIds The cohort method comparator cohort id
#' @param comparatorNames Friendly names for the comparators
#' @param covariateIds A vector of covariateIds to include in the characterization
#' @param details a list with the studyPeriod and restrictions 
#' @param title A title for the presentation
#' @param lead The name of the presentor
#' @param date The date of the presentation
#' @param backgroundText a character with any background text
#' @param evaluationText a list of bullet points for the evaluation 
#' @param outputLocation The file location and name to save the protocol 
#' @param outputName The name of the html protocol that is created
#' @param intermediateDir The work directory for quarto
#' 
#' @return
#' An named R list with the elements 'standard' and 'source'
#' 
#' @family Reporting
#'
#' @export
#' 
generatePresentationMultiple <- function(
    server,
    username,
    password,
    dbms,
    resultsSchema = NULL,
    targetId = 1,
    targetName = "target cohort",
    cmSubsetId = 2,
    sccsSubsetId = NULL,
    indicationName = NULL,
    outcomeIds = 3,
    outcomeNames = 'outcome cohort',
    comparatorIds = c(2,4),
    comparatorNames = c("comparator cohort 1", "comparator cohort 2"),
    covariateIds = NULL,
    details = list(
      studyPeriod = 'All Time',
      restrictions = "Age - None"
    ),
    title = 'ASSURE 001 ...',
    lead = 'add name',
    date = Sys.Date(),
    backgroundText = '',
    evaluationText = '',
    outputLocation,
    outputName = paste0('presentation_', gsub(':', '_',gsub(' ','_',as.character(date()))),'.html'),
    intermediateDir = tempdir()
){
  
  warning('This function has been depreciated please use generatePresentation() instead - calling generatePresentation() with the limited inputs')
   
  # call the new function with the old inputs
  result <- generatePresentation(
    server = server, 
    username = username, 
    password = password, 
    dbms = dbms,
    resultsSchema = resultsSchema, 
    dbDetails = '', 
    
    lead = lead, 
    team = '', 
    trigger = backgroundText,
    safetyQuestion = '', 
    objective = '', 
    topline1 = '', 
    topline2 = '', 
    topline3 = '', 
    
    targetId = targetId, 
    outcomeIds = outcomeIds, 
    cohortNames = c(targetName, outcomeNames, comparatorNames), 
    cohortIds = c(targetId, outcomeIds, comparatorIds), 
    covariateIds = covariateIds,  
    details = details, 
    evaluationText = evaluationText, 
    
    outputLocation = outputLocation, 
    outputName = outputName
    )
  
  return(invisible(result))
}