## ----echo = FALSE, message = FALSE, warning = FALSE---------------------------
library(PheValuator)

## ----tidy=FALSE,eval=FALSE----------------------------------------------------
# options(andromedaTempFolder = "c:/temp2/ff") #place to store large temporary files
# 
# CovSettings <- createDefaultCovariateSettings(excludedCovariateConceptIds = c(201254),
#                                               addDescendantsToExclude = TRUE,
#                                               startDayWindow1 = 0,
#                                               endDayWindow1 = 30,
#                                               startDayWindow2 = 31,
#                                               endDayWindow2 = 180,
#                                               startDayWindow3 = 181,
#                                               endDayWindow3 = 365)
# 

## ----tidy=FALSE,eval=FALSE----------------------------------------------------
# options(andromedaTempFolder = "c:/temp2/ff") #place to store large temporary files
# 
# CovSettings <- createDefaultCovariateSettings(startDayWindow1 = 0,
#                                               endDayWindow1 = 10,
#                                               startDayWindow2 = 11,
#                                               endDayWindow2 = 20,
#                                               startDayWindow3 = 21,
#                                               endDayWindow3 = 30)
# 

## ----tidy=FALSE,eval=FALSE----------------------------------------------------
# CohortArgs <- createCreateEvaluationCohortArgs(xSpecCohortId = 1769699,
#                                                xSensCohortId = 1770120,
#                                                prevalenceCohortId = 1770119,
#                                                evaluationPopulationCohortId = 1778258,
#                                                covariateSettings = CovSettings)

## ----tidy=FALSE,eval=FALSE----------------------------------------------------
# #First phenotype algorithm to test
# conditionAlg1TestArgs <- createTestPhenotypeAlgorithmArgs(phenotypeCohortId =  1778259)

## ----tidy=FALSE,eval=FALSE----------------------------------------------------
# analysis1 <- createPheValuatorAnalysis(analysisId = 1,
#                                        description = "[PheValuator] Type 2 Diabetes Mellitus
#                                                     (prevalent)",
#                                        createEvaluationCohortArgs = CohortArgs,
#                                        testPhenotypeAlgorithmArgs = conditionAlg1TestArgs)
# 

## ----tidy=FALSE,eval=FALSE----------------------------------------------------
# #Second phenotype algorithm to test
# conditionAlg2TestArgs <- createTestPhenotypeAlgorithmArgs(phenotypeCohortId = 1778260,
#                                                           washoutPeriod = 0)
# 
# analysis2 <- createPheValuatorAnalysis(analysisId = 2,
#                                        description = "[PheValuator] Type 2 diabetes mellitus
#                                                     with second code 31-365 days after index",
#                                        createEvaluationCohortArgs = CohortArgs,
#                                        testPhenotypeAlgorithmArgs = conditionAlg2TestArgs)
# 
# #save the analyses
# pheValuatorAnalysisList <- list(analysis1, analysis2)

## ----tidy=FALSE,eval=FALSE----------------------------------------------------
# #create database connection details
# connectionDetails <- createConnectionDetails(dbms = "postgresql",
#                                              server = "localhost/ohdsi",
#                                              user = "joe",
#                                              password = "supersecret")
# 
# #run the PheValuator process
# referenceTable <- runPheValuatorAnalyses(connectionDetails = connectionDetails,
#                                          cdmDatabaseSchema = "yourCDMSchema",
#                                          cohortDatabaseSchema = "yourCohortSchema",
#                                          cohortTable = "yourCohortTableSchema",
#                                          workDatabaseSchema = "yourWritableSchema",
#                                          outputFolder = "yourOutputFolderSchema",
#                                          pheValuatorAnalysisList = pheValuatorAnalysisList)

## ----tidy=FALSE,eval=FALSE----------------------------------------------------
# #view the results of the phenotype evaluation
# View(summarizePheValuatorAnalyses(referenceTable, "yourOutputFolderSchema"))
# write.csv(phenotypeResults, "c:/phenotyping/diabetes_results.csv", row.names = FALSE)