extras/00_setUp.R

In gowthamrao/StudyManagement: An OHDSI R package to conduct reproducible research.

#library(StudyManagement)
### update the parametes below
# baseUrl <-  "http://api.ohdsi.org:80/WebAPI"
# basePath <- 'd:/study/project' # location on local drive to store RDS
# StudyManagement::createDefaultProjectDirectory(basePath)
# targetIds <- c(1772958)
# comparatorIds <- c(1772956)
# outcomeIds <- c(1772966)
# cohortIds = c(targetIds, comparatorIds, outcomeIds)
# sourceKeys <- c('synpuf1k','synpuf5pct') #,
# conceptSetIds <- c(1861604, 1861603,1861606)
# cohortPathways <- c(22800)
# incidenceRateIds <- c(1747184)
# estimationId <- 273 #only one estimation id per project
# characterizationIds <- c(19)

##################

#cohortIds <- c()
# for (i in (1:length(cohortIds))) { #i = 1
#   definitionId = cohortIds[i]
#   for (j in (1:length(sourceKeys))) { #j = 1
#     sourceKey = sourceKeys[j]
#     ROhdsiWebApi::invokeCohortSetGeneration(baseUrl, sourceKeys= sourceKey, definitionIds = definitionId)
#   }
# }


estimationResultsFolders <- c(sourceKeys)
createDefaultProjectDirectory(basePath = basePath, estimationResultsFolders = estimationResultsFolders)
# Create folders if it does not exist
if (is.null(basePath)) {
   basePath <- getwd()
   return(basePath)
}
rdsLoc <- paste0(basePath, '/studySpecificationAndResults/01_rds/rdsFileName.rds')
estimationCohortMethodOutputLoc <- paste0(basePath, "/studySpecificationAndResults/04_executable/estimation/results")