extras/codeToRun.R

In ohdsi-studies/CovidDeath: Add the title of the package here

 library(CovidDeath)
  # USER INPUTS
#=======================
# The folder where the study intermediate and result files will be written:
outputFolder <- "./covidDeathResults"

# Details for connecting to the server:
dbms <- "you dbms"
user <- 'your username'
pw <- 'your password'
server <- 'your server'
port <- 'your port'

connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,
                                                                server = server,
                                                                user = user,
                                                                password = pw,
                                                                port = port)

# Add the database containing the OMOP CDM data
cdmDatabaseSchema <- 'cdm database schema'
# Add a sharebale name for the database containing the OMOP CDM data
cdmDatabaseName <- 'a friendly shareable  name for your database'
# Add a database with read/write access as this is where the cohorts will be generated
cohortDatabaseSchema <- 'work database schema'

oracleTempSchema <- NULL

# table name where the cohorts will be generated
cohortTable <- 'covidDeathValidationCohort'
#=======================
execute(connectionDetails = connectionDetails,
                                 databaseName = cdmDatabaseName,
                                 cdmDatabaseSchema = cdmDatabaseSchema,
                                 cohortDatabaseSchema = cohortDatabaseSchema,
                                 oracleTempSchema = oracleTempSchema,
                                 cohortTable = cohortTable,
                                 outputFolder = outputFolder,
                                 createCohorts = T,
                                 runValidation = T,
                                 packageResults = F,
                                 minCellCount = 5,
                                 sampleSize = NULL)