library(remote)
# Build the package
# Build, install and restart
if("diagCovVaxExposures" %in% (.packages())){
detach("package:diagCovVaxExposures", unload=TRUE)}
library(DatabaseConnector)
library(CohortDiagnostics)
library(diagCovVaxExposures)
#install.packages("renv") # if not already installed, install renv from CRAN
renv::activate() # activate renv
renv::restore() # this should prompt you to install the various packages required for the study
library(shiny)
library(shinydashboard)
library(shinyWidgets)
library(plotly)
library(magrittr)
# Specify where the results files will be saved:
outputFolder <- "/output"
# Optional: specify where the temporary files will be created:
options(andromedaTempFolder = "/andromedaTemp")
# Maximum number of cores to be used:
maxCores <- parallel::detectCores()
# Details for connecting to the server:
server<-Sys.getenv("...")
server_dbi<-Sys.getenv("...")
db.name<-"..."
user<-Sys.getenv("DB_USER")
password<- Sys.getenv("DB_PASSWORD")
port<-Sys.getenv("DB_PORT")
host<-Sys.getenv("DB_HOST")
connectionDetails <-DatabaseConnector::downloadJdbcDrivers("postgresql", here::here())
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "postgresql",
server =server,
user = user,
password = password,
port = port ,
pathToDriver = here::here())
#connectionDetails <- DatabaseConnector::createConnectionDetails("....")
oracleTempSchema <- NULL
cdmDatabaseSchema <- "public"
cohortDatabaseSchema <- "results"
cohortTable <- "diagCovVaxExposuresCohorts"
databaseId <- "1"
databaseName <- "..."
databaseDescription <- "..."
# Use this to run the cohorttDiagnostics.
# The results will be stored in the diagnosticsExport subfolder of the outputFolder.
# This can be shared between sites.
diagCovVaxExposures::runCohortDiagnostics(connectionDetails = connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
cohortDatabaseSchema = cohortDatabaseSchema,
cohortTable = cohortTable,
oracleTempSchema = oracleTempSchema,
outputFolder = outputFolder,
databaseId = databaseId,
databaseName = databaseName,
databaseDescription = databaseDescription,
createCohorts = TRUE,
runInclusionStatistics = TRUE,
runIncludedSourceConcepts = TRUE,
runOrphanConcepts = TRUE,
runTimeDistributions = TRUE,
runBreakdownIndexEvents = TRUE,
runIncidenceRates = TRUE,
runCohortOverlap = TRUE,
runCohortCharacterization = TRUE,
runTemporalCohortCharacterization = TRUE,
minCellCount = 5)
# To view your results:
CohortDiagnostics::preMergeDiagnosticsFiles(file.path(outputFolder, "diagnosticsExport"))
CohortDiagnostics::launchDiagnosticsExplorer(file.path(outputFolder, "diagnosticsExport"))
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