extras/CodeToRun.R

In Tsemharb/PIONEERCharacterization: Characterizing patients with PCa

# *******************************************************
# -----------------INSTRUCTIONS -------------------------
# *******************************************************
#
#-----------------------------------------------------------------------------------------------
#-----------------------------------------------------------------------------------------------
# This CodeToRun.R is provided as an example of how to run this study package.
# Below you will find 2 sections: the 1st is for installing the dependencies 
# required to run the study and the 2nd for running the package.
#
# The code below makes use of R environment variables (denoted by "Sys.getenv(<setting>)") to 
# allow for protection of sensitive information. If you'd like to use R environment variables stored
# in an external file, this can be done by creating an .Renviron file in the root of the folder
# where you have cloned this code. For more information on setting environment variables please refer to: 
# https://stat.ethz.ch/R-manual/R-devel/library/base/html/readRenviron.html
#
#
# Below is an example .Renviron file's contents: (please remove)
# the "#" below as these too are interprted as comments in the .Renviron file:
#
#    DBMS = "postgresql"
#    DB_SERVER = "database.server.com"
#    DB_PORT = 5432
#    DB_USER = "database_user_name_goes_here"
#    DB_PASSWORD = "your_secret_password"
#    FFTEMP_DIR = "E:/fftemp"
#
# The following describes the settings
#    DBMS, DB_SERVER, DB_PORT, DB_USER, DB_PASSWORD := These are the details used to connect
#    to your database server. For more information on how these are set, please refer to:
#    http://ohdsi.github.io/DatabaseConnector/
#
#    FFTEMP_DIR = A directory where temporary files used by the FF package are stored while running.
#
#
# Once you have established an .Renviron file, you must restart your R session for R to pick up these new
# variables. 
#
# In section 2 below, you will also need to update the code to use your site specific values. Please scroll
# down for specific instructions.
#-----------------------------------------------------------------------------------------------
#
# 
# *******************************************************
# SECTION 1: Make sure to install all dependencies (not needed if already done) -------------------------------
# *******************************************************
# 
# Prevents errors due to packages being built for other R versions: 
Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = TRUE)
# 
# First, it probably is best to make sure you are up-to-date on all existing packages.
# Important: This code is best run in R, not RStudio, as RStudio may have some libraries
# (like 'rlang') in use.
#update.packages(ask = "graphics")

# When asked to update packages, select '1' ('update all') (could be multiple times)
# When asked whether to install from source, select 'No' (could be multiple times)

# *******************************************************
# SECTION 2: Running the package -------------------------------------------------------------------------------
# *******************************************************
library(PIONEERCharacterization)

# Optional: specify where the temporary files (used by the ff package) will be created:
fftempdir <- if (Sys.getenv("FFTEMP_DIR") == "") "~/fftemp" else Sys.getenv("FFTEMP_DIR")
options(fftempdir = fftempdir)

# Details for connecting to the server:
dbms = Sys.getenv("DBMS")
user <- if (Sys.getenv("DB_USER") == "") NULL else Sys.getenv("DB_USER")
password <- if (Sys.getenv("DB_PASSWORD") == "") NULL else Sys.getenv("DB_PASSWORD")
server = Sys.getenv("DB_SERVER")
port = Sys.getenv("DB_PORT")
extraSettings <- if (Sys.getenv("DB_EXTRA_SETTINGS") == "") NULL else Sys.getenv("DB_EXTRA_SETTINGS")
pathToDriver <- if (Sys.getenv("PATH_TO_DRIVER") == "") NULL else Sys.getenv("PATH_TO_DRIVER")
connectionString <- Sys.getenv("CONNECTION_STRING")

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



# For Oracle: define a schema that can be used to emulate temp tables:
oracleTempSchema <- NULL

# Details specific to the database:
databaseId <- "SP"
databaseName <- "Synpuf"
databaseDescription <- "Testing"
outputFolderPath <- "" # set up a path for results

# Details for connecting to the CDM and storing the results
outputFolder <- file.path(outputFolderPath, databaseId)
cdmDatabaseSchema <- Sys.getenv("CDM_SCHEMA")
cohortDatabaseSchema <- Sys.getenv("COHORT_SCHEMA")
cohortTable <- paste0("PIONEER_", databaseId)
cohortStagingTable <- paste0(cohortTable, "_stg")
featureSummaryTable <- paste0(cohortTable, "_smry")
minCellCount <- 5
useBulkCharacterization <- TRUE
cohortIdsToExcludeFromExecution <- c()
cohortIdsToExcludeFromResultsExport <- NULL



# Run cohort diagnostics -----------------------------------
runCohortDiagnostics(connectionDetails = connectionDetails,
                     cdmDatabaseSchema = cdmDatabaseSchema,
                     cohortDatabaseSchema = cohortDatabaseSchema,
                     cohortStagingTable = cohortStagingTable,
                     oracleTempSchema = oracleTempSchema,
                     cohortIdsToExcludeFromExecution = cohortIdsToExcludeFromExecution,
                     exportFolder = outputFolder,
                     # cohortGroupNames = c("target", "outcome", "strata"), # Optional - will use all groups by default
                     databaseId = databaseId,
                     databaseName = databaseName,
                     databaseDescription = databaseDescription,
                     minCellCount = minCellCount)

# preMerge the data for shiny App. Replace "target" with
# one of these options: "target", "outcome", "strata"
# preMergeDiagnosticsFiles(file.path(outputFolder, "diagnostics", "strata"))
# Use the next command to review cohort diagnostics and replace "target" with
# one of these options: "target", "outcome", "strata"
# CohortDiagnostics::launchDiagnosticsExplorer(file.path(outputFolder, "diagnostics", "target"))




# Use this to run the study. The results will be stored in a zip file called
# 'Results_<databaseId>.zip in the outputFolder.
runStudy(connectionDetails = connectionDetails,
         cdmDatabaseSchema = cdmDatabaseSchema,
         cohortDatabaseSchema = cohortDatabaseSchema,
         cohortStagingTable = cohortStagingTable,
         cohortTable = cohortTable,
         featureSummaryTable = featureSummaryTable,
         oracleTempSchema = cohortDatabaseSchema,
         exportFolder = outputFolder,
         databaseId = databaseId,
         databaseName = databaseName,
         databaseDescription = databaseDescription,
         #cohortGroups = c("target"), # Optional - will use all groups by default
         cohortIdsToExcludeFromExecution = cohortIdsToExcludeFromExecution,
         cohortIdsToExcludeFromResultsExport = cohortIdsToExcludeFromResultsExport,
         incremental = TRUE,
         useBulkCharacterization = useBulkCharacterization,
         minCellCount = minCellCount)


# Use the next set of commands to compress results
# and view the output.
preMergeResultsFiles(outputFolder)
launchShinyApp(outputFolder)