README.md

In lhjohn/EmcWaltersDementiaModel: A Package Skeleton for Replicating Published Prediction Models

A Package Skeleton for Validating Prognositic Models Over OHDSI

A skeleton package, to be used as a starting point when replicating existing models

Vignette: Using the package skeleton for validating exisitng prediction studies

Instructions To Prepare Package Outside Atlas

To create the package outside of ATLAS please see Populating the settings in the package skeleton for validating exisitng prediction studies

Instructions To Install and Run Package From Github

• Make sure you have PatientLevelPrediction installed:

  # get the latest PatientLevelPrediction
  install.packages("devtools")
  devtools::install_github("OHDSI/PatientLevelPrediction")
  # check the package
  PatientLevelPrediction::checkPlpInstallation()

• Then install the study package:

  # install the network package
  devtools::install_github("ohdsi-studies/EmcWaltersDementiaModel")

• Execute the study by running the code in (extras/CodeToRun.R) but make sure to edit the settings:

library(EmcWaltersDementiaModel)
# USER INPUTS
#=======================

# The folder where the study intermediate and result files will be written:
outputFolder <- "./EmcWaltersDementiaModelResults"

# 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 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 <- 'EmcWaltersDementiaModelCohort'

# TAR settings
sampleSize <- NULL
riskWindowStart <- 1
startAnchor <- 'cohort start'
riskWindowEnd <- 365
endAnchor <- 'cohort start'
firstExposureOnly <- F
removeSubjectsWithPriorOutcome <- F
priorOutcomeLookback <- 99999
requireTimeAtRisk <- F
minTimeAtRisk <- 1
includeAllOutcomes <- T


#=======================


execute(connectionDetails = connectionDetails,
                                    cdmDatabaseSchema = cdmDatabaseSchema,
                                    cdmDatabaseName = cdmDatabaseName,
                                    cohortDatabaseSchema = cohortDatabaseSchema,
                                    cohortTable = cohortTable,
                                    sampleSize = sampleSize,
                                    riskWindowStart = riskWindowStart,
                                    startAnchor = startAnchor,
                                    riskWindowEnd = riskWindowEnd,
                                    endAnchor = endAnchor,
                                    firstExposureOnly = firstExposureOnly,
                                    removeSubjectsWithPriorOutcome = removeSubjectsWithPriorOutcome,
                                    priorOutcomeLookback = priorOutcomeLookback,
                                    requireTimeAtRisk = requireTimeAtRisk,
                                    minTimeAtRisk = minTimeAtRisk,
                                    includeAllOutcomes = includeAllOutcomes,
                                    outputFolder = outputFolder,
                                    createCohorts = T,
                                    runAnalyses = T,
                                    viewShiny = T,
                                    packageResults = F,
                                    minCellCount= 5,
                                    verbosity = "INFO",
                                    cdmVersion = 5)

Development status

Under development.

lhjohn/EmcWaltersDementiaModel documentation built on Feb. 25, 2021, 2:54 p.m.