README.md

In ohdsi-studies/BipolarMisclassificationValidation: External Validation of Model Predicting Bipolar Misdiagnosed as MDD

External Validation of Model Predicting Bipolar Misdiagnosed as MDD

• Analytics use case(s): Patient-Level Prediction
• Study type: Clinical Application
• Tags: -
• Study lead: Jenna Reps, Christophe Lambert
• Study lead forums tag: jreps , Christophe_Lambert
• Study start date: Jan 1, 2020
• Study end date: April 30, 2020
• Protocol: Protocol
• Publications: -
• Results explorer: -

This study applies and evaluates a simple score model to OMOP CDM data that predicts which newly diagnosed MDD patients will be diagnosed with bipolar within the next 1 year.

If you would like to participate, please let us know by March 27, 2020. We hope to have all of the data analysis performed by the end of April 2020, and then will submit a manuscript with participants as co-authors.

You may contact us at the following emails:

Christophe Lambert: cglambert[at]unm.edu Jenna Reps: jreps[at]its.jnj.com

Background

Patients with BD are often misdiagnosed as having MDD. We have developed a simple score based prediction model that can predict the risk that a patient who is newly diagnosed with MDD will be diagnosed with BD within the next year. We now aim to externally validate this model across the OHDSI network. If this model works then it may help patients with bipolar get diagnosed years earlier.

Code to Install

To install this package run :

  # install the network package
  # install.packages('devtools')
  devtools::install_github("OHDSI/OhdsiSharing")
  devtools::install_github("OHDSI/FeatureExtraction")
  devtools::install_github("OHDSI/PatientLevelPrediction")
  devtools::install_github("ohdsi-studies/BipolarMisclassificationValidation")

Code to Run

Execute the study by running the code in (extras/CodeToRun.R) but update using your database configuration and settings:

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

# Specify where the temporary files (used by the ff package) will be created:
options(fftempdir = "location with space to save big data")

# 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 cdmDatabaseSchema database
databaseName <- 'Validation Data Name'
# 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 <- 'bipolarValidationCohort'

# the study runs n patients aged 10+ you can restrict to 18+ by setting restrictToAdults to TRUE
restrictToAdults <- FALSE
#=======================

execute(connectionDetails = connectionDetails,
        cdmDatabaseSchema = cdmDatabaseSchema,
        cohortDatabaseSchema = cohortDatabaseSchema,
        cohortTable = cohortTable,
        outputFolder = outputFolder,
        databaseName = databaseName,
        oracleTempSchema = oracleTempSchema,
        viewModel = F,
        createCohorts = T,
        runValidation = T,
        packageResults = T,
        minCellCount = 5,
        sampleSize = NULL,
        restrictToAdults = restrictToAdults)

Submitting Results

Once you have sucessfully executed the study you will find a compressed folder in the location specified by '[outputFolder]/[databaseName]' named '[databaseName].zip'. The study should remove sensitive data but we encourage researchers to also check the contents of this folder (it will contain an rds file with the results which can be loaded via readRDS('[file location]').

To send the compressed folder results please message one of the leads (jreps , Christophe_Lambert) and we will give you the privateKeyFileName and userName. You can then run the following R code to share the results:

# If you don't have the R package OhdsiSharing then install it using github (uncomment the line below)
# install_github("ohdsi/OhdsiSharing")

library("OhdsiSharing")
privateKeyFileName <- "message us for this"
userName <- "message us for this"
fileName <- file.path(outputFolder, databaseName, paste0(databaseName,'.zip'))
sftpUploadFile(privateKeyFileName, userName, fileName)

Result object

After running the study you will get an rds object saved to: '[outputFolder]/[databaseName]/[databaseName]/validationResults.rds' you can load this object using the R function readRDS:

result <- readRDS('[outputFolder]/[databaseName]/[databaseName]/validationResults.rds')

the 'result' object is a list containing the following:

| Object | Description | Edited by minCellCount | | ----------| ---------------------------------------------------| ----------------------- | | result$inputSetting | The outcome and cohort ids and the databaseName | No | | result$executionSummary | Information about the R version, PatientLevelPrediction version and execution platform info | No | | result$model | Information about the model (name and type) | No | | result$analysisRef | Used to store a unique reference for the study | No | | result$covariateSummary | A dataframe with summary information about how often the covariates occured for those with and without the outcome | Yes | | result$spline | Fit and plot of cox regression for predicted risk ~ outcome over 10 years | Yes | | result$scoreThreshold | Operating characteristics per score | Yes | | result$survInfo | Dataframe containing the surivial plot data per 30 day window per risk score - number surviving, number censored and number with outcome | Yes | | result$yauc | The AUC when restricted the data per year of target cohort start | Yes | | result$performanceEvaluation$evaluationStatistics | Performance metrics and sizes | No | | result$performanceEvaluation$thresholdSummary | Operating characteristcs @ 100 thresholds | No | | result$performanceEvaluation$demographicSummary | Calibration per age group | Yes | | result$performanceEvaluation$calibrationSummary | Calibration at risk score deciles | No | | result$performanceEvaluation$predictionDistribution | Distribution of risk score for those with and without the outcome | Yes |

After running execute() with packageResults = T you will get the sharable results as: '[outputFolder]/[databaseName]/[databaseName].zip' and the corresponding contents are at:

result <- readRDS('[outputFolder]/[databaseName]/[databaseName]/resultsToShare/validationResults.rds')

This will be the same obejct as before but any cell counts less than minCellCount are replaced by -1 and if you specified a minCellCount >0 then 'result$survInfo' will be removed.

ohdsi-studies/BipolarMisclassificationValidation documentation built on July 13, 2020, 10:32 p.m.