https://github.com/ablack3/tkrpredictsimple

https://github.com/ablack3/tkrpredictsimple

Last synced: 29 days ago
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• Host: GitHub
• URL: https://github.com/ablack3/tkrpredictsimple
• Owner: ablack3
• Created: 2023-03-17T23:35:18.000Z (almost 2 years ago)
• Default Branch: replicateathon
• Last Pushed: 2023-03-17T23:59:11.000Z (almost 2 years ago)
• Last Synced: 2023-08-17T02:06:06.057Z (over 1 year ago)
• Language: R
• Size: 37.1 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
Predicting 90-day mortality following total knee replacement

======================



- Analytics use case(s): **Patient-Level Prediction**

- Study type: **Clinical Application**

- Tags: **Study-a-thon, COVID-19**

- Study lead: **Jenna Reps, Ross Williams**

- Study lead forums tag: **[jreps](https://forums.ohdsi.org/u/jreps), [RossW](https://forums.ohdsi.org/u/RossW),**

- Study start date: **Dec 16, 2018**

- Study end date: **-**

- Protocol: **[Link](https://github.com/OHDSI/StudyProtocols/blob/master/UkaTkaSafetyEffectiveness/documents/OHDSI%20Oxford%20PLE%20Protocol%2030dec2018.docx)**

- Publications: **-**

- Results explorer: [Link](https://data.ohdsi.org/TKROutcomesExplorer/)

The objective of this study is to develop and validate various patient-level prediction models for total knee replacement patients. 

Introduction

============

This repo contains the simple models needed for validation of the Oxford Ehden study-athon simple models to predict mortality following a total knee replacement

Features

========

  - Validates the full models developed in Thin and OptumDod as well as a user designed simple and a data driven simple developed in optumDod

  

  - Included in the package are 4 models they are:

    - Analysis_1: the full mdoel developed in optumDod

    - Analysis_1001: the simple model using user defined inputs

    - Analysis_1002: the simple model using data driven development methods (high penalisation)

    - Analysis_2: the full model developed on THIN

Technology

==========

  oxfordKneeValidation is an R package.

System Requirements

===================

  Requires R (version 3.3.0 or higher).

Dependencies

============

  * PatientLevelPrediction

Getting Started

===============

  1. In R, use the following commands to run the study:

  ```r

library(oxfordKneeValidation)

# USER INPUTS

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

# Specify where the temporary files (used by the ff package) will be created:

options(andromedatempdir = "S://temp//tempandromeda")

# The folder where the study intermediate and result files will be written:

outputFolder <- "./tkrSimpleResults"

dbms <-

user <-

pw <-

server <-

port <-

connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,

                                                                server = server,

                                                                user = user,

                                                                password = pw,

                                                                port = port)

# Add the database containing the OMOP CDM data

cdmDatabaseSchema <- ''

# Add the name of database containing the OMOP CDM data

cdmDatabaseName <- ''

# Add a database with read/write access as this is where the cohorts will be generated

cohortDatabaseSchema <- ''

oracleTempSchema <- NULL

# table name where the cohorts will be generated

cohortTable <- 'tkrSimpleTest'

#============== Pick Study Parts To Run: ===========

createCohorts = FALSE

predictTkrSimple = TRUE

runValidation = TRUE

packageResults = TRUE

minCellCount <- 5

sampleSize <- NULL

#============== Pick T and O cohorts ===========

# [option 1] use default cohorts

usePackageCohorts <- TRUE

newTargetCohortId <- NULL

newOutcomeCohortId <- NULL

newCohortDatabaseSchema <- NULL

newCohortTable <- NULL

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

# TAR settings - recommended to not edit

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

riskWindowStart <- 0

startAnchor <- 'cohort start'

riskWindowEnd <- 90

endAnchor <- 'cohort start'

firstExposureOnly <- F

removeSubjectsWithPriorOutcome <- F

priorOutcomeLookback <- 99999

requireTimeAtRisk <- F

minTimeAtRisk <- 1

includeAllOutcomes <- T

execute(connectionDetails = connectionDetails,

        usePackageCohorts = usePackageCohorts,

        newTargetCohortId = newTargetCohortId,

        newOutcomeCohortId = newOutcomeCohortId,

        newCohortDatabaseSchema = newCohortDatabaseSchema,

        newCohortTable = newCohortTable,

        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 = createCohorts,

        predictTkrSimple = predictTkrSimple,

        runValidation = runValidation,

        packageResults = packageResults,

        minCellCount = minCellCount,

        verbosity = "INFO",

        cdmVersion = 5)

```

License

=======

  oxfordKneeValidation is licensed under Apache License 2.0

Development

===========

  oxfordKneeValidation is being developed in R Studio.