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EHDEN Alopecia

Analytic software to perform large-scale distributed analysis of patients with Alopecia as part of the EHDEN study-athon

Study Status: Started

  • Analytics use case(s): Population-Level Estimation
  • Study type: Clinical Application
  • Tags: -
  • Study lead:
  • Study lead forums tag:
  • Study start date: 1 November 2023
  • Study end date: -
  • Protocol: To be added
  • Publications: -
  • Results explorer: -

Requirements

A database in Common Data Model version 5 in one of these platforms: SQL Server, Oracle, PostgreSQL, IBM Netezza, Apache Impala, Amazon RedShift, Google BigQuery, or Microsoft APS. R version 4.0.5 On Windows: RTools Java 100 GB of free disk space

How to run

See the instructions at https://ohdsi.github.io/Hades/rSetup.html for configuring your R environment, including Java and RStudio.

Clone the EhdenAlopecia package into your local R environment.

Open your study package in RStudio. Use the following code to install all the dependencies:

install.packages(c("DBI",
    "dplyr",
    "glue",
    "zip",
    "magrittr",
    "checkmate",
    "log4r",
    "lubridate",
    "rlang",
    "readr")
)

In RStudio, select 'Build' then 'Install and Restart' to install the package.

After succesfully installing the package. Open the extras/codeTorun.R and run the following code

#Load the library

library(EhdenAlopecia)
# database metadata and connection details -----
# The name/ acronym for the database
databaseId <- ""

# Database connection details -----
#connection details
#User specified input


# Details for connecting to the server:
dbms <- ""
user <- ""
pw <- ""
server <- ""
port <- ""

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


cdmDatabaseSchema <- ""
cohortDatabaseSchema <- ""


# Name of table prefix to use in the result schema for tables created during the study.
# Notes:
# - if there is an existing table in your results schema with the same names it
#   will be overwritten
# - name must be lower case
cohortTable <- "alopecia_ehden"


# minimum counts that can be displayed according to data governance
minCellCount <- 5

#specify where to save the results
outputFolder <- "results"


#choose analysis to run
instantiateCohorts <- TRUE
runDiagnostics <- TRUE


### Do not edit below here

EhdenAlopecia::runStudy(
  connectionDetails = connectionDetails, 
  cohortTable = cohortTable, 
  cdmDatabaseSchema = cdmDatabaseSchema, 
  cohortDatabaseSchema = cohortDatabaseSchema,
  instantiateCohorts = instantiateCohorts,
  runDiagnostics = runDiagnostics,
  outputFolder = outputFolder,
  databaseId = databaseId,
  minCellCount = minCellCount
)