Phenotype Phebruary 2024

• Analytics use case(s): Characterization
• Study type: Methods Research
• Tags: Phenotype Phebruary 2024
• Study lead: James Weaver
• Study lead forums tag: jweave17
• Study start date: Feb 1, 2024
• Study end date: Feb 29, 2024
• Protocol: https://forums.ohdsi.org/t/ohdsi-phenotype-phebruary-2024
• Publications: TBD
• Results explorer: https://results.ohdsi.org/app/16_PhenotypePhebAlzh

How to run

1. In R, use the following code to install dependencies: (Update any additional dependencies if prompted)

install.packages("remotes")
remotes::install_github("ohdsi/SqlRender")
remotes::install_github("ohdsi/DatabaseConnector")
remotes::install_github("ohdsi/OhdsiSharing")
remotes::install_github("ohdsi/FeatureExtraction")
remotes::install_github("ohdsi/CohortGenerator")
remotes::install_github("ohdsi/CohortDiagnostics")
remotes::install_github("ohdsi/CohortIncidence")

2. In 'R', use the following code to install the PhePheb2024 package:

remotes::install_github("ohdsi-studies/PhePheb2024")

3. Once installed, you can execute the study by modifying and using the following code:

library(magrittr)
options(fftempdir = "") # directory location where any temporary files will be stored

outputFolder <- "" # directory location where study results will be saved; e.g. "G:/PhePhebAlzh"
if(!file.exists(outputFolder)){
  dir.create(outputFolder)
}

cohortDatabaseSchema <- "" # database schema name with write access
cohortTable <- "phe_pheb_cohort"

cdmDatabaseSchema <- "" # database schema where your CDM is located
databaseId <- "" # short, concise name of your database, e.g. "cuimc"

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

PhePheb2024::execute(
  connectionDetails = connectionDetails,
  outputFolder = outputFolder,
  targetCohortIds = targetCohortIds,
  outcomeCohortIds = outcomeCohortIds,
  databaseId = databaseId,
  cdmDatabaseSchema = cdmDatabaseSchema,
  cohortDatabaseSchema = cohortDatabaseSchema,
  cohortTable = cohortTable,
  createCohortTable = TRUE,
  createCohorts = TRUE,
  runCohortDiagnostics = TRUE,
  runIncidenceAnalysis = TRUE
)

# Sharing: TODO