- 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
- 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")
- In 'R', use the following code to install the PhePheb2024 package:
remotes::install_github("ohdsi-studies/PhePheb2024")
- 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