OhdsiReportGenerator (version 2.0.2)

generateFullReport: generateFullReport

Description

Generates a full report from a Strategus analysis

Usage

generateFullReport(
  server,
  username,
  password,
  dbms,
  resultsSchema = NULL,
  targetId = 1,
  outcomeIds = 3,
  comparatorIds = 2,
  indicationIds = "",
  cohortNames = c("target name", "outcome name", "comp name"),
  cohortIds = c(1, 3, 2),
  includeCI = TRUE,
  includeCharacterization = TRUE,
  includeCohortMethod = TRUE,
  includeSccs = TRUE,
  includePrediction = TRUE,
  webAPI = NULL,
  authMethod = NULL,
  webApiUsername = NULL,
  webApiPassword = NULL,
  outputLocation,
  outputName = paste0("full_report_", gsub(":", "_", gsub(" ", "_",
    as.character(date()))), ".html"),
  intermediateDir = tempdir(),
  pathToDriver = Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
)

Value

An html document containing the full results for the target, comparators, indications and outcomes specified.

Arguments

server

The server containing the result database

username

The username for an account that can access the result database

password

The password for an account that can access the result database

dbms

The dbms used to access the result database

resultsSchema

The result database schema

targetId

The cohort definition id for the target cohort

outcomeIds

The cohort definition id for the outcome

comparatorIds

(optional) The cohort definition id for any comparator cohorts. If NULL the report will find and include all possible comparators in the results if includeCohortMethod is TRUE.

indicationIds

The cohort definition id for any indication cohorts. If no indication use '' and if you want some indications plus no indication use c('', indicationId1, indicationId2). Use 'Any' to include all children of targetId.

cohortNames

Friendly names for any cohort used in the study

cohortIds

The corresponding Ids for the cohortNames

includeCI

Whether to include the cohort incidence slides

includeCharacterization

Whether to include the characterization slides

includeCohortMethod

Whether to include the cohort method slides

includeSccs

Whether to include the self controlled case series slides

includePrediction

Whether to include the patient level prediction slides

webAPI

The ATLAS web API to use for the characterization index breakdown (set to NULL to not include)

authMethod

The authorization method for the webAPI

webApiUsername

The username for the webAPI authorization

webApiPassword

The password for the webAPI authorization

outputLocation

The file location and name to save the protocol

outputName

The name of the html protocol that is created

intermediateDir

The work directory for quarto

pathToDriver

Path to a folder containing the JDBC driver JAR files.

Details

Specify the connection details to the result database and the schema name to generate the full report.

See Also

Other Reporting: createPredictionReport(), generatePresentation(), generatePresentationMultiple(), generateSummaryPredictionReport()