man-roxygen/CohortSetSpecs.R

In anthonysena/CohortGenerator: Used to generate OHDSI cohorts

#' @param packageName          The name of the package containing the cohort definitions. Can be left
#'                             NULL if \code{baseUrl} and \code{cohortSetReference} have been
#'                             specified.
#' @param cohortToCreateFile   The location of the cohortToCreate file within the package. Is ignored
#'                             if \code{baseUrl} and \code{cohortSetReference} have been specified. The
#'                             cohortToCreateFile must be .csv file that is expected to be read into a
#'                             dataframe object identical to requirements for \code{cohortSetReference}
#'                             argument. This csv file is expected to be encoded in either ASCII or
#'                             UTF-8, if not, an error message will be displayed and process stopped.
#' @param baseUrl              The base URL for the WebApi instance, for example:
#'                             "http://server.org:80/WebAPI". Can be left NULL if \code{packageName}
#'                             and \code{cohortToCreateFile} have been specified.
#' @param cohortSetReference   A data frame with four columns, as described in the details. Can be left
#'                             NULL if \code{packageName} and \code{cohortToCreateFile} have been
#'                             specified.
#'
#' @details
#' Currently two ways of executing this function are supported, either (1) [Package Mode] embedded in
#' a study package, assuming the cohort definitions are stored in that package using the
#' \code{ROhdsiWebApi::insertCohortDefinitionSetInPackage}, or (2) [WebApi Mode] By using a WebApi
#' interface to retrieve the cohort definitions.
#' When using this function in Package Mode: Use the \code{packageName} and \code{cohortToCreateFile}
#' to specify the name of the study package, and the name of the cohortToCreate file within that
#' package, respectively
#' When using this function in WebApi Mode: use the \code{baseUrl} and \code{cohortSetReference} to
#' specify how to connect to the WebApi, and which cohorts to fetch, respectively.
#' Note: if the parameters for both Package Mode and WebApi Mode are provided, then Package mode is
#' preferred.