#' Extract radiology reports
#'
#' Extracts radiology reports from the Caisis database and returns a data frame.
#'
#' @param connection ODBC connection object returned by dbConnect.
#' @param patients A character vector of patient medical record numbers. If no
#' limit is desired then set as NULL.
#' @param n Number of records to retrieve. Use n = -1 to retrieve all records.
#' @return Returns a data frame with radiology reports from the Caisis database.
#' @export
#' @import DBI
extractRadiology <- function(connection, patients = NULL, n = -1) {
if(is.null(patients)){
patients <- "LIKE '%'"
} else {
patients <- paste("IN ('", paste(patients, collapse = "', '"), "')", sep = "")
}
data <- DBI::dbGetQuery(connection, paste("SELECT
PtMRN as 'PatientMRN',
CaisisProd.dbo.vDatasetDiagnostics.DxDataSource,
CaisisProd.dbo.vDatasetDiagnostics.DxType,
CaisisProd.dbo.vDatasetDiagnostics.DxAcc,
CaisisProd.dbo.vDatasetDiagnostics.DxDate,
CaisisProd.dbo.vDatasetDiagnostics.DxIndication,
CaisisProd.dbo.vDatasetDiagnostics.DxNotes,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgNumofFocalBonyLesions_DD,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgTotalNumberOfBonyLesions,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgSiteFocalBonyLesions,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSizeofFocalBonyLesions_DD,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSizeofFocalBonyLesions,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSUVofFocalBonyLesions_DD,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSUVofFocalBonyLesions,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSizeofEnlargedLymphNodes_DD,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSizeofEnlargedLymphNodes,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSUVofEnlargedLymphNodes_DD,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSUVofEnlargedLymphNodes,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgSiteofMassLesions,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSizeofMassLesions_DD,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSizeofMassLesions,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSUVofMassLesions_DD,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgMaxSUVofMassLesions,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgNumofLyticLesions_DD,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgTotalNumofLyticLesions,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgNumofLucentLesions_DD,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgNumofLucentLesions,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgSiteofLyticLesions,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgSiteofLucentLesions,
CaisisProd.dbo.vDatasetDxImageMyeloma.ImgSiteofFractures,
CaisisProd.dbo.vDatasetDxImageMyeloma.EnteredTime
FROM CaisisProd.dbo.vDatasetPatients
INNER JOIN CaisisProd.dbo.vDatasetDiagnostics ON CaisisProd.dbo.vDatasetPatients.PatientId = CaisisProd.dbo.vDatasetDiagnostics.PatientId
FULL JOIN CaisisProd.dbo.vDatasetDxImageMyeloma ON CaisisProd.dbo.vDatasetDxImageMyeloma.DiagnosticId = CaisisProd.dbo.vDatasetDiagnostics.DiagnosticId
WHERE CaisisProd.dbo.vDatasetPatients.PtMRN ", patients, sep = ""), n=-1)
data$PatientMRN = as.factor(data$PatientMRN)
data$DxDate = as.Date(data$DxDate, format = "%Y-%m-%d")
data$EnteredTime = as.Date(data$EnteredTime, format = "%Y-%m-%d")
return(data)
}
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