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#' Trial Inclusion Exclusion Criteria Domain
#'
#' @name Trial Inclusion Exclusion Criteria Domain
#' @description The Trial Inclusion Exclusion Criteria data of an ImmPort study is reformated to the
#' CDISC SDTM Trial Inclusion Exclusion Criteria (TI) domain model, and is a list of 2 data frames
#' containing 1) Trial Inclusion Exclusion Criteria data \code{\link{TI}}
#' and 2) any supplemental Trial Inclusion Exclusion Criteria data \code{\link{SUPP}}
NULL
#> NULL
# Get Trial Inclusion Exclusion Criteria data of a specific study
#
# The function \code{getTrialInclusionExclusionCriteria} queries the ImmPort database for Trial Inclusion Exclusion Criteria data and
# reformats it to the CDISC SDTM Trial Inclusion Exclusion Criteria (TI) domain model
#
# @param data_src A connection handle to ImmPort (MySQL or SQLite) database instance or
# a directory handle to folder where study RDS files are located
# @param study_id Identifier of a specific study
# @return a list of 2 data frames containing 1) Trial Inclusion Exclusion Criteria data \code{\link{TI}} and 2) any supplemental
# Trial Inclusion Exclusion Criteria data \code{\link{SUPP}}
# @examples
# \dontrun{
# getTrialInclusionExclusionCriteria(data_src, "SDY1")
# }
getTrialInclusionExclusionCriteria <- function(data_src, study_id) {
cat("loading TrialInclusionExclusionCriteria data....")
ti_cols <- c("STUDYID", "DOMAIN", "IETEST", "IECAT")
sql_stmt <- paste("SELECT distinct
ie.study_accession,
\"TI\" as domain,
ie.criterion,
ie.criterion_category
FROM inclusion_exclusion ie
WHERE ie.study_accession in ('", study_id, "')
ORDER BY ie.criterion_accession", sep = "")
if ((class(data_src)[1] == 'MySQLConnection') ||
(class(data_src)[1] == 'SQLiteConnection')) {
ti_df <- dbGetQuery(data_src, statement = sql_stmt)
colnames(ti_df) <- ti_cols
suppti_df <- data.frame()
if (nrow(ti_df) > 0) {
}
} else {
l <- loadSerializedStudyData(data_src, study_id, "Trial Inclusion Exclusion Criteria")
ti_df <- l[[1]]
suppti_df <- l[[2]]
}
cat("done", "\n")
ti_l <- list()
if (nrow(ti_df) > 0)
ti_l <- list(ti_df=ti_df, suppti_df=suppti_df)
ti_l
}
# Get count of Trial Inclusion Exclusion Criteria data of a specific study
#
# The function \code{getCountOfTrialInclusionExclusionCriteria} queries the ImmPort database for count
# of Trial Inclusion Exclusion Criteria data
#
# @param conn A connection handle to ImmPort database instance
# @param study_id Identifier of a specific study
# @return a count of Trial Inclusion Exclusion Criteria data
# @examples
# \dontrun{
# # get count of study SDY1's Trial Inclusion Exclusion Criteria data
# count <- getCountOfTrialInclusionExclusionCriteria(conn, "SDY1")
# }
getCountOfTrialInclusionExclusionCriteria <- function(conn, study_id) {
sql_stmt <- paste("SELECT count(*)
FROM inclusion_exclusion ie
WHERE ie.study_accession in ('", study_id, "')", sep = "")
count <- dbGetQuery(conn, statement = sql_stmt)
count
}
##' Trial Inclusion Exclusion Criteria Domain Variables
##' @name TI
##' @description {
##' \tabular{ll}{
##' \strong{Variable Name } \tab \strong{Variable Label} \cr
##' STUDYID \tab Study Identifier \cr
##' DOMAIN \tab Domain Abbreviation \cr
##' IETEST \tab Inclusion/Exclusion Criterion \cr
##' IECAT \tab Inclusion/Exclusion Category
##' }
##' }
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#> NULL
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