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#' Trial Visits Domain
#'
#' @name Trial Visits Domain
#' @description Information on the planned visits of an ImmPort study is reformated to the CDISC SDTM Trial Visits (TV)
#' domain model, and is a list of 2 data frames containing 1) Trial Visits data \code{\link{TV}}
#' and 2) any supplemental Trial Visits data \code{\link{SUPP}}
NULL
#> NULL
# Get Trial Visits data of a specific study
#
# The function \code{getTrialVisits} queries the ImmPort database for Trial Visits data and
# reformats it to the CDISC SDTM Trial Visits (TV) 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 Visits data \code{\link{TV}} and 2) any supplemental
# Trial Visits data \code{\link{SUPP}}
# @examples
# \dontrun{
# getTrialVisits(data_src, "SDY1")
# }
getTrialVisits <- function(data_src, study_id) {
cat("loading Trial Visits data....")
tv_cols <- c("STUDYID", "DOMAIN", "VISITNUM", "VISIT", "ARMCD", "ARM", "TVSTRL", "TVENRL")
trialVisitsSQL <- paste("SELECT distinct
pv.study_accession,
\"TV\" as domain,
pv.order_number,
pv.name,
ac.arm_accession,
ac.name,
pv.start_rule,
pv.end_rule
FROM planned_visit pv
INNER JOIN
planned_visit_2_arm pv2a ON pv2a.planned_visit_accession=pv.planned_visit_accession
INNER JOIN
arm_or_cohort ac ON ac.arm_accession=pv2a.arm_accession
WHERE pv.study_accession in ('", study_id, "')
ORDER BY pv.order_number", sep = "")
if ((class(data_src)[1] == 'MySQLConnection') ||
(class(data_src)[1] == 'SQLiteConnection')) {
tv_df <- dbGetQuery(data_src, statement = trialVisitsSQL)
colnames(tv_df) <- tv_cols
supptv_df <- data.frame()
if (nrow(tv_df) > 0) {
}
} else {
l <- loadSerializedStudyData(data_src, study_id, "Trial Visits")
tv_df <- l[[1]]
supptv_df <- l[[2]]
}
cat("done", "\n")
tv_l <- list()
if (nrow(tv_df) > 0)
tv_l <- list(tv_df=tv_df, supptv_df=supptv_df)
tv_l
}
# Get count of Trial Visits data of a specific study
#
# The function \code{getCountOfTrialVisits} queries the ImmPort database for count
# of Trial Visits data
#
# @param conn A connection handle to ImmPort database instance
# @param study_id Identifier of a specific study
# @return a count of Trial Visits data
# @examples
# \dontrun{
# # get count of study SDY1's Trial Visits data
# count <- getCountOfTrialVisits(conn, "SDY1")
# }
getCountOfTrialVisits <- function(conn, study_id) {
sql_stmt <- paste("SELECT count(*)
FROM planned_visit pv
WHERE pv.study_accession in ('", study_id, "')", sep = "")
count <- dbGetQuery(conn, statement = sql_stmt)
count[1, 1]
}
##' Trial Visits Domain Variables
##' @name TV
##' @description {
##' \tabular{ll}{
##' \strong{Variable Name } \tab \strong{Variable Label} \cr
##' STUDYID \tab Study Identifier \cr
##' DOMAIN \tab Domain Abbreviation \cr
##' VISITNUM \tab Visit Number \cr
##' VISIT \tab Visit Name \cr
##' ARMCD \tab Planned Arm Code \cr
##' ARM \tab Name of Planned Arm \cr
##' TVSTRL \tab Visit Start Rule \cr
##' TVENRL \tab Visit End Rule
##' }
##' }
NULL
#> NULL
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