BODC flag scheme added

R/AllClass.R

@@ -776,26 +776,26 @@ initializeFlagSchemeInternal <- function(object, name=NULL, mapping=NULL, debug=
     if (!is.null(object@metadata$flagScheme))
         warning("cannot alter a flagScheme that is already is place")
     else {
-        predefined <- c("WHP CTD", "WHP bottle", "argo")
+        predefined <- c("argo", "BODC", "WHP bottle", "WHP CTD")
         if (name %in% predefined) {
-            if (name == "WHP CTD") {
-                if (!is.null(mapping))
-                    stop("cannot redefine the mapping for existing scheme named \"WHP CTD\"")
-                mapping <- list(not_calibrated=1, acceptable=2, questionable=3,
-                                bad=4, not_reported=5, interpolated=6,
-                                despiked=7, missing=9)
+            if (!is.null(mapping))
+                stop("cannot redefine the mapping for existing scheme named \"", name, "\"")
+            if (name == "argo") {
+                mapping <- list(not_assessed=0, passed_all_tests=1, probably_good=2,
+                                probably_bad=3, bad=4, averaged=7,
+                                interpolated=8, missing=9)
+            } else  if (name == "BODC") {
+                mapping <- list(no_quality_control=0, good=1, probably_good=2,
+                                probably_bad=3, bad=4, changed=5, below_detection=6,
+                                in_excess=7, interpolated=8, missing=9)
             } else if (name == "WHP bottle") {
-                if (!is.null(mapping))
-                    stop("cannot redefine the mapping for existing scheme named \"WHP bottle\"")
                 mapping <- list(no_information=1, no_problems_noted=2, leaking=3,
                                 did_not_trip=4, not_reported=5, discrepency=6,
                                 unknown_problem=7, did_not_trip=8, no_sample=9)
-            } else if (name == "argo") {
-                if (!is.null(mapping))
-                    stop("cannot redefine the mapping for existing scheme named \"argo\"")
-                mapping <- list(not_assessed=0, passed_all_tests=1, probably_good=2,
-                                probably_bad=3, bad=4, averaged=7,
-                                interpolated=8, missing=9)
+            } else if (name == "WHP CTD") {
+                mapping <- list(not_calibrated=1, acceptable=2, questionable=3,
+                                bad=4, not_reported=5, interpolated=6,
+                                despiked=7, missing=9)
             } else {
                 stop("internal coding error in initializeFlagSchemeInternal(); please report to developer")
             }

man-roxygen/initializeFlagSchemeTemplate.R

@@ -18,19 +18,36 @@
 #' The following pre-defined schemes are available (note that the
 #' names are simplified from the phrases used in defining
 #' documentation):
+#'
 #' \itemize{
-#' \item \code{name="WHP CTD"} defaults \code{mapping} to
-#' \code{list(not_calibrated=1, acceptable=2, questionable=3,
-#'     bad=4, not_reported=5, interpolated=6,
-#'     despiked=7, missing=9)}
-#' \item \code{name="WHP bottle"} defaults \code{mapping} to
-#' \code{list(no_information=1, no_problems_noted=2, leaking=3,
-#'     did_not_trip=4, not_reported=5, discrepency=6,
-#'     unknown_problem=7, did_not_trip=8, missing=9)}
+#'
 #' \item \code{name="argo"} defaults \code{mapping} to
 #' \code{list(not_assessed=0, passed_all_tests=1, probably_good=2,
-#'     probably_bad=3, bad=4, averaged=7,
-#'     interpolated=8, missing=9)}
+#'            probably_bad=3, bad=4, averaged=7,
+#'            interpolated=8, missing=9)}.
+#' See [1] for a deeper explanation of the meanings of these codes.
+#'
+#' \item \code{name="BODC"} defaults \code{mapping} to
+#' \code{list(no_quality_control=0, good=1, probably_good=2,
+#'            probably_bad=3, bad=4, changed=5,
+#'            below_detection=6, in_excess=7, interpolated=8,
+#'            missing=9)}.
+#' See [2] for a deeper explanation of the meanings of these codes,
+#' and note that codes \code{A} and \code{Q} are not provided in
+#' oce.
+#'
+#' \item \code{name="WHP bottle"} defaults \code{mapping} to
+#' \code{list(no_information=1, no_problems_noted=2, leaking=3,
+#'                 did_not_trip=4, not_reported=5, discrepency=6,
+#'                 unknown_problem=7, did_not_trip=8, no_sample=9)}.
+#' See [3] for a deeper explanation of the meanings of these codes.
+#'
+#' \item \code{name="WHP CTD"} defaults \code{mapping} to
+#' \code{list(not_calibrated=1, acceptable=2, questionable=3,
+#'                 bad=4, not_reported=5, interpolated=6,
+#'                 despiked=7, missing=9)}.
+#' See [3] for a deeper explanation of the meanings of these codes.
+#'
 #'}
 #'
 #' \strong{Specific to the <%=class%> objects:}
@@ -54,11 +71,14 @@
 #' @return An object with the \code{metadata} slot containing \code{flagScheme}.
 #'
 #' @references
-#' 1. The codes for \code{"WHP CTD"} and \code{"WHP bottle"} are defined at
-#' \url{https://www.nodc.noaa.gov/woce/woce_v3/wocedata_1/whp/exchange/exchange_format_desc.htm}
-#'
-#' 2. The codes for \code{"Argo"} are defined at
+#' 1. The codes for \code{"Argo"} are defined at
 #' \url{http://www.oceannetworks.ca/data-tools/data-quality}
 #'
+#' 2. The codes for \code{"BODC"} are defined at
+#' \url{http://seadatanet.maris2.nl/v_bodc_vocab_v2/browse.asp?order=conceptid&formname=search&screen=0&lib=l20}
+#'
+#' 3. The codes for \code{"WHP CTD"} and \code{"WHP bottle"} are defined at
+#' \url{https://www.nodc.noaa.gov/woce/woce_v3/wocedata_1/whp/exchange/exchange_format_desc.htm}
+#'
 #' @family functions relating to data-quality flags
 

tests/testthat/test_flags.R

@@ -11,24 +11,30 @@ test_that("argument existence", {
 
 test_that("predefined flag schemes", {
           data(ctd)
-          a <- initializeFlagScheme(ctd, "WHP CTD")
+          a <- initializeFlagScheme(ctd, "argo")
           expect_equal(a[["flagScheme"]],
-                       list(name="WHP CTD",
-                            mapping=list(not_calibrated=1, acceptable=2, questionable=3,
-                                         bad=4, not_reported=5, interpolated=6,
-                                         despiked=7, missing=9)))
+                       list(name="argo",
+                            mapping=list(not_assessed=0, passed_all_tests=1, probably_good=2,
+                                         probably_bad=3, bad=4, averaged=7,
+                                         interpolated=8, missing=9)))
+          a <- initializeFlagScheme(ctd, "BODC")
+          expect_equal(a[["flagScheme"]],
+                       list(name="BODC",
+                            mapping=list(no_quality_control=0, good=1, probably_good=2,
+                                         probably_bad=3, bad=4, changed=5, below_detection=6,
+                                         in_excess=7, interpolated=8, missing=9)))
           a <- initializeFlagScheme(ctd, "WHP bottle")
           expect_equal(a[["flagScheme"]],
                        list(name="WHP bottle",
                             mapping=list(no_information=1, no_problems_noted=2, leaking=3,
                                          did_not_trip=4, not_reported=5, discrepency=6,
                                          unknown_problem=7, did_not_trip=8, no_sample=9)))
-          a <- initializeFlagScheme(ctd, "argo")
+          a <- initializeFlagScheme(ctd, "WHP CTD")
           expect_equal(a[["flagScheme"]],
-                       list(name="argo",
-                            mapping=list(not_assessed=0, passed_all_tests=1, probably_good=2,
-                                         probably_bad=3, bad=4, averaged=7,
-                                         interpolated=8, missing=9)))
+                       list(name="WHP CTD",
+                            mapping=list(not_calibrated=1, acceptable=2, questionable=3,
+                                         bad=4, not_reported=5, interpolated=6,
+                                         despiked=7, missing=9)))
 })
 
 test_that("user-created flag scheme", {