v0.1.122 Added validation_occurrencestatus_notstandard data check

Author: PoGibas

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bdchecks
 Title: Biodiversity Data Checks
 Description: Supplies a set of functions to perform and manage data checks for biodiversity data. 
-Version: 0.1.121
+Version: 0.1.122
 Date: 2019-12-22
 License: GPL-3 | file LICENSE
 URL: https://github.com/bd-R/bdchecks

NAMESPACE

@@ -41,6 +41,7 @@ export(dc_validation_month_notstandard)
 export(dc_validation_occurrenceid_empty)
 export(dc_validation_occurrenceid_notstandard)
 export(dc_validation_occurrencestatus_empty)
+export(dc_validation_occurrencestatus_notstandard)
 export(dc_validation_order_notfound)
 export(dc_validation_phylum_notfound)
 export(dc_validation_scientificname_empty)

R/dc_validation_occurrencestatus_notstandard.R

@@ -0,0 +1,20 @@
+#' @rdname dc_validation_occurrencestatus_notstandard
+#' 
+#' @param TARGET a vector of occurrenceStatus information. To pass it must be
+#' within given reference dictionary.
+#' @param sources a vector of available sources.
+#' 
+dc_validation_occurrencestatus_notstandard <- function(
+  TARGET = NULL,
+  sources = c(
+    "present",
+    "absent"
+  )
+) {
+  result <- TARGET %>%
+    gsub(" ", "", .) %>% # Remove possible spaces
+    gsub("_| |\\.|-", "", .) %>% # Remove seperators
+    tolower()
+  result <- result %in% sources
+  return(perform_dc_missing(result, TARGET))
+}

R/documentation_validation_occurrencestatus_notstandard.R

@@ -0,0 +1,21 @@
+#'
+#' Data check validation_occurrencestatus_notstandard Check if occurrenceStatus is specified source authority service.
+#'
+#'     This data check answers: "Is occurrenceStatus within given source authority list?" question.\cr Data check will pass if \strong{The value for occurrenceStatus is present and correct.} and will fail if \strong{The value for occurrenceStatus is missing or incorrect.}.\cr Dimension of this data check is \strong{} and it's flagging type is: \strong{FLAG}\cr Example of entries that will pass: \code{occurrenceStatus=present}, such data check would return \code{TRUE}.\cr Example of entries that will fail: \code{occurrenceStatus=observed}, such data check would return \code{FALSE}.
+#' @name dc_validation_occurrencestatus_notstandard
+#' @format An object of class function to perform a specific data check.
+#' @references None
+#' @examples 
+#' perform_dc(data_bats, 'validation_occurrencestatus_notstandard')
+#' @section samplePassData:
+#' The value for occurrenceStatus is present and correct.
+#' @section sampleFailData:
+#' The value for occurrenceStatus is missing or incorrect.
+#' @section targetDWCField:
+#' occurrenceStatus
+#' @section checkCategory:
+#'  occurrence
+#' @importFrom magrittr %>%
+#' @export
+#' @keywords vocabulary,validation
+NULL

R/sysdata.rda

@@ -2210,3 +2210,50 @@ DC_validation_dateidentified_notstandard:
     output_standard_fail: not_compliant 
     output_standard_missing: internal_prerequisites_not_met
     merge_targets: FALSE
+DC_validation_occurrencestatus_notstandard:
+  name: validation_occurrencestatus_notstandard
+  meta:
+    information:
+      description: Check if occurrenceStatus is specified source authority service.
+      question: Is occurrenceStatus within given source authority list?
+      darwin_core_class: occurrence
+      data_quality_dimension: conformance
+      dimension: other
+      output: validation
+      severity:
+      warning: invalid
+      resolution:
+        record: single_record
+        term:
+      keywords: vocabulary,validation
+      guid: 7af25f1e-a4e2-4ff4-b161-d1f25a5c3e47
+    example:
+      pass: The value for occurrenceStatus is present and correct.
+      fail: The value for occurrenceStatus is missing or incorrect.
+      input_pass: occurrenceStatus=present
+      input_fail: occurrenceStatus=observed
+      output_pass: TRUE
+      output_fail: FALSE
+    pseudocode: |
+      occurrenceStatus %in% reference
+    source:
+      resource: https://github.com/tdwg/bdq/issues/116
+      reference: http://rs.tdwg.org/dwc/terms/index.htm#occurrenceStatus
+      creator: 
+      creation:
+      maintainer: Povilas Gibas
+      modification: 2019-12-22
+    notes:
+  input:
+    target: occurrenceStatus
+    target2:
+    dependency:
+      dependency_type: internal
+      data_checks:
+      rpackages:
+      data:
+  output:
+    output_standard_pass: compliant
+    output_standard_fail: not_compliant 
+    output_standard_missing: internal_prerequisites_not_met
+    merge_targets: FALSE

inst/extdata/data_check.yaml

@@ -495,3 +495,15 @@ validation_dateidentified_notstandard:
     - [Orange, irrelevent, fail]
     - ["", missing, fail]
   comment:
+validation_occurrencestatus_notstandard:
+  data:
+    - [occurrenceStatus, type, expected]
+    - [present, correct, pass]
+    - [absent, correct, pass]
+    - [Present, correct, pass]
+    - [ABSENT, correct, pass]
+    - [' present ', correct, pass]
+    - [Observed, incorrect, fail]
+    - [-2000, irrelevent, fail]
+    - ["", missing, fail]
+  comment: