Testdata

DESCRIPTION

@@ -43,8 +43,8 @@ Imports:
 Depends: 
     R (>= 3.5.0)
 Suggests: 
+    rlang,
     remotes, 
-    rlang, 
     tidyverse,
     knitr,
     rmarkdown,

R/DataDiscoveryRetrieval.R

@@ -271,11 +271,43 @@ autoclean <- function(.data) {
 
   # run MeasureValueSpecialCharacters function
   .data <- MeasureValueSpecialCharacters(.data)
-
+
+  #convert 'meters' to 'm'
+  .data$ActivityDepthHeightMeasure.MeasureUnitCode[.data$ActivityDepthHeightMeasure.MeasureUnitCode == 'meters'] <- 'm'
+  .data$ActivityTopDepthHeightMeasure.MeasureUnitCode[.data$ActivityTopDepthHeightMeasure.MeasureUnitCode == 'meters'] <- 'm'
+  .data$ActivityBottomDepthHeightMeasure.MeasureUnitCode[.data$ActivityBottomDepthHeightMeasure.MeasureUnitCode == 'meters'] <- 'm'
+  .data$ResultDepthHeightMeasure.MeasureUnitCode[.data$ResultDepthHeightMeasure.MeasureUnitCode == 'meters'] <- 'm'
+  .data$ResultMeasure.MeasureUnitCode[.data$ResultMeasure.MeasureUnitCode == 'meters'] <- 'm'
+
   return(.data)
 }
 
 
+#' autoclean
+#'
+#' Removes complex biological data. Removes non-water media samples.
+#' Removes rows of data that are true duplicates. Capitalizes fields to harmonize
+#' data. This function includes and runs the TADA "MeasureValueSpecialCharacters" 
+#' function as well. 
+#'
+#' Within "BiologicalIntentName", only the allowable values "tissue", "toxicity",
+#' and "NA" apply to non-biological data (the function removes all others).
+#' Toxicity and fish tissue data will be kept, but other types of biological
+#' monitoring data will not.
+#'
+#' We decided to make some fields uppercase that way they're more compatible
+#' with the WQX validation reference tables and to avoid any issues with
+#' case-sensitivity when joining data. Therefore, we might need to tack on any
+#' immediate QA steps (removing true duplicates, converting result values to numeric,
+#' capitalizing letters, etc.) to this function, as well as the other retrieval functions.
+#'
+#' @param .data TADA dataframe
+#'
+#' @return cleaned TADA data profile
+#'
+
+
+
 #' TADA Profile Check
 #'
 #' This function checks if the column names in a dataframe include the TADA

R/Transformations.R

@@ -312,7 +312,7 @@ WQXTargetUnits <- function(.data, transform = TRUE) {
 #' Function generates a harmonization reference table that is specific to
 #' the input dataset. Users can review how their input data relates to standard
 #' TADA values for CharacteristicName, ResultSampleFractionText,
-#' MethodSpecicationName, and ResultMeasure.MeasureUnitCode and they can optionally
+#' MethodSpecificationName, and ResultMeasure.MeasureUnitCode and they can optionally
 #' edit the reference file to meet their needs.
 #'
 #' @param .data TADA dataframe