testing vignette

R/Utilities.R

@@ -1,26 +1,3 @@
-#' Apply Conversions
-#' 
-#' **placeholder text for function description
-#'
-#' @param .data TADA dataset
-#' @param Include Conversions to execute (should input be a column name? Or 
-#' groups of columns, which have their own group ID? Where would we put this
-#' group ID info, another reference table? within the function?)
-#' @param Exclude ibid, but conversions to not execute
-#'
-#' @return Full TADA dataset with data conversions executed. Function defaults 
-#' to convert the following: (**note all columns/type of data included in 
-#' conversions).
-#' Users can specify which conversions to exclude.
-#' @export
-#' 
-
-
-ApplyConversions <- function(.data, Include, Exclude){
-
-}
-
-
 #' AutoFilter
 #' 
 #' This function can be used to autofilter and simplify a WQP dataset. 
@@ -39,7 +16,6 @@ ApplyConversions <- function(.data, Include, Exclude){
 #' @export
 
 
-
 AutoFilter <- function(.data, clean = TRUE){
 
   field.names <- colnames(.data)
@@ -71,24 +47,6 @@ AutoFilter <- function(.data, clean = TRUE){
 }
 
 
-#' Filter
-#' 
-#' @param .data TADA dataset
-#' 
-#' @return Full TADA dataset with data removed
-#' 
-#' @export
-
-
-Filter <- function(.data){
-
-# Remove all data where media name does NOT equal WATER (ignore punctuation)
-dplyr::filter(.data, ActivityMediaName == "Water")
-
-  return(.data)
-}
-
-
 #' RemoveEmptyColumns
 #' 
 #' @param .data TADA dataset

vignettes/testing.Rmd

@@ -16,8 +16,12 @@ knitr::opts_chunk$set(
 )
 ```
 
+Load TADA library and update internal TADA package validation and reference tables
 ```{r setup}
 library(TADA)
+UpdateWQXCharValRef()
+#UpdateMeasureUnitRef()
+#HarmonizationRefTable()
 ```
 
 Read in WQP data using WQP web services directly 
@@ -43,12 +47,44 @@ original data filters, but it cannot be used to download the data.
 WQP query URL: https://www.waterqualitydata.us/#statecode=US%3A42&characteristicType=Nutrient&mimeType=csv&dataProfile=resultPhysChem&providers=NWIS&providers=STEWARDS&providers=STORET
 
 ```{r}
+#get PA nutrient data
 TADAProfileRaw=readWQPwebservice("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A42&characteristicType=Nutrient&mimeType=csv&zip=yes&dataProfile=resultPhysChem&providers=NWIS&providers=STEWARDS&providers=STORET")
 ```
 
 
+Clean raw data for TADA use case
 ```{r}
+#autoclean
+TADAProfileClean=AggregatedContinuousData(TADAProfileClean)
+```
+
+Run result flag functions and address flagged data
+```{r}
+#TADAProfileClean=UncommonAnalyticalMethodID(TADAProfileClean)
+TADAProfileClean=PotentialDuplicateRowID(TADAProfileClean)
+TADAProfileClean=AboveNationalWQXUpperThreshold(TADAProfileClean)
+TADAProfileClean=BelowNationalWQXUpperThreshold(TADAProfileClean)
+TADAProfileClean=QAPPapproved(TADAProfileClean)
+TADAProfileClean=QAPPDocAvailable(TADAProfileClean)
+TADAProfileClean=InvalidCoordinates(TADAProfileClean)
+TADAProfileClean=InvalidFraction(TADAProfileClean)
+TADAProfileClean=InvalidSpeciation(TADAProfileClean)
+TADAProfileClean=InvalidResultUnit(TADAProfileClean)
+```
+
+Address result values with special characters
+```{r}
+MeasureValueSpecialCharacters
+```
 
+Apply unit conversions
+```{r}
+DepthProfileData
+WQXTargetUnits
 ```
 
+Transform Characteristic, Speciation, and Unit values to TADA Standards
+```{r}
+HarmonizeData
+```