USEPA · mthawley · Jul 7, 2022 · Jul 6, 2022 · Jul 6, 2022
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,10 @@
+## Welcome!
+
+We’re so glad you’re thinking about contributing to an EPA open source project! If you’re unsure about anything, just ask — or submit your issue or pull request anyway. The worst that can happen is we’ll politely ask you to change something. We appreciate all friendly contributions.
+
+We encourage you to read this project’s CONTRIBUTING policy (you are here), its
+LICENSE, and its [README](https://github.com/USEPA/TADA/blob/develop/readme.md).
+
+All contributions to this project will be released under the CCO dedication. By submitting a pull request or issue, you are agreeing to comply with this waiver of copyright interest.
+
+If you have any questions or want to read more, check out the [EPA Open Source Project Repo](https://github.com/USEPA/open-source-projects) and [EPA's Interim Open Source Code Guidance](https://developer.epa.gov/guide/open-source-code/).
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: TADA
 Type: Package
-Title: Tools for Automated Data Assessment (TADA)
+Title: Tools for Automated Data Assessment (TADA) R Package
 Version: 0.0.1
 Author: U.S. Environmental Protection Agency
 Maintainer: Cristina Mullin <[email protected]>

diff --git a/LICENSE → LICENSE.md b/LICENSE → LICENSE.md
diff --git a/R/DataDiscoveryRetrieval.R b/R/DataDiscoveryRetrieval.R
@@ -114,7 +114,7 @@ readWQPwebservice <- function(webservice) {
 #' @return autocleaned TADA data profile 
 #' 
 
-autoclean <- function(.data, clean=TRUE){
+autoclean <- function(.data){
   # check that .data object is compatible with TADA
   # check .data is of class data.frame
   if("data.frame" %in% class(.data) == FALSE) {

diff --git a/R/ResultFlagsIndependent.R b/R/ResultFlagsIndependent.R
@@ -489,11 +489,11 @@ BelowNationalWQXUpperThreshold <- function(.data, clean = TRUE){
 #' Some organizations submit data for this field to indicate if the data 
 #' produced has an approved Quality Assurance Project Plan (QAPP) or not. 
 #' Y indicates yes, N indicates no.  This function has two default inputs: 
-#' clean = TRUE, cleanNA = FALSE. The default removes rows of data where the 
+#' clean = TRUE and cleanNA = FALSE. The default removes rows of data where the 
 #' QAPPApprovedIndicator equals "N". Users could alternatively remove both N's
-#' and NA's using the inputs clean = TRUE, cleanNA = TRUE. If both 
+#' and NA's using the inputs clean = TRUE and cleanNA = TRUE. If both 
 #' clean = FALSE and cleanNA = FALSE, the function will not make any changes to
-#' the dataset.
+#' the data.
 #' 
 #' Note: This is not a required field, so it is often left blank (NA) even if 
 #' the data has an associated QAPP. All states and tribes that collect 
@@ -503,12 +503,15 @@ BelowNationalWQXUpperThreshold <- function(.data, clean = TRUE){
 #' submitted to WQP is NA.
 #'
 #' @param .data TADA dataframe
-#' @param clean Two boolean arguments: 1) remove data where the 
-#' QAPPApprovedIndicator = "N"  when clean = TRUE; 2) remove data where the 
-#' QAPPApprovedIndicator = NA  when cleanNA = TRUE. Default is clean = TRUE and 
-#' cleanNA = FALSE.
-#' @param cleanNA 
-#'
+#' @param clean Boolean argument with two possible values called "TRUE" and 
+#' "FALSE". When clean=TRUE, rows of data where the QAPPApprovedIndicator equals
+#' "N" will be removed. When, clean=FALSE, rows of data where the 
+#' QAPPApprovedIndicator equals "N" will be retained.
+#' @param cleanNA Boolean argument with two possible values called "TRUE" and 
+#' "FALSE". When cleanNA=TRUE, rows of data where the QAPPApprovedIndicator 
+#' equals "NA" will be removed. When, cleanNA=FALSE, rows of data where the 
+#' the QAPPApprovedIndicator equals "NA" will be retained.
+#' 
 #' @return When clean = FALSE and cleanNA = FALSE, no data is removed from the 
 #' dataset.
 #' 

diff --git a/R/Transformations.R b/R/Transformations.R
@@ -1,36 +1,57 @@
 #' Transform Units to WQX Target Units
 #' 
-#' Function compares measure units in the input data to the Water Quality 
-#' Exchange (WQX) 3.0 QAQC Characteristic Validation table. Optional outputs 
-#' include: 1) the dataset with flag columns appended, indicating if data can be 
-#' converted, to which unit it can be converted, and the conversion factor
-#' required to convert measure values, 2) the datset with units and result values
-#' converted to the WQX target unit, or 3) converted result values and units with
-#' flag columns appended, specifying if data can be converted. Default is 
-#' transform = TRUE and flag = TRUE.
-#'
+#' This function compares measure units in the input data to the Water Quality 
+#' Exchange (WQX) 3.0 QAQC Characteristic Validation table. 
+#' 
+#' This function will ALWAYS add the following two columns to the input dataset:
+#' 1) "WQX.ResultMeasureValue.UnitConversion", 
+#' 2) "WQX.DetectionLimitMeasureValue.UnitConversion"
+#' These two fields indicate if data can be converted."NoResultValue" means data
+#' cannot be converted because there is no ResultMeasureValue, and "NoTargetUnit"
+#' means data cannot be converted because the original unit is not associated with a target unit in WQX. 
+#' "Convert" means the data can be transformed, and "Converted" means that this function 
+#' has been run with the input transform = TRUE, and the values were already converted.
+#' 
+#' It also uses the following six fields from the input dataset:
+#' 1) "CharacteristicName",
+#' 2) "ActivityMediaName",
+#' 3) "ResultMeasureValue",
+#' 4) "ResultMeasure.MeasureUnitCode",
+#' 5) "DetectionQuantitationLimitMeasure.MeasureValue",
+#' 6) "DetectionQuantitationLimitMeasure.MeasureUnitCode"
+#' 
+#' This function adds the following two fields and transforms values within the 
+#' following four fields ONLY when transform=TRUE:
+#' Adds: "ResultMeasureUnitCode.Original", and "DetectionLimitMeasureUnitCode.Original".
+#' Transforms: "ResultMeasureValue", "ResultMeasure.MeasureUnitCode", "DetectionQuantitationLimitMeasure.MeasureValue", and "DetectionQuantitationLimitMeasure.MeasureUnitCode".
+#' 
+#' This function adds the following two fields ONLY when transform=FALSE:
+#' Adds: "WQX.ConversionFactor" and "WQX.TargetUnit".
+#' 
 #' @param .data TADA dataset
-#' @param transform Boolean argument; changes ResultMeasure.MeasureUnitCode and 
-#' DetectionQuantitationLimitMeasure.MeasureUnitCode to WQX target unit and 
-#' converts ResultMeasureValue and DetectionQuantitationLimitMeasure.MeasureValue
-#' to corresponding target unit when transform = TRUE. Default is transform = TRUE.
-#' @param flag Boolean argument; appends WQX.ResultMeasureValue.UnitConversion and
-#' WQX.DetectionLimitMeasureValue.UnitConversion columns, indicating if data can be
-#' converted. "Transform" means data can be converted, "NoResultValue" means data
-#' cannot be converted because there is no ResultMeasureValue, and "NoTargetUnit" 
-#' means data cannot be converted because the original unit is not associated 
-#' with a target unit in WQX. Default is flag = TRUE.
+#' 
+#' @param transform Boolean argument with two possible values, “TRUE” and “FALSE”.
+#' Default is transform = TRUE.
 #'
-#' @return When transform = FALSE and flag = TRUE, flag columns are appended to 
-#' the dataset only. When transform = TRUE and flag = TRUE, flag columns are 
-#' appended to the dataset and unit conversions are executed. When transform = TRUE
-#' and flag = FALSE, unit conversions are executed only. When transform = FALSE and
-#' flag = FALSE, an error is returned (function would return the input dataframe
-#' unchanged if input was allowed).
+#' @return When transform=TRUE, result values and units are converted to WQX target units. 
+#' This function changes the values within the "ResultMeasure.MeasureUnitCode"
+#' and "DetectionQuantitationLimitMeasure.MeasureUnitCode" to the WQX target units and 
+#' converts respective values within the "ResultMeasureValue" and "DetectionQuantitationLimitMeasure.MeasureValue"
+#' fields. In addition to "WQX.ResultMeasureValue.UnitConversion"
+#' and "WQX.DetectionLimitMeasureValue.UnitConversion", transform=TRUE will add
+#' the following two fields to the input dataset, "ResultMeasureUnitCode.Original", 
+#' and "DetectionLimitMeasureUnitCode.Original", to retain the original result
+#' and unit values.
+#' 
+#' When transform = FALSE, result values and units are NOT converted to WQX target units, 
+#' but columns are appended to indicate what the target units and conversion factors are,
+#' and if the data can be converted. In addition to "WQX.ResultMeasureValue.UnitConversion"
+#' and "WQX.DetectionLimitMeasureValue.UnitConversion",  transform=FALSE will add the 
+#' following two fields to the input dataset: "WQX.ConversionFactor" and "WQX.TargetUnit".
 #' 
 #' @export
 
-WQXTargetUnits <- function(.data, transform = TRUE, flag = TRUE){
+WQXTargetUnits <- function(.data, transform = TRUE){
 
   # check that .data object is compatible with TADA
   # check .data is of class data.frame
@@ -49,14 +70,6 @@ WQXTargetUnits <- function(.data, transform = TRUE, flag = TRUE){
   if(is.logical(transform) == FALSE){
     stop("transform argument must be Boolean (TRUE or FALSE)")
   }
-  # check if flag is boolean
-  if(is.logical(flag) == FALSE){
-    stop("flag argument must be Boolean (TRUE or FALSE)")
-  }
-  # check that both transform and flag do NOT equal FALSE
-  if(transform == FALSE & flag == FALSE){
-    stop("Both 'transform' and 'flag' arguments equal FALSE, which would return the input dataset unchanged. One or both arguments must be equal to TRUE.")
-  }
 
   # execute function after checks are passed
   if(all(c("CharacteristicName", "ActivityMediaName", "ResultMeasureValue",
@@ -102,8 +115,7 @@ WQXTargetUnits <- function(.data, transform = TRUE, flag = TRUE){
             TRUE ~ WQX.ConversionFactor))
       }
 
-    # add flag column when flag = TRUE
-    if(flag == TRUE) {
+
     # add WQX.ResultMeasureValue.UnitConversion column
     flag.data <- flag.data %>%
       # apply function row by row
@@ -124,7 +136,6 @@ WQXTargetUnits <- function(.data, transform = TRUE, flag = TRUE){
            !is.na(WQX.TargetUnit)) ~ as.character("Convert"),
         is.na(DetectionQuantitationLimitMeasure.MeasureValue) ~ as.character("NoDetectionLimitValue"),
         is.na(WQX.TargetUnit) ~ as.character("NoTargetUnit")))
-    }
 
     if(transform == FALSE) {
 
@@ -148,7 +159,7 @@ WQXTargetUnits <- function(.data, transform = TRUE, flag = TRUE){
                         .after = "DetectionQuantitationLimitMeasure.MeasureUnitCode")
 
 
-      warning("Conversions required for range checks and TADATargetUnit conversions -- Unit conversions, data summaries, and data calculations may be affected.")
+      print("Conversions required for range checks and TADATargetUnit conversions -- Unit conversions, data summaries, and data calculations may be affected.")
       return(flag.data)
     }
 
@@ -200,7 +211,7 @@ WQXTargetUnits <- function(.data, transform = TRUE, flag = TRUE){
           !is.na(WQX.TargetUnit) ~ WQX.TargetUnit,
           is.na(WQX.TargetUnit) ~ DetectionQuantitationLimitMeasure.MeasureUnitCode))
 
-      if(flag == TRUE) {
+
       # edit WQX.ResultMeasureValue.UnitConversion column
       clean.data <- clean.data %>%
         # apply function row by row
@@ -218,7 +229,7 @@ WQXTargetUnits <- function(.data, transform = TRUE, flag = TRUE){
         dplyr::mutate(WQX.DetectionLimitMeasureValue.UnitConversion = dplyr::case_when(
           (!is.na(DetectionQuantitationLimitMeasure.MeasureValue) & !is.na(WQX.TargetUnit)) ~ as.character("Converted"),
           TRUE ~ WQX.DetectionLimitMeasureValue.UnitConversion))
-      }
+
 
       # remove extraneous columns, fix field names
       clean.data <- clean.data %>%
@@ -228,27 +239,27 @@ WQXTargetUnits <- function(.data, transform = TRUE, flag = TRUE){
       # get .data column names
       col.order <- colnames(.data)
       # add ResultUnitConversion column to the list if flag = TRUE
-      if(flag == TRUE){
-        col.order <- append(col.order, c("WQX.ResultMeasureValue.UnitConversion",
+
+      col.order <- append(col.order, c("WQX.ResultMeasureValue.UnitConversion",
                                         "WQX.DetectionLimitMeasureValue.UnitConversion"))
-      }
+
       # add original units to list if transform = TRUE
       if(transform == TRUE){
         col.order <- append(col.order, c("ResultMeasureUnitCode.Original",
                                          "DetectionLimitMeasureUnitCode.Original"))
-      }
+
       # reorder columns in clean.data
       clean.data <- clean.data[, col.order]
-      # place flag columns next to relevant fields if flag = TRUE
-      if(flag == TRUE){
+
+      # place flag columns next to relevant fields
         clean.data <- clean.data %>%
           dplyr::relocate("ResultMeasureUnitCode.Original", 
                           .after = "ResultMeasure.MeasureUnitCode") %>%
           dplyr::relocate("WQX.DetectionLimitMeasureValue.UnitConversion", 
                           .after = "DetectionQuantitationLimitMeasure.MeasureUnitCode")
-      }
+
       # Place original unit columns next to original columns
-      if(transform == TRUE){
+
         clean.data <- clean.data %>%
           dplyr::relocate("WQX.ResultMeasureValue.UnitConversion", 
                           .after = "ResultMeasure.MeasureUnitCode") %>%

diff --git a/R/Utilities.R b/R/Utilities.R
@@ -69,7 +69,7 @@ RemoveEmptyColumns <- function(.data){
 #' 
 #' for numeric data type
 #'
-#' @param .data TADA dataset
+#' @param x Numeric data field from TADA profile
 #' 
 #' @return Number of values to the right of the decimal point for numeric type data.
 #' 
@@ -87,12 +87,12 @@ decimalplaces <- function(x) {
 #' 
 #' for character data type
 #'
-#' @param .data TADA dataset
+#' @param x Numeric data field from TADA profile
 #' 
 #' @return Number of values to the right of the decimal point for character type data.
 #' 
 #'  
 
 decimalnumcount<-function(x){stopifnot(class(x)=="character")
   x<-gsub("(.*)(\\.)|(*$)","",x)
-  nchar(x)}
+  nchar(x)}
diff --git a/man/QAPPapproved.Rd b/man/QAPPapproved.Rd