USEPA · cristinamullin · Oct 20, 2025 · Feb 1, 2024 · Feb 2, 2024 · May 10, 2024
diff --git a/R/ATTAINSCrosswalks.R b/R/ATTAINSCrosswalks.R
@@ -162,7 +162,6 @@ TADA_GetATTAINSAUMLCrosswalk <- function(org_id = NULL,
 }
 
 
-
 #' Update Monitoring Location Identifier and Assessment Unit Identifier
 #' Crosswalk in ATTAINS
 #'
@@ -1456,7 +1455,6 @@ TADA_CreateParamRef <- function(.data, org_id = NULL, paramRef = NULL, auto_assi
 }
 
 
-
 #' Create or Update ATTAINS Parameter and Use crosswalk
 #'
 #' This function generates a crosswalk of all parameters and uses applicable to
@@ -2161,7 +2159,6 @@ TADA_CreateUseParamRef <- function(.data, org_id = NULL, paramRef = NULL, usePar
 }
 
 
-
 #' ATTAINS Assessment Unit and Use Name Crosswalk
 #'
 #' This function pulls in all prior ATTAINS Use names associated with each
@@ -2606,7 +2603,6 @@ TADA_CreateUseAURef <- function(.data, org_id = NULL, AUMLRef = NULL, # Required
 }
 
 
-
 #' Helper Function to Apply Uses to Unassigned Assessment Units by Water Type
 #'
 #' This is a helper function to TADA_CreateUseAURef and is meant to help users
@@ -2725,7 +2721,6 @@ TADA_CreateWaterUseRef <- function(.data, org_id = NULL, waterUseRef = NULL) {
 }
 
 
-
 #' Review and Apply Any Site-specific Criteria to Monitoring Location Sites or Assessment Units
 #'
 #' This function will pull in all unique MonitoringLocationName, MonitoringLocationType,

diff --git a/R/ContinuousDataFunctions.R b/R/ContinuousDataFunctions.R
@@ -205,9 +205,7 @@ TADA_listNWIS <- function(aoi_sf = "null", statecode = "null", siteid = "null")
               err_msg <- as.character(e$message)
 
               # Check for HTTP 404 in the error message
-              if (grepl("404", err_msg)) {
-
-              } else {
+              if (grepl("404", err_msg)) {} else {
                 # For any other error, stop with server error message
                 stop(paste0("Something went wrong:", err_msg, " See https://waterservices.usgs.gov/docs/site-service/site-service-details/#error-codes."))
               }
@@ -302,9 +300,7 @@ TADA_listNWIS <- function(aoi_sf = "null", statecode = "null", siteid = "null")
               err_msg <- as.character(e$message)
 
               # Check for HTTP 404 in the error message
-              if (grepl("404", err_msg)) {
-
-              } else {
+              if (grepl("404", err_msg)) {} else {
                 # For any other error, stop with server error message
                 stop(paste0("Something went wrong:", err_msg, " See https://waterservices.usgs.gov/docs/site-service/site-service-details/#error-codes."))
               }
@@ -532,9 +528,7 @@ TADA_getNWIS <- function(aoi_sf = "null", statecode = "null", siteid = "null", p
               err_msg <- as.character(e$message)
 
               # Check for HTTP 404 in the error message
-              if (grepl("404", err_msg)) {
-
-              } else {
+              if (grepl("404", err_msg)) {} else {
                 # For any other error, stop with server error message
                 stop(paste0("Something went wrong: ", err_msg, " See https://waterservices.usgs.gov/docs/site-service/site-service-details/#error-codes."))
               }
@@ -579,9 +573,7 @@ TADA_getNWIS <- function(aoi_sf = "null", statecode = "null", siteid = "null", p
               err_msg <- as.character(e$message)
 
               # Check for HTTP 404 in the error message
-              if (grepl("404", err_msg)) {
-
-              } else {
+              if (grepl("404", err_msg)) {} else {
                 # For any other error, stop with server error message
                 stop(paste0("Something went wrong:", err_msg, " See https://waterservices.usgs.gov/docs/site-service/site-service-details/#error-codes."))
               }

diff --git a/R/CriteriaComparison.R b/R/CriteriaComparison.R
@@ -300,7 +300,6 @@ TADA_PairForCriteriaCalc <- function(.data, ref = "null", hours_range = 4) {
       dplyr::rename_with(~ paste0("TADA.", group.id, "MethodSpeciationName"), TADA.MethodSpeciationName)
 
 
-
     # identify dynamically named columns
     pair_char_name <- paste0("TADA.", group.id, "Name")
     pair_result_val <- paste0("TADA.", group.id, ".ResultMeasureValue")

diff --git a/R/CriteriaMethods.R b/R/CriteriaMethods.R
@@ -988,7 +988,6 @@ TADA_DefineCriteriaMethodology <- function(.data,
 }
 
 
-
 #' Data Dictionary for Criteria and Methodology
 #'
 #' Defines and summarizes the column names found in the TADA format for the

diff --git a/R/Figures.R b/R/Figures.R
@@ -795,7 +795,6 @@ TADA_FieldValuesPie <- function(.data, field = "null", characteristicName = "nul
 }
 
 
-
 #' Create Scatterplot(s)
 #'
 #' @param .data TADA dataframe containing the data downloaded from the

diff --git a/R/GeospatialFunctions.R b/R/GeospatialFunctions.R
@@ -544,7 +544,6 @@ fetchATTAINS <- function(.data, catchments_only = FALSE) {
     )
 
 
-
     return(final_features)
 
     # If area is small (< 6e+9 square meters), just use the bbox in one pull:
@@ -2589,7 +2588,6 @@ TADA_ViewATTAINS <- function(.data, ref_icons = TRUE) {
 }
 
 
-
 #' Identify and group nearby monitoring locations (UNDER ACTIVE DEVELOPMENT)
 #'
 #' This function takes a TADA dataset and identifies the NHD catchments that
@@ -3124,7 +3122,6 @@ TADA_FindNearbySites <- function(.data, dist_buffer = 100,
 }
 
 
-
 #' Get grouped monitoring stations that are near each other
 #'
 #' This function takes a TADA dataset that contains grouped nearby monitoring stations
@@ -3167,7 +3164,6 @@ TADA_GetUniqueNearbySites <- function(.data) {
 }
 
 
-
 #' Generate a random WQP dataset
 #'
 #' Retrieves data for a period of time in the past 20 years using
@@ -3261,7 +3257,6 @@ TADA_RandomTestingData <- function(number_of_days = 1, choose_random_state = FAL
 }
 
 
-
 #' TADA_CreateAUMLCrosswalk
 #'
 #' Create the assessment unit and monitoring location ref by utilizing an optional

diff --git a/R/RequiredCols.R b/R/RequiredCols.R
@@ -341,7 +341,6 @@ TADA_OrderCols <- function(.data) {
 }
 
 
-
 #' Get TADA Template
 #'
 #' This function returns a blank TADA template that can be used as a starting
@@ -365,7 +364,6 @@ TADA_GetTemplate <- function() {
 }
 
 
-
 #' TADA Required Fields Check
 #'
 #' This function checks if all fields required to run TADA functions are included in the input

diff --git a/R/ResultFlagsDependent.R b/R/ResultFlagsDependent.R
@@ -61,9 +61,12 @@ TADA_FlagFraction <- function(.data, clean = TRUE, flaggedonly = FALSE) {
   if (("TADA.SampleFraction.Flag" %in% colnames(.data)) == TRUE) {
     .data <- dplyr::select(.data, -TADA.SampleFraction.Flag)
   }
-  # read in sample fraction reference table from extdata and filter
-  frac.ref <- utils::read.csv(system.file("extdata", "WQXcharValRef.csv", package = "EPATADA")) %>%
-    dplyr::filter(Type == "CharacteristicFraction")
+  # read in fraction reference table from extdata and filter
+  file_path <- system.file("extdata", "WQXcharValRef.rda", package = "EPATADA")
+  load(file_path)
+  rm(file_path)
+  frac.ref <- dplyr::filter(WQXcharValRef, Type == "CharacteristicFraction")
+  rm(WQXcharValRef)
 
   # join "TADA.WQXVal.Flag" column to .data by CharacteristicName and Value (SampleFraction)
   check.data <- merge(.data, frac.ref[, c("Characteristic", "TADA.WQXVal.Flag", "Value")],
@@ -217,8 +220,11 @@ TADA_FlagSpeciation <- function(.data, clean = c("suspect_only", "nonstandardize
   }
 
   # read in speciation reference table from extdata and filter
-  spec.ref <- utils::read.csv(system.file("extdata", "WQXcharValRef.csv", package = "EPATADA")) %>%
-    dplyr::filter(Type == "CharacteristicSpeciation")
+  file_path <- system.file("extdata", "WQXcharValRef.rda", package = "EPATADA")
+  load(file_path)
+  rm(file_path)
+  spec.ref <- dplyr::filter(WQXcharValRef, Type == "CharacteristicSpeciation")
+  rm(WQXcharValRef)
 
   # join "TADA.WQXVal.Flag" column to .data by CharacteristicName and Value (Speciation)
   check.data <- merge(.data, spec.ref[, c("Characteristic", "TADA.WQXVal.Flag", "Value")],
@@ -299,7 +305,6 @@ TADA_FlagSpeciation <- function(.data, clean = c("suspect_only", "nonstandardize
 }
 
 
-
 #' Check Result Unit Validity
 #'
 #' Function checks the validity of each characteristic-media-result unit
@@ -416,8 +421,11 @@ TADA_FlagResultUnit <- function(.data, clean = c("suspect_only", "nonstandardize
   }
 
   # read in unit reference table from extdata and filter
-  unit.ref <- utils::read.csv(system.file("extdata", "WQXcharValRef.csv", package = "EPATADA")) %>%
-    dplyr::filter(Type == "CharacteristicUnit")
+  file_path <- system.file("extdata", "WQXcharValRef.rda", package = "EPATADA")
+  load(file_path)
+  rm(file_path)
+  unit.ref <- dplyr::filter(WQXcharValRef, Type == "CharacteristicUnit")
+  rm(WQXcharValRef)
 
   # join "TADA.WQXVal.Flag" column to .data by CharacteristicName, Source (Media), and Value (unit)
   check.data <- merge(.data, unit.ref[, c("Characteristic", "Source", "TADA.WQXVal.Flag", "Value")],
@@ -633,7 +641,6 @@ TADA_FindQCActivities <- function(.data, clean = FALSE, flaggedonly = FALSE) {
 }
 
 
-
 #' Pair Replicates with Original Samples
 #'
 #' This function looks for replicate samples and pairs them to their original or
@@ -781,7 +788,6 @@ TADA_PairReplicates <- function(.data, type = c("QC_replicate"), time_difference
 }
 
 
-
 #' Check for results with suspect result Measure Qualifier Codes
 #'
 #' This function checks for and flags or removes samples denoted as suspect
-Original file line number
+Diff line change
@@ Expand Up / @@ -988,7 +988,6 @@ TADA_DefineCriteriaMethodology <- function(.data, @@
     }
     #' Data Dictionary for Criteria and Methodology
     #'
     #' Defines and summarizes the column names found in the TADA format for the
@@ Expand Down @@