USEPA · cristinamullin · Jun 16, 2025 · Jun 13, 2025 · Jun 13, 2025 · Jun 14, 2025
diff --git a/R/DataDiscoveryRetrieval.R b/R/DataDiscoveryRetrieval.R
@@ -1070,11 +1070,11 @@ TADA_TribalOptions <- function(tribal_area_type, return_sf = FALSE) {
 #' @examples
 #' \dontrun{
 #' # construct the WQP web service URL for each profile
-#' baseurl <- "https://www.waterqualitydata.us/data/"
-#' profile_station <- "Station"
-#' profile_result <- "Result"
+#' baseurl <- "https://www.waterqualitydata.us"
+#' profile_station <- "/data/Station"
+#' profile_result <- "/data/Result"
 #' profile_result_2 <- "&dataProfile=biological"
-#' profile_project <- "Project"
+#' profile_project <- "/data/Project"
 #' filters <- "/search?statecode=US%3A09&sampleMedia=water&sampleMedia=Water"
 #' dates <- "&startDateLo=01-01-2021&startDateHi=02-01-2021"
 #' type <- "&mimeType=csv&zip=yes"
@@ -1291,11 +1291,11 @@ TADA_BigDataHelper <- function(record_summary, WQPquery, maxrecs = 250000, maxsi
 #' @examples
 #' \dontrun{
 #' # construct the WQP web service URL for each profile
-#' baseurl <- "https://www.waterqualitydata.us/data/"
-#' profile_station <- "Station"
-#' profile_result <- "Result"
+#' baseurl <- "https://www.waterqualitydata.us"
+#' profile_station <- "/data/Station"
+#' profile_result <- "/data/Result"
 #' profile_result_2 <- "&dataProfile=resultPhysChem"
-#' profile_project <- "Project"
+#' profile_project <- "/data/Project"
 #' filters <- "/search?statecode=US%3A09&characteristicType=Nutrient"
 #' dates <- "&startDateLo=04-01-2023&startDateHi=11-01-2023"
 #' type <- "&mimeType=csv&zip=yes"
@@ -1392,7 +1392,16 @@ TADA_JoinWQPProfiles <- function(FullPhysChem = "null",
   } else {
     join2 <- join1
   }
-
+  # check to make sure project cols have been added (a few of these are
+  # required TADA cols for the shiny app to run & for package checks to pass)
+  # even if blank
+  if (all(Filter(function(x) !any(grepl("TADA.", x)), require.cols) %in% names(join2)) == FALSE) {
+    join2[c(
+      "ProjectDescriptionText",
+      "SamplingDesignTypeCode", "QAPPApprovedIndicator", "QAPPApprovalAgencyName",
+      "ProjectFileUrl", "ProjectMonitoringLocationWeightingUrl"
+    )] <- NA
+  }
   return(join2)
 }
 

diff --git a/R/ExampleData.R b/R/ExampleData.R
@@ -121,14 +121,3 @@ NULL
 #' @usage data(Data_HUC8_02070004_Mod1Output)
 #' @format A data frame with 84 rows and 161 variables
 NULL
-
-#' cybertown
-#'
-#' See TADACybertown2025.Rmd in vignettes folder.
-#'
-#' @docType data
-#' @keywords data frame
-#' @name cybertown
-#' @usage data(cybertown)
-#' @format A data frame with 990 rows and 150 variables
-NULL
diff --git a/R/Utilities.R b/R/Utilities.R
@@ -1899,7 +1899,7 @@ TADA_CreateCSV <- function(.data) {
 
   downloads_path <- file.path(Sys.getenv("USERPROFILE"), "Downloads", paste0(df_name, ".csv"))
 
-  write.csv(.data, file = downloads_path, row.names = FALSE)
+  utils::write.csv(.data, file = downloads_path, row.names = FALSE)
 
   cat("File saved to:", gsub("/", "\\\\", downloads_path), "\n")
 }
diff --git a/data/Data_6Tribes_5y_Harmonized.rda b/data/Data_6Tribes_5y_Harmonized.rda
diff --git a/data/Data_HUC8_02070004_Mod1Output.rda b/data/Data_HUC8_02070004_Mod1Output.rda
diff --git a/data/Data_NCTCShepherdstown_HUC12.rda b/data/Data_NCTCShepherdstown_HUC12.rda
diff --git a/data/Data_Nutrients_UT.rda b/data/Data_Nutrients_UT.rda
diff --git a/data/Data_R5_TADAPackageDemo.rda b/data/Data_R5_TADAPackageDemo.rda
diff --git a/data/cybertown.rda b/data/cybertown.rda
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -381,7 +381,6 @@ crs
 csv
 cwa
 dailyagg
-dataProfile
 dataRetrieval
 dateTime
 datetimes

diff --git a/inst/extdata/WQXCharacteristicRef.csv b/inst/extdata/WQXCharacteristicRef.csv
@@ -521,7 +521,6 @@
 "(Z)-Octadec-9-enyl (5-(((2-(((perfluorooctyl)sulphonyl)methylamino)ethoxy)carbonyl)amino)-o-tolyl)carbamate","Accepted",""
 "(Z,Z)-11,13-Hexadecadienal","Accepted",""
 "({4-[(1,2,3,3,4,4,5,5,6,6,6-Undecafluorohex-1-en-1-yl)oxy]phenyl}methyl)phosphonic acid","Accepted",""
-".Alpha.-Pinene","Accepted",""
 ".alpha.,.alpha.-Dimethylphenethylamine","Accepted",""
 ".alpha.,2,6-Trichlorotoluene","Accepted",""
 ".alpha.-1,2,3,4,5,6-Hexachlorocyclohexane-D6 or alpha-HCH D6","Accepted",""
@@ -540,6 +539,7 @@
 ".alpha.-Methylstyrene","Accepted",""
 ".alpha.-Naphthylthiourea","Accepted",""
 ".alpha.-Nitrotoluene","Accepted",""
+".alpha.-Pinene","Accepted",""
 ".alpha.-Terpineol","Accepted",""
 ".alpha.-[2-Hydroxy-3-[.alpha.-perfluoroisopropylpoly(degree of polymerization 7-15)(difluoromethylene)]propyl]-.omega.-methoxy-poly(degree of polymerization 1-25)(oxyethylene)","Accepted",""
 ".beta.-1,2,5,6-Tetrabromocyclooctane","Accepted",""
@@ -4541,7 +4541,6 @@
 "2,2-Dimethyldecane","Accepted",""
 "2,2-Dimethylheptane","Accepted",""
 "2,2-Dimethylhexane","Accepted",""
-"2,2-Dimethylpentane","Accepted",""
 "2,2-Dimethylpropane","Accepted",""
 "2,2-Oxybis(2-chloropropane)","Accepted",""
 "2,2-Propanediamine, 1,1,1,3,3,3-hexafluoro-","Accepted",""
@@ -11966,7 +11965,7 @@
 "Condition class, recreational (Microcystin)","Accepted",""
 "Condition class, recreational Cyanobacteria (bluegreen)","Accepted",""
 "Conditions Preventing Sampling","Accepted",""
-"Conductance","Accepted",""
+"Conductance","Accepted","Conductivity"
 "Conductivity","Accepted",""
 "Conductivity, Debye-Huckel-Onsager","Accepted",""
 "Consolidated-Undrained Triaxial C","Accepted",""
@@ -12166,6 +12165,7 @@
 "Cyclohexane, 1,1,2,2,3,3,4,5,5,6-decafluoro-4,6-bis(trifluoromethyl)-","Accepted",""
 "Cyclohexane, 1,2,3,4,5-pentafluoro-6-(1,1,2,2,3,3,3-heptafluoropropyl)-","Accepted",""
 "Cyclohexane, 1,2,4-trimethyl-, (1R,2R,4R)-rel-","Accepted",""
+"Cyclohexane, 2-ethyl-1,1,3-trimethyl-","Accepted",""
 "Cyclohexane, 4-chloro-1,1-bis(trifluoromethyl)-","Accepted",""
 "Cyclohexane, butyl-","Accepted",""
 "Cyclohexane, decafluoro-","Accepted",""
@@ -12546,7 +12546,8 @@
 "Depth, Photic zone includes bottom (Y/N) (choice list)","Accepted",""
 "Depth, Secchi disk depth","Accepted",""
 "Depth, Secchi disk depth (choice list)","Accepted",""
-"Depth, Secchi disk depth reappears","Accepted",""
+"Depth, Secchi disk depth disappears","Accepted","Depth, Secchi disk depth"
+"Depth, Secchi disk depth reappears","Accepted","Depth, Secchi disk depth"
 "Depth, Secchi disk visible at bottom (Y/N) (choice list)","Accepted",""
 "Depth, below bottom surface","Accepted",""
 "Depth, bottom","Accepted",""
@@ -14014,6 +14015,7 @@
 "Forchlorfenuron","Accepted",""
 "Forest Age (choice list)","Accepted",""
 "Formaldehyde","Accepted",""
+"Formamide, N,N'-[dithiobis[2-(2-hydroxyethyl)-1-methyl-2,1-ethenediyl]]bis[N-[(4-amino-2-methyl-5-pyrimidinyl)methyl]-","Accepted",""
 "Formate","Accepted",""
 "Formation code","Accepted",""
 "Formetanate","Accepted",""
@@ -16959,6 +16961,7 @@
 "Nonane, 1,1,1,2,3,3,7,7,8,9,9,9-dodecafluoro-4-methyl-","Accepted",""
 "Nonane, 1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8-hexadecafluoro-9-methoxy-","Accepted",""
 "Nonane, 1-[(1,1,2,2,3,3,4,4,5,5,6,6,6-tridecafluorohexyl)oxy]-","Accepted",""
+"Nonane, 2,2,4,4,6,8,8-heptamethyl-","Accepted",""
 "Nonane, heptadecafluoro-1-[(2,2,3,3,4,4,5,5,6,6,7,7,8,8,8-pentadecafluorooctyl)oxy]-","Accepted",""
 "Nonanedioic acid, 4,4,5,5,6,6-hexafluoro-3,7-dioxo-2,8-bis(triphenylphosphoranylidene)-, diethyl ester","Accepted",""
 "Nonanethioic acid, 2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,9-heptadecafluoro-, S-[3-(trimethoxysilyl)propyl] ester","Accepted",""
@@ -17909,6 +17912,7 @@
 "Pentane, 1,1,1,2,3,3-hexafluoro-4-(1,1,2,3,3,3-hexafluoropropoxy)-","Accepted",""
 "Pentane, 1,1,1,2,3,3-hexafluoro-4-methyl-","Accepted",""
 "Pentane, 1,1-dichloro-2,2,3,3,4,4,5,5-octafluoro-1-(propylthio)-","Accepted",""
+"Pentane, 2,2-dimethyl-","Accepted",""
 "Pentane, 3,3-dimethyl-","Accepted",""
 "Pentane, 5-chloro-1,1,2,2,3,3,4,4-octafluoro-","Accepted",""
 "Pentanedioic acid","Accepted",""
@@ -20622,16 +20626,16 @@
 "Site Disturbance (text)","Accepted",""
 "Site Disturbance Evident (choice list)","Accepted",""
 "Site Erosion (text)","Accepted",""
+"Site NOT Verified (Y/N) (choice list)","Accepted",""
 "Site Sampleability Detail","Accepted",""
 "Site Sampleability Status","Accepted",""
 "Site Sampled (Y/N) (choice list)","Accepted",""
-"Site Verified (Y/N) (choice list)","Accepted",""
-"Site Verified By GPS","Accepted",""
-"Site Verified By Local Contact","Accepted",""
-"Site Verified By Other","Accepted",""
-"Site Verified By Roads","Accepted",""
-"Site Verified By Signs","Accepted",""
-"Site Verified By Topographic Map","Accepted",""
+"Site Verified by GPS","Accepted",""
+"Site Verified by Local Contact","Accepted",""
+"Site Verified by Other","Accepted",""
+"Site Verified by Roads","Accepted",""
+"Site Verified by Signs","Accepted",""
+"Site Verified by Topographic Map","Accepted",""
 "Site Visit Number","Accepted",""
 "Sky Code (CA SWAMP) (choice list)","Accepted",""
 "Slavina","Accepted",""
@@ -21765,7 +21769,9 @@
 "Toxicity sediment survival","Accepted",""
 "Toxicity sediment survival significant","Accepted",""
 "Toxicity water 100%/ LC50 (% effluent)","Accepted",""
+"Toxicity water IC25","Accepted",""
 "Toxicity water LC50","Accepted",""
+"Toxicity water LOEC","Accepted",""
 "Toxicity water microtox","Accepted",""
 "Toxicity water norm embryo","Accepted",""
 "Toxicity, A. abdita, coefficient of variation**retired**useBiologicalSample,SubjectTaxon,IntentToxicity","Deprecated",""
@@ -21811,6 +21817,7 @@
 "Transect Spacing - Actual","Accepted",""
 "Transect Spacing - Intended","Accepted",""
 "Transit Rate, sampler","Accepted",""
+"Transmittance at 254 nm","Accepted",""
 "Transmittance, Horizontal","Accepted",""
 "Transparency, Secchi tube with disk","Accepted",""
 "Transparency, tube with disk","Accepted",""