TADA_CreateParamRef() and TADA_CreateParamUseRef()

.Rbuildignore

@@ -9,3 +9,5 @@ readme.html
 .gitignore
 ^articles
 ^vignettes/articles$
+^vignettes/articles/\.quarto$
+^vignettes/articles/*_files$

.gitignore

@@ -26,3 +26,9 @@ testing_log.txt
 
 # test data from AK
 AK_EPATADA_troubleshooting
+
+# built and rendered vignettes aren't tracked
+inst/doc
+vignettes/*.html
+vignettes/*.R
+**/.quarto/

DESCRIPTION

@@ -72,13 +72,14 @@ Imports:
     nhdplusTools,
     arcgislayers,
     httr,
-    jsonlite,
-    rATTAINS
+    jsonlite, 
+    openxlsx,
+    rATTAINS,
+    DT
 Depends: 
     R (>= 3.5.0)
 Suggests:
     lwgeom,
-    DT,
     RColorBrewer,
     rmarkdown,
     readr,
@@ -91,11 +92,14 @@ Suggests:
     pkgdown,
     spelling,
     htmltools,
-    yaml
+    yaml, 
+    quarto, 
+    remotes
 VignetteBuilder: knitr, rmarkdown
 Language: en-US
 Config/testthat/edition: 3
 Config/testthat/load-all: list(export_all = FALSE, helpers = FALSE)
-URL: https://usepa.github.io/EPATADA/, https://github.com/USEPA/EPATADA, usepa.github.io/EPATADA
+URL: https://usepa.github.io/EPATADA/, https://github.com/USEPA/EPATADA
 LazyData: true
 LazyDataCompression: xz
+Config/Needs/website: quarto, rmarkdown

NAMESPACE

@@ -7,6 +7,7 @@ export(TADA_AutoClean)
 export(TADA_AutoFilter)
 export(TADA_BigDataRetrieval)
 export(TADA_Boxplot)
+export(TADA_CSVExport)
 export(TADA_CalculateTotalNP)
 export(TADA_CharStringRemoveNA)
 export(TADA_CheckRequiredFields)
@@ -16,6 +17,8 @@ export(TADA_ConvertResultUnits)
 export(TADA_ConvertSpecialChars)
 export(TADA_CreateComparableID)
 export(TADA_CreatePairRef)
+export(TADA_CreateParamRef)
+export(TADA_CreateParamUseRef)
 export(TADA_CreateUnitRef)
 export(TADA_DataRetrieval)
 export(TADA_DepthProfilePlot)
@@ -43,10 +46,12 @@ export(TADA_FormatDelimitedString)
 export(TADA_GetATTAINS)
 export(TADA_GetATTAINSAUSiteCrosswalk)
 export(TADA_GetATTAINSOrgIDsRef)
+export(TADA_GetATTAINSParamUseOrgRef)
 export(TADA_GetActivityTypeRef)
 export(TADA_GetCharacteristicRef)
 export(TADA_GetDetCondRef)
 export(TADA_GetDetLimitRef)
+export(TADA_GetEPA304aRef)
 export(TADA_GetMeasureQualifierCodeRef)
 export(TADA_GetMeasureUnitRef)
 export(TADA_GetMonLocByOrgId)

R/ATTAINSRefTables.R

@@ -15,32 +15,32 @@ TADA_GetATTAINSOrgIDsRef <- function() {
   if (!is.null(ATTAINSOrgIDsRef_Cached)) {
     return(ATTAINSOrgIDsRef_Cached)
   }
-  
+
   # Try to download up-to-date raw data
-  
+
   raw.data <- tryCatch(
     {
       # get data from ATTAINS
-    rATTAINS::domain_values(domain_name = "OrgName")
+      rATTAINS::domain_values(domain_name = "OrgName")
     },
     error = function(err) {
       NULL
     }
   )
-  
+
   # If the download failed fall back to internal data (and report it)
   if (is.null(raw.data)) {
     message("Downloading latest ATTAINS Organization Reference Table failed!")
     message("Falling back to (possibly outdated) internal file.")
     return(utils::read.csv(system.file("extdata", "ATTAINSOrgIDsRef.csv", package = "EPATADA")))
   }
-  
+
   ATTAINSOrgIDsRef <- raw.data %>%
     dplyr::distinct()
-  
+
   # Save updated table in cache
   ATTAINSOrgIDsRef_Cached <- ATTAINSOrgIDsRef
-  
+
   ATTAINSOrgIDsRef
 }
 
@@ -53,4 +53,4 @@ TADA_UpdateATTAINSOrgIDsRef <- function() {
 
 
 # Used to store cached Measure Unit Reference Table
-ATTAINSOrgIDsRef_Cached <- NULL
+ATTAINSOrgIDsRef_Cached <- NULL

R/CrosswalksFromATTAINS.R

@@ -2,19 +2,19 @@
 #' Crosswalk from ATTAINS
 #'
 #' Tribes and States who participate in electronic reporting of water quality
-#' conditions through EPA ATTAINS may also submit a crosswalk of WQP 
-#' MonitoringLocationIdentifiers associated with their Assessment Units to 
-#' ATTAINS. If the organization has recorded MonitoringLocationIdentifiers 
+#' conditions through EPA ATTAINS may also submit a crosswalk of WQP
+#' MonitoringLocationIdentifiers associated with their Assessment Units to
+#' ATTAINS. If the organization has recorded MonitoringLocationIdentifiers
 #' associated with their Assessment Units in ATTAINS, this function can be used
 #' to create a crosswalk of known MonitoringLocationIdentifiers and Assessment
-#' Units. All tribal nations record this crosswalk in ATTAINS but only a few 
-#' states. If a state has not supplied Monitoring Location information to 
+#' Units. All tribal nations record this crosswalk in ATTAINS but only a few
+#' states. If a state has not supplied Monitoring Location information to
 #' ATTAINS, the function will not return a data frame.
 #'
-#' @param org_id The ATTAINS organization identifier must be supplied by the 
-#' user. A list of organization identifiers can be found by downloading the 
-#' ATTAINS Domains Excel file: 
-#' https://www.epa.gov/system/files/other-files/2023-09/DOMAINS.xlsx. 
+#' @param org_id The ATTAINS organization identifier must be supplied by the
+#' user. A list of organization identifiers can be found by downloading the
+#' ATTAINS Domains Excel file:
+#' https://www.epa.gov/system/files/other-files/2023-09/DOMAINS.xlsx.
 #' Organization identifiers are listed in the "OrgName" tab. The "code" column
 #' contains the organization identifiers that should be used for this param.
 #'
@@ -32,7 +32,8 @@
 #'
 #' # Pueblo of Tesuque example
 #' PUEBLOOFTESUQUE_crosswalk <- TADA_GetATTAINSAUSiteCrosswalk(
-#' org_id = "PUEBLOOFTESUQUE")
+#'   org_id = "PUEBLOOFTESUQUE"
+#' )
 #'
 #' # Arizona example, returns blank dataframe as of 1/21/25
 #' AZ_crosswalk <- TADA_GetATTAINSAUSiteCrosswalk(org_id = "21ARIZ")
@@ -68,12 +69,13 @@ TADA_GetATTAINSAUSiteCrosswalk <- function(org_id = NULL) {
         MonitoringDataLinkText = monitoring_data_link_text
       ) %>%
       # paste org_id in front of MLs from the specified org if they are missing
-      #from ATTAINS
+      # from ATTAINS
       dplyr::mutate(MonitoringLocationIdentifier = ifelse((
         OrganizationIdentifier == org_id &
-          stringr::str_detect(MonitoringLocationIdentifier, 
-                              org_id, 
-                              negate = TRUE)),
+          stringr::str_detect(MonitoringLocationIdentifier,
+            org_id,
+            negate = TRUE
+          )),
       paste0(org_id, "-", MonitoringLocationIdentifier),
       MonitoringLocationIdentifier
       ))
@@ -108,7 +110,7 @@ TADA_GetATTAINSAUSiteCrosswalk <- function(org_id = NULL) {
 #' This function creates the batch upload files needed to add or update
 #' Monitoring Location Identifiers in ATTAINS Assessment Unit profiles. Users
 #' can specify whether all records should be overwritten (replaced) or if new
-#' Monitoring Location Identifiers should be appended (added) to existing 
+#' Monitoring Location Identifiers should be appended (added) to existing
 #' records.
 #'
 #' @param org_id Character argument. The ATTAINS organization identifier must
@@ -118,39 +120,39 @@ TADA_GetATTAINSAUSiteCrosswalk <- function(org_id = NULL) {
 #' Organization identifiers are listed in the "OrgName" tab. The "code" column
 #' contains the organization identifiers that should be used for this param.
 #'
-#' @param wqp_data_links Character argument. When wqp_data_links is equal to 
-#' "add" or "replace", the function will build the URL for the Water Quality 
-#' Portal Data Site page for each Monitoring Location Identifier in the data 
-#' frame. It will examine the response code of each URL and only retain those 
-#' with a 200 response, which indicates the URL is valid. When 
-#' wqp_data_links = "add", the URL will be added to any existing text in the 
-#' MS_DATA_LINK_TEXT column. When wqp_data_links = "replace", the URL will 
-#' replace any existing text in the MS_DATA_LINK_TEXT column. When 
-#' wqp_data_links = "none", no URLs will be created or added to the returned 
+#' @param wqp_data_links Character argument. When wqp_data_links is equal to
+#' "add" or "replace", the function will build the URL for the Water Quality
+#' Portal Data Site page for each Monitoring Location Identifier in the data
+#' frame. It will examine the response code of each URL and only retain those
+#' with a 200 response, which indicates the URL is valid. When
+#' wqp_data_links = "add", the URL will be added to any existing text in the
+#' MS_DATA_LINK_TEXT column. When wqp_data_links = "replace", the URL will
+#' replace any existing text in the MS_DATA_LINK_TEXT column. When
+#' wqp_data_links = "none", no URLs will be created or added to the returned
 #' data frame. Default is wqp_data_links = "add".
 #'
 #' @param attains_replace Character argument. When attains_replace = FALSE, all
-#' Monitoring Location Identifiers in the user supplied crosswalk will be 
-#' appended to the existing ATTAINS crosswalk. When attains_replace = TRUE, 
-#' Monitoring Location Identifiers will only be retained if they are in the 
+#' Monitoring Location Identifiers in the user supplied crosswalk will be
+#' appended to the existing ATTAINS crosswalk. When attains_replace = TRUE,
+#' Monitoring Location Identifiers will only be retained if they are in the
 #' user supplied crosswalk. Default equals FALSE.
 #'
-#' @param crosswalk A user-supplied dataframe with the columns 
+#' @param crosswalk A user-supplied dataframe with the columns
 #' ASSESSMENT_UNIT_ID, MS_LOCATION_ID, MS_ORG_ID, and MONITORING_DATA_LINK_TEXT
-#' is required. The ASSESSMENT_UNIT_ID and MS_LOCATION_ID must be filled out 
-#' in order to use this function. The additional columns, 
-#' MONITORING_DATA_LINK_TEXT, containing a single URL or "; " separated URLs 
-#' linking to information about the Monitoring Location, and MS_ORG_ID, 
-#' containing the WQP organization identifier for the Monitoring Location can 
-#' be left blank and the function will still run. Data link URLS to WQP site 
-#' pages cannot be automatically generated by this function unless the 
-#' MS_ORG_ID column is populated with the WQP OrganizationIdentifier. When 
+#' is required. The ASSESSMENT_UNIT_ID and MS_LOCATION_ID must be filled out
+#' in order to use this function. The additional columns,
+#' MONITORING_DATA_LINK_TEXT, containing a single URL or "; " separated URLs
+#' linking to information about the Monitoring Location, and MS_ORG_ID,
+#' containing the WQP organization identifier for the Monitoring Location can
+#' be left blank and the function will still run. Data link URLS to WQP site
+#' pages cannot be automatically generated by this function unless the
+#' MS_ORG_ID column is populated with the WQP OrganizationIdentifier. When
 #' crosswalk = NULL, the crosswalk will be downloaded from ATTAINS. This allows
 #' users to add URLs for the Water Quality Portal Data Site pages to the ATTAINS
 #' Assessment Unit profile where possible without updating other information
 #' in ATTAINS.
 #'
-#' @return The csv batch upload files for ATTAINS to add or update 
+#' @return The csv batch upload files for ATTAINS to add or update
 #' Monitoring Locations.
 #'
 #' @export
@@ -165,7 +167,7 @@ TADA_GetATTAINSAUSiteCrosswalk <- function(org_id = NULL) {
 #'   wqp_data_links = "replace"
 #' )
 #'
-#' # Alaska example using a user supplied crosswalk to update entries in 
+#' # Alaska example using a user supplied crosswalk to update entries in
 #' # ATTAINS by appending user supplied information to ATTAINS crosswalk
 #'
 #' # example monitoring location identifiers
@@ -174,40 +176,46 @@ TADA_GetATTAINSAUSiteCrosswalk <- function(org_id = NULL) {
 #'   "AK_M_1021109_013", "AK_M_1021109_013",
 #'   "AK_M_1021109_013"
 #' )
-#' 
+#'
 #' # example organization identifiers
 #' MS_ORG_ID <- c("AKDECWQ", "AKDECWQ", "AKDECWQ", "AKDECWQ", "AKDECWQ")
-#' 
+#'
 #' # example assessment units
-#' MS_LOCATION_ID <- c("ExampleSite1", "ExampleSite2", "ExampleSite3",
-#'                        "ExampleSite4", "ExampleSite5")
+#' MS_LOCATION_ID <- c(
+#'   "ExampleSite1", "ExampleSite2", "ExampleSite3",
+#'   "ExampleSite4", "ExampleSite5"
+#' )
 #' # example urls
 #' MONITORING_DATA_LINK_TEXT <- c(
-#' "https://www.waterqualitydata.us/provider/STORET/AKDECWQ/",
-#' "https://www.waterqualitydata.us/provider/STORET/AKDECWQ/",
-#' "https://www.waterqualitydata.us/provider/STORET/AKDECWQ/",
-#' "https://www.waterqualitydata.us/provider/STORET/AKDECWQ/",
-#' "https://www.waterqualitydata.us/provider/STORET/AKDECWQ/")
+#'   "https://www.waterqualitydata.us/provider/STORET/AKDECWQ/",
+#'   "https://www.waterqualitydata.us/provider/STORET/AKDECWQ/",
+#'   "https://www.waterqualitydata.us/provider/STORET/AKDECWQ/",
+#'   "https://www.waterqualitydata.us/provider/STORET/AKDECWQ/",
+#'   "https://www.waterqualitydata.us/provider/STORET/AKDECWQ/"
+#' )
 #'
 #' # create example crosswalk data frame
-#' ex.user.cw <- data.frame(MS_LOCATION_ID, MS_ORG_ID, ASSESSMENT_UNIT_ID,
-#'                          MONITORING_DATA_LINK_TEXT)
+#' ex.user.cw <- data.frame(
+#'   MS_LOCATION_ID, MS_ORG_ID, ASSESSMENT_UNIT_ID,
+#'   MONITORING_DATA_LINK_TEXT
+#' )
 #'
 #' AK_appenduserdata <- TADA_UpdateMonitoringLocationsInATTAINS(
-#' org_id = "AKDECWQ", 
-#' crosswalk = ex.user.cw, 
-#' attains_replace = FALSE, 
-#' wqp_data_links = "none")
-#'
+#'   org_id = "AKDECWQ",
+#'   crosswalk = ex.user.cw,
+#'   attains_replace = FALSE,
+#'   wqp_data_links = "none"
+#' )
 #' }
 #'
 TADA_UpdateMonitoringLocationsInATTAINS <- function(org_id = NULL,
                                                     crosswalk = NULL,
                                                     attains_replace = FALSE,
                                                     wqp_data_links = "add") {
   # get list of organization identifiers from ATTAINS
-  org.ref <- utils::read.csv(system.file("extdata", "ATTAINSOrgIDsRef.csv", 
-                                         package = "EPATADA"))
+  org.ref <- utils::read.csv(system.file("extdata", "ATTAINSOrgIDsRef.csv",
+    package = "EPATADA"
+  ))
 
   # stop function if organization identifiers is not found in ATTAINS
   if (!org_id %in% org.ref$code) {
@@ -373,8 +381,10 @@ TADA_UpdateMonitoringLocationsInATTAINS <- function(org_id = NULL,
         dplyr::mutate(
           MONITORING_DATA_LINK_TEXT = ifelse(
             grepl("200", response.code),
-            paste0(MONITORING_DATA_LINK_TEXT, "; ", 
-                   MONITORING_DATA_LINK_TEXT.New),
+            paste0(
+              MONITORING_DATA_LINK_TEXT, "; ",
+              MONITORING_DATA_LINK_TEXT.New
+            ),
             MONITORING_DATA_LINK_TEXT
           ),
           MONITORING_DATA_LINK_TEXT = stringr::str_remove_all(
@@ -384,14 +394,20 @@ TADA_UpdateMonitoringLocationsInATTAINS <- function(org_id = NULL,
         ) %>%
         tidyr::separate_rows(MONITORING_DATA_LINK_TEXT, sep = ", ") %>%
         dplyr::group_by(ASSESSMENT_UNIT_ID, MS_ORG_ID, MS_LOCATION_ID) %>%
-        suppressMessages(dplyr::summarise(MONITORING_DATA_LINK_TEXT = 
-                                            paste(
-                                              unique(
-                                                MONITORING_DATA_LINK_TEXT),
-                                              collapse = ", "))) %>%
-        dplyr::select(ASSESSMENT_UNIT_ID, 
-                      MS_ORG_ID, MS_LOCATION_ID, 
-                      MONITORING_DATA_LINK_TEXT) %>%
+        suppressMessages(dplyr::summarise(
+          MONITORING_DATA_LINK_TEXT =
+            paste(
+              unique(
+                MONITORING_DATA_LINK_TEXT
+              ),
+              collapse = ", "
+            )
+        )) %>%
+        dplyr::select(
+          ASSESSMENT_UNIT_ID,
+          MS_ORG_ID, MS_LOCATION_ID,
+          MONITORING_DATA_LINK_TEXT
+        ) %>%
         dplyr::distinct()
     }
     return(update.crosswalk)

R/DataDiscoveryRetrieval.R

@@ -18,7 +18,6 @@
 #' characteristicName and Characteristic Group also work as an AND, therefore the
 #' characteristicName must fall within the Characteristic Group when both are entered.
 #'
-#'
 #' Users can reference the \href{https://www.epa.gov/waterdata/storage-and-retrieval-and-water-quality-exchange-domain-services-and-downloads}{WQX domain tables}
 #' to find allowable values for queries, e.g., reference the WQX domain table to find countycode and statecode: https://cdx.epa.gov/wqx/download/DomainValues/County_CSV.zip
 #' Alternatively, you can use the WQP services to find areas where data is available in the US: https://www.waterqualitydata.us/Codes/countycode
@@ -27,7 +26,7 @@
 #' is important for categorizing result value and detection limit data, as well as
 #' harmonizing key columns used in TADA. See ?TADA_AutoClean for more information.
 #'
-#' Note: TADA_DataRetrieval (by leveraging dataRetrieval),  automatically converts
+#' Note: TADA_DataRetrieval (by leveraging dataRetrieval), automatically converts
 #' the date times to UTC. It also automatically converts the data to dates,
 #' datetimes, numerics based on a standard algorithm. See: ?dataRetrieval::readWQPdata
 #'

R/DepthProfile.R

@@ -661,7 +661,7 @@ TADA_IDDepthProfiles <- function(.data, nresults = TRUE, nvalue = 2, aggregates
 #' data(Data_6Tribes_5y_Harmonized)
 #' # Create a depth profile figure with three parameters for a single monitoring location and date
 #' TADA_DepthProfilePlot(Data_6Tribes_5y_Harmonized,
-#'   groups = c("TEMPERATURE_NA_NA_DEG C", "PH_NA_NA_NA", "DEPTH, SECCHI DISK DEPTH_NA_NA_M"),
+#'   groups = c("TEMPERATURE_NA_NA_DEG C", "PH_NA_NA_STD UNITS", "DEPTH, SECCHI DISK DEPTH_NA_NA_M"),
 #'   location = "REDLAKE_WQX-ANKE",
 #'   activity_date = "2018-10-04"
 #' )