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Merged
cristinamullin merged 6 commits into from
Sep 2, 2025
Merged

Assign Use to AU workflow in ExampleMod2 vignette #645

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15cb38a
Assign Use to AU workflow in ExampleMod2 vignette
wokenny13 Aug 22, 2025
a45b7a3
Update ExampleMod2Workflow.Rmd
hillarymarler Aug 25, 2025
e25f1be
when batch_upload = TRUE in TADA_UpdateATTAINSAUMLCrosswalk, filter o…
hillarymarler Aug 25, 2025
27129c0
address check notes and update ExampleMod2Workflow.Rmd
cristinamullin Aug 25, 2025
f78534b
fix documentation and dontrun TADA_CreateWaterUseRef example
cristinamullin Aug 25, 2025
ce0b3a9
update example data and refs
cristinamullin Aug 26, 2025
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25 changes: 18 additions & 7 deletions R/ATTAINSCrosswalks.R
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Original file line number Diff line number Diff line change
Expand Up @@ -204,8 +204,12 @@ TADA_GetATTAINSAUMLCrosswalk <- function(org_id = NULL,
#'
#' @param batch_upload Boolean argument. When batch_upload = TRUE, the column
#' names in the returned df will match the column names required for ATTAINS
#' batch upload. When batch_upload = FALSE, the column names will match those in
#' the TADA workflow. Default is batch_upload = FALSE.
#' batch upload and all WQP Monitoring Locations that have not been matched to
#' an existing Assessment Unit from the user-specified organization are removed
#' from the dataframe. When batch_upload = FALSE, the column names will match
#' those in the TADA workflow and Monitoring Locations not assigned to existing
#' Assessment Units from the user-specified organization will be retained.
#' Default is batch_upload = FALSE.
#'
#' @return When batch_upload = FALSE, A dataframe with six columns:
#' OrganizationIdentifier, ATTAINS.OrganizationIdentifier,
Expand Down Expand Up @@ -252,13 +256,13 @@ TADA_GetATTAINSAUMLCrosswalk <- function(org_id = NULL,
#' "ExampleSite1", "ExampleSite2", "ExampleSite3",
#' "ExampleSite4", "ExampleSite5"
#' )
#'
#'
#' # example water types
#' ATTAINS.WaterType <- c(
#' "BEACH", "BAY", "CREEK",
#' "ESTUARY", "CREEK"
#' )
#'
#'
#' # example urls
#' ATTAINS.MonitoringDataLinkText <- c(
#' "https://www.waterqualitydata.us/provider/STORET/AKDECWQ/",
Expand Down Expand Up @@ -358,8 +362,12 @@ TADA_UpdateATTAINSAUMLCrosswalk <- function(org_id = NULL,
ATTAINS.MonitoringLocationIdentifier = MS_LOCATION_ID,
OrganizationIdentifier = MS_ORG_ID,
ATTAINS.MonitoringDataLinkText = MS_DATA_LINK) %>%
dplyr::rowwise() %>%
dplyr::mutate(ATTAINS.OrganizationIdentifier = org_id,
ATTAINS.WaterType = NA)
ATTAINS.WaterType =
ifelse(
"ATTAINS.WaterType" %in% names(.), ATTAINS.WaterType,
NA_character_ ))
}
}

Expand Down Expand Up @@ -694,6 +702,7 @@ TADA_UpdateATTAINSAUMLCrosswalk <- function(org_id = NULL,
# If batch upload is desired, format the output in the required format.
if (batch_upload == TRUE) {
update.crosswalk <- update.crosswalk %>%
dplyr::filter(!is.na(ATTAINS.AssessmentUnitIdentifier)) %>%
dplyr::select(-c(ATTAINS.WaterType, ATTAINS.OrganizationIdentifier)) %>%
dplyr::rename(ASSESSMENT_UNIT_ID = ATTAINS.AssessmentUnitIdentifier,
MS_ORG_ID = ATTAINS.MonitoringLocationIdentifier,
Expand Down Expand Up @@ -2515,8 +2524,8 @@ 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
#' with reviewing all water type and use name combination from their org.
#' This is a helper function to TADA_CreateUseAURef and is meant to assist users
#' with reviewing all water type and use name combinations from their organization.
#' This function will help to assign ATTAINS use names to any new or modified
#' assessment unit provided from a user's AUMLRef if there are any.
#'
Expand Down Expand Up @@ -2550,7 +2559,9 @@ TADA_CreateUseAURef <- function(.data, org_id = NULL, AUMLRef = NULL, # Required
#' @export
#'
#' @examples
#' \dontrun{
#' TADA_CreateWaterUseRef(TADA_AK_EXAMPLE, org_id = "AKDECWQ")
#' }
#'
TADA_CreateWaterUseRef <- function(.data, org_id = NULL, waterUseRef = NULL) {
# If org_id argument is not provided, this will attempt to pull in org_id from TADA_GetATTAINS.
Expand Down
125 changes: 63 additions & 62 deletions R/DataDiscoveryRetrieval.R
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Expand Up @@ -1051,10 +1051,8 @@ TADA_TribalOptions <- function(tribal_area_type, return_sf = FALSE) {
#'
#' Note: It may be useful to save the Query URL from the WQP as well as a
#' comment within your code. This URL let's you return to the WQP query page
#' with all your selected data filters. For example, this is the query used
#' in the examples for this function:
#' https://www.waterqualitydata.us/#statecode=US%3A09&sampleMedia=water&sampleMedia=Water&startDateLo=01-01-2021&startDateHi=02-01-2021&mimeType=csv&providers=NWIS&providers=STORET
#'
#' with all your selected data filters. See example below.
#'
#' **Extra tip:** Note that the web service call built using the Water
#' Quality Portal uses the inputs startDateLo and startDateHi rather than
#' startDate and endDate, and dates are in the format MM-DD-YYYY rather
Expand All @@ -1071,47 +1069,31 @@ TADA_TribalOptions <- function(tribal_area_type, return_sf = FALSE) {
#' @return WQP Data Profile
#'
#' @export
#'
#'
#' @examples
#' \dontrun{
#' # construct the WQP web service URL for each profile
#' # Define base URL and common components
#' baseurl <- "https://www.waterqualitydata.us"
#' profile_station <- "/data/Station"
#' profile_result <- "/data/Result"
#' profile_result_2 <- "&dataProfile=biological"
#' 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"
#' providers <- "&providers=NWIS&providers=STEWARDS&providers=STORET"
#'
#' physchemresults1 <- TADA_ReadWQPWebServices(paste0(
#' baseurl,
#' profile_station,
#' filters,
#' dates,
#' type,
#' providers
#' ))
#'
#' sites1 <- TADA_ReadWQPWebServices(paste0(
#' baseurl,
#' profile_result,
#' filters,
#' dates,
#' type,
#' profile_result_2,
#' providers
#' ))
#'
#' projects1 <- TADA_ReadWQPWebServices(paste0(
#' baseurl,
#' profile_project,
#' filters,
#' dates,
#' type,
#' providers
#' ))
#' # Construct URLs for different profiles
#' station_url <- paste0(
#' baseurl, "/data/Station", filters, dates, type, providers
#' )
#' result_url <- paste0(
#' baseurl, "/data/Result", filters, dates, type, "&dataProfile=biological", providers
#' )
#' project_url <- paste0(
#' baseurl, "/data/Project", filters, dates, type, providers
#' )
#'
#' # Retrieve data from Water Quality Portal web services
#' physchemresults1 <- TADA_ReadWQPWebServices(station_url)
#' sites1 <- TADA_ReadWQPWebServices(result_url)
#' projects1 <- TADA_ReadWQPWebServices(project_url)
#' }
#'
TADA_ReadWQPWebServices <- function(webservice) {
Expand Down Expand Up @@ -1298,28 +1280,23 @@ TADA_BigDataHelper <- function(record_summary, WQPquery, maxrecs = 250000, maxsi
#'
#' @examples
#' \dontrun{
#' # construct the WQP web service URL for each profile
#' # Define base URL and common components
#' baseurl <- "https://www.waterqualitydata.us"
#' profile_station <- "/data/Station"
#' profile_result <- "/data/Result"
#' profile_result_2 <- "&dataProfile=resultPhysChem"
#' 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"
#' providers <- "&providers=NWIS&providers=STEWARDS&providers=STORET"
#'
#' stationProfile <- TADA_ReadWQPWebServices(
#' paste0(baseurl, profile_station, filters, dates, type, providers)
#' )
#' # Construct URLs for different profiles
#' station_url <- paste0(baseurl, "/data/Station", filters, dates, type, providers)
#' result_url <- paste0(baseurl, "/data/Result", filters,
#' dates, type, "&dataProfile=resultPhysChem", providers)
#' project_url <- paste0(baseurl, "/data/Project", filters, dates, type, providers)
#'
#' physchemProfile <- TADA_ReadWQPWebServices(
#' paste0(baseurl, profile_result, filters, dates, type, profile_result_2, providers)
#' )
#'
#' projectProfile <- TADA_ReadWQPWebServices(
#' paste0(baseurl, profile_project, filters, dates, type, providers)
#' )
#' # Retrieve data from Water Quality Portal web services
#' stationProfile <- TADA_ReadWQPWebServices(station_url)
#' physchemProfile <- TADA_ReadWQPWebServices(result_url)
#' projectProfile <- TADA_ReadWQPWebServices(project_url)
#'
#' # Join all three profiles using TADA_JoinWQPProfiles
#' TADAProfile <- TADA_JoinWQPProfiles(
Expand Down Expand Up @@ -1476,25 +1453,49 @@ make_groups <- function(x, maxrecs) {
#'
#' @examples
#' \dontrun{
#' # Find web service URLs for each Profile using WQP User Interface (https://www.waterqualitydata.us/)
#' # Example WQP URL: https://www.waterqualitydata.us/#statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&providers=NWIS&providers=STEWARDS&providers=STORET
#' # Find web service URLs for each Profile using WQP User Interface
#' # (https://www.waterqualitydata.us/)
#' # Example WQP URL:
#' # https://www.waterqualitydata.us/#statecode=US%3A09&characteristicType=Nutrient&
#' # startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&providers=NWIS&
#' # providers=STEWARDS&providers=STORET
#'
#' # Define base URL and common components
#' baseurl <- "https://www.waterqualitydata.us"
#' filters <- "/search?statecode=US%3A09&characteristicType=Nutrient"
#' dates <- "&startDateLo=04-01-2023&startDateHi=11-01-2023"
#' type <- "&mimeType=csv&zip=yes"
#' providers <- "&providers=NWIS&providers=STEWARDS&providers=STORET"
#'
#' # Construct URLs for different profiles
#' station_url <- paste0(
#' baseurl, "/data/Station", filters, dates, type, providers
#' )
#' result_url <- paste0(
#' baseurl, "/data/Result", filters, dates, type,
#' "&dataProfile=resultPhysChem", providers
#' )
#' project_url <- paste0(
#' baseurl, "/data/Project", filters, dates, type, providers
#' )
#'
#' # Use TADA_ReadWQPWebServices to load the Station, Project, and Phys-Chem Result profiles
#' stationProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Station/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&providers=NWIS&providers=STEWARDS&providers=STORET")
#' physchemProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&dataProfile=resultPhysChem&providers=NWIS&providers=STEWARDS&providers=STORET")
#' projectProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Project/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&providers=NWIS&providers=STEWARDS&providers=STORET")
#' # Use TADA_ReadWQPWebServices to load Station, Project,
#' # and Phys-Chem Result profiles
#' stationProfile <- TADA_ReadWQPWebServices(station_url)
#' physchemProfile <- TADA_ReadWQPWebServices(result_url)
#' projectProfile <- TADA_ReadWQPWebServices(project_url)
#'
#' # Join all three profiles using TADA_JoinWQPProfiles
#' TADAProfile <- TADA_JoinWQPProfiles(
#' FullPhysChem = physchemProfile, Sites = stationProfile,
#' FullPhysChem = physchemProfile,
#' Sites = stationProfile,
#' Projects = projectProfile
#' )
#'
#' # Run TADA_CheckRequiredFields, returns error message,
#' # 'The dataframe does not contain the required fields: ActivityStartDateTime'
#' # Run TADA_CheckRequiredFields, returns error message
#' TADA_CheckRequiredFields(TADAProfile)
#'
#' # Add missing col
#' # Add missing column
#' TADAProfile1 <- TADA_CreateDateTime(
#' .data = TADAProfile,
#' date_col = "ActivityStartDate",
Expand Down
5 changes: 3 additions & 2 deletions R/GeospatialFunctions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3542,14 +3542,15 @@ TADA_CreateAUMLCrosswalk <- function(.data, au_ref = NULL,
sf::st_drop_geometry() %>%
dplyr::select(TADA.MonitoringLocationIdentifier,
ATTAINS.AssessmentUnitIdentifier,
OrganizationIdentifier) %>%
OrganizationIdentifier,
ATTAINS.WaterType) %>%
dplyr::distinct() %>%
dplyr::rename(MS_LOCATION_ID = TADA.MonitoringLocationIdentifier,
ASSESSMENT_UNIT_ID = ATTAINS.AssessmentUnitIdentifier,
MS_ORG_ID = OrganizationIdentifier) %>%
dplyr::mutate(MS_DATA_LINK = NA) %>%
dplyr::select(ASSESSMENT_UNIT_ID, MS_ORG_ID, MS_LOCATION_ID,
MS_DATA_LINK)
MS_DATA_LINK, ATTAINS.WaterType)

final_list <- c(final_list, list("ATTAINS_batchupload" = ATTAINS_batchupload))
}
Expand Down
81 changes: 61 additions & 20 deletions R/RequiredCols.R
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Original file line number Diff line number Diff line change
Expand Up @@ -282,18 +282,36 @@ last.cols <- c(
#'
#' @examples
#' \dontrun{
#' # Find web service URLs for each Profile using WQP User Interface (https://www.waterqualitydata.us/)
#' # Example WQP URL: https://www.waterqualitydata.us/#statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&providers=NWIS&providers=STEWARDS&providers=STORET
#'
#' # Use TADA_ReadWQPWebServices to load the Station, Project, and Phys-Chem Result profiles
#' stationProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Station/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&providers=NWIS&providers=STEWARDS&providers=STORET")
#' physchemProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&dataProfile=resultPhysChem&providers=NWIS&providers=STEWARDS&providers=STORET")
#' projectProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Project/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&providers=NWIS&providers=STEWARDS&providers=STORET")
#' # Find web service URLs for each Profile using WQP User Interface
#' # (https://www.waterqualitydata.us/)
#' # Example WQP URL:
#' # https://www.waterqualitydata.us/#statecode=US%3A09&characteristicType=Nutrient&
#' # startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&providers=NWIS&
#' # providers=STEWARDS&providers=STORET
#'
#' # Define base URL and common components
#' baseurl <- "https://www.waterqualitydata.us"
#' filters <- "/search?statecode=US%3A09&characteristicType=Nutrient"
#' dates <- "&startDateLo=04-01-2023&startDateHi=11-01-2023"
#' type <- "&mimeType=csv&zip=yes"
#' providers <- "&providers=NWIS&providers=STEWARDS&providers=STORET"
#'
#' # Construct URLs for different profiles
#' station_url <- paste0(baseurl, "/data/Station", filters, dates, type, providers)
#' result_url <- paste0(baseurl, "/data/Result", filters, dates, type,
#' "&dataProfile=resultPhysChem", providers)
#' project_url <- paste0(baseurl, "/data/Project", filters, dates, type, providers)
#'
#' # Use TADA_ReadWQPWebServices to load Station, Project, and Phys-Chem Result profiles
#' stationProfile <- TADA_ReadWQPWebServices(station_url)
#' physchemProfile <- TADA_ReadWQPWebServices(result_url)
#' projectProfile <- TADA_ReadWQPWebServices(project_url)
#'
#' # Join all three profiles using TADA_JoinWQPProfiles
#' TADAProfile <- TADA_JoinWQPProfiles(
#' FullPhysChem = physchemProfile,
#' Sites = stationProfile, Projects = projectProfile
#' Sites = stationProfile,
#' Projects = projectProfile
#' )
#'
#' # Run TADA_OrderCols
Expand Down Expand Up @@ -362,25 +380,48 @@ TADA_GetTemplate <- function() {
#'
#' @examples
#' \dontrun{
#' # Find web service URLs for each Profile using WQP User Interface (https://www.waterqualitydata.us/)
#' # Example WQP URL: https://www.waterqualitydata.us/#statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&providers=NWIS&providers=STEWARDS&providers=STORET
#' # Find web service URLs for each Profile using WQP User Interface
#' # (https://www.waterqualitydata.us/)
#' # Example WQP URL:
#' # https://www.waterqualitydata.us/#statecode=US%3A09&characteristicType=Nutrient&
#' # startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&providers=NWIS&
#' # providers=STEWARDS&providers=STORET
#'
#' # Define base URL and common components
#' baseurl <- "https://www.waterqualitydata.us"
#' filters <- "/search?statecode=US%3A09&characteristicType=Nutrient"
#' dates <- "&startDateLo=04-01-2023&startDateHi=11-01-2023"
#' type <- "&mimeType=csv&zip=yes"
#' providers <- "&providers=NWIS&providers=STEWARDS&providers=STORET"
#'
#' # Construct URLs for different profiles
#' station_url <- paste0(
#' baseurl, "/data/Station", filters, dates, type, providers
#' )
#' result_url <- paste0(
#' baseurl, "/data/Result", filters, dates, type,
#' "&dataProfile=resultPhysChem", providers
#' )
#' project_url <- paste0(
#' baseurl, "/data/Project", filters, dates, type, providers
#' )
#'
#' # Use TADA_ReadWQPWebServices to load the Station, Project, and Phys-Chem Result profiles
#' stationProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Station/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&providers=NWIS&providers=STEWARDS&providers=STORET")
#' physchemProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&dataProfile=resultPhysChem&providers=NWIS&providers=STEWARDS&providers=STORET")
#' projectProfile <- TADA_ReadWQPWebServices("https://www.waterqualitydata.us/data/Project/search?statecode=US%3A09&characteristicType=Nutrient&startDateLo=04-01-2023&startDateHi=11-01-2023&mimeType=csv&zip=yes&providers=NWIS&providers=STEWARDS&providers=STORET")
#' # Use TADA_ReadWQPWebServices to load Station, Project, and Phys-Chem profiles
#' stationProfile <- TADA_ReadWQPWebServices(station_url)
#' physchemProfile <- TADA_ReadWQPWebServices(result_url)
#' projectProfile <- TADA_ReadWQPWebServices(project_url)
#'
#' # Join all three profiles using TADA_JoinWQPProfiles
#' # Join profiles using TADA_JoinWQPProfiles
#' TADAProfile <- TADA_JoinWQPProfiles(
#' FullPhysChem = physchemProfile, Sites = stationProfile,
#' FullPhysChem = physchemProfile,
#' Sites = stationProfile,
#' Projects = projectProfile
#' )
#'
#' # Run TADA_CheckRequiredFields, returns error message,
#' # 'The dataframe does not contain the required fields: ActivityStartDateTime'
#' # Run TADA_CheckRequiredFields, returns error message
#' TADA_CheckRequiredFields(TADAProfile)
#'
#' # Add missing col
#' # Add missing column
#' TADAProfile1 <- TADA_CreateDateTime(
#' .data = TADAProfile,
#' date_col = "ActivityStartDate",
Expand All @@ -397,7 +438,7 @@ TADA_GetTemplate <- function() {
#' "ActivityStartTime.TimeZoneCode_offset"
#' ))
#'
#' # re-run TADA_CheckRequiredFields, returns TRUE
#' # Re-run TADA_CheckRequiredFields, returns TRUE
#' TADA_CheckRequiredFields(TADAProfile1)
#' }
#'
Expand Down
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