USEPA · cristinamullin · May 27, 2025 · May 20, 2025 · May 20, 2025 · May 21, 2025
diff --git a/R/ContinuousDataFunctions.R b/R/ContinuousDataFunctions.R
@@ -5,7 +5,7 @@
 #' @description
 #' Retrieves available metadata from USGS National Water Information System (NWIS) based on
 #' different spatial queries: area of interest (AOI), specific sites, or state boundaries.
-#' Returns a spatial sf object containing continuous monitoring site information and 
+#' Returns a spatial sf object containing continuous monitoring site information and
 #' available parameters and statistics.
 #' If no data is found, returns an empty sf object with appropriate column structure.
 #'
@@ -15,7 +15,7 @@
 #' @param statecode Character vector of two-letter state codes (e.g., c("CA", "OR")).
 #' @param siteid Character vector of USGS site numbers.
 #'
-#' @return An sf object containing NWIS continuous monitoring site summary 
+#' @return An sf object containing NWIS continuous monitoring site summary
 #' information including:
 #'   \itemize{
 #'     \item site_no: USGS site identification number
@@ -129,22 +129,20 @@ TADA_listNWIS <- function(aoi_sf = "null", statecode = "null", siteid = "null")
   }
 
   # Daily stats info grabber:
-  
+
   stats_table <- function() {
-
     site_url <- "https://help.waterdata.usgs.gov/stat_code"
-    
+
     table <- rvest::read_html(site_url) %>%
       rvest::html_nodes("table") %>%
       rvest::html_table() %>%
       .[[1]] %>%
       dplyr::mutate(stat_cd = sprintf("%05d", `Statistic Type Code`)) %>%
       dplyr::select(stat_cd, stat_type = `Statistic Type Description`)
-    
+
     return(table)
-
   }
-  
+
   # Grab NWIS by an area of interest:
   if ((unlist(aoi_sf)[1] != "null")) {
     og_epsg <- sf::st_crs(aoi_sf)$epsg
@@ -388,7 +386,7 @@ TADA_listNWIS <- function(aoi_sf = "null", statecode = "null", siteid = "null")
     ) %>%
     # Remove any duplicates if they exist (precautionary - they shouldn't!)
     dplyr::distinct(., .keep_all = TRUE)
-  
+
   # If no data, return empty data frame
   if (nrow(inventory) == 0) {
     message("No daily USGS-NWIS data in specified query.")
@@ -401,7 +399,7 @@ TADA_listNWIS <- function(aoi_sf = "null", statecode = "null", siteid = "null")
 #' Retrieve and tidy daily values from NWIS
 #'
 #' This function interfaces with the USGS National Water Information System (NWIS) to
-#' retrieve daily values (DV) water quality data using the TADA (Tools for Automated 
+#' retrieve daily values (DV) water quality data using the TADA (Tools for Automated
 #' Data Analysis) framework. Users can query data based on a spatial area of interest
 #' (AOI), a vector of state abbreviations, or a vector of specific site ids, along
 #' with relevant USGS parameter codes, statistics to return, and a date range.
@@ -434,16 +432,16 @@ TADA_listNWIS <- function(aoi_sf = "null", statecode = "null", siteid = "null")
 #'   dplyr::filter(NAME %in% c("Spokane", "Navajo Nation"))
 #' sites_aoi_sf <- TADA_getNWIS(
 #'   aoi_sf = locs_sf,
-#'    parameter_codes =
-#'     c("00060", "00010"), 
-#'     start_date = "2020-01-01", 
-#'     end_date = "2020-01-31"
+#'   parameter_codes =
+#'     c("00060", "00010"),
+#'   start_date = "2020-01-01",
+#'   end_date = "2020-01-31"
 #' )
 #'
 #' # Example 2: Query by specific site numbers
 #' sites_specific <- TADA_getNWIS(
 #'   siteid = c("11530500", "11532500"),
-#'   parameter_codes = c("00060", "00010"), 
+#'   parameter_codes = c("00060", "00010"),
 #'   start_date = "2020-01-01",
 #'   end_date = "2020-12-31"
 #' )
@@ -452,7 +450,7 @@ TADA_listNWIS <- function(aoi_sf = "null", statecode = "null", siteid = "null")
 #' nwis_data <- TADA_getNWIS(
 #'   statecode = c("RI", "CO"),
 #'   stat_codes = c("00001"),
-#'   parameter_codes = c("00010"), 
+#'   parameter_codes = c("00010"),
 #'   start_date = "2020-01-01",
 #'   end_date = "2020-01-02"
 #' )

diff --git a/R/DataDiscoveryRetrieval.R b/R/DataDiscoveryRetrieval.R
@@ -83,6 +83,7 @@
 #'        See https://www.waterqualitydata.us/Codes/project for options.
 #' @param providers Leave blank to include all, or specify "STEWARDS", "STORET" (i.e., WQX), and/or
 #'        "NWIS". See https://www.waterqualitydata.us/Codes/providers for options.
+#' @param bBox The latitude and longitude extent. Includes four numbers, e.g. bBox <- c(-xmin, ymin, -xmax, ymax).
 #' @param maxrecs Maximum number of records to query at once (i.e., without breaking into smaller
 #'        queries).
 #' @param ask A logical value (TRUE or FALSE) indicating whether the user should be asked for approval before
@@ -165,6 +166,9 @@
 #'   endDate = "2023-12-31",
 #'   ask = FALSE
 #' )
+#'
+#' bbox <- c(-86.9736, 34.4883, -86.6135, 34.6562)
+#' tada8 <- TADA_DataRetrieval(bBox = bbox)
 #' }
 #'
 TADA_DataRetrieval <- function(startDate = "null",
@@ -184,6 +188,7 @@ TADA_DataRetrieval <- function(startDate = "null",
                                organization = "null",
                                project = "null",
                                providers = "null",
+                               bBox = "null",
                                maxrecs = 350000,
                                ask = TRUE,
                                applyautoclean = TRUE) {
@@ -312,6 +317,14 @@ TADA_DataRetrieval <- function(startDate = "null",
     } else if (providers != "null") {
       WQPquery <- c(WQPquery, providers = providers)
     }
+
+    # bbox
+    if (length(bBox) > 1) {
+      WQPquery <- c(WQPquery, bBox = list(bBox))
+    } else if (bBox != "null") {
+      WQPquery <- c(WQPquery, bBox = bBox)
+    }
+
     # Organization
     if (length(organization) > 1) {
       WQPquery <- c(WQPquery, organization = list(organization))
@@ -744,6 +757,13 @@ TADA_DataRetrieval <- function(startDate = "null",
       WQPquery <- c(WQPquery, providers = providers)
     }
 
+    # bbox
+    if (length(bBox) > 1) {
+      WQPquery <- c(WQPquery, bBox = list(bBox))
+    } else if (bBox != "null") {
+      WQPquery <- c(WQPquery, bBox = bBox)
+    }
+
     if (length(organization) > 1) {
       WQPquery <- c(WQPquery, organization = list(organization))
     } else if (organization != "null") {

diff --git a/R/ExampleData.R b/R/ExampleData.R
@@ -121,3 +121,14 @@ 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/Figures.R b/R/Figures.R
@@ -647,7 +647,7 @@ TADA_FlaggedSitesMap <- function(.data) {
 #'
 #' @param .data TADA dataframe after running TADA.FindNearbySites.
 #' @param dist_buffer Distance in m to show a radius around each site marker.
-#' 
+#'
 #'
 #' @return A leaflet map that shows all sites in the dataframe that contain
 #' flagged data in the form of near other sites - groups of sites that are spatially located within
@@ -668,61 +668,69 @@ TADA_FlaggedSitesMap <- function(.data) {
 #' }
 #'
 TADA_NearbySitesMap <- function(.data, dist_buffer = 100) {
-
-  if(c("TADA.NearbySiteGroup") %in% colnames(.data) == FALSE) {
+  if (c("TADA.NearbySiteGroup") %in% colnames(.data) == FALSE) {
     .data <- TADA_FindNearbySites(.data)
   }
 
   .data <- .data %>%
     dplyr::filter(!is.na(TADA.NearbySiteGroup)) %>%
-    dplyr::mutate(LatitudeMeasure = as.numeric(LatitudeMeasure),
-                  LongitudeMeasure = as.numeric(LongitudeMeasure)) %>%
-    dplyr::select(LongitudeMeasure, LatitudeMeasure, TADA.MonitoringLocationIdentifier,
-                  MonitoringLocationIdentifier, MonitoringLocationName, TADA.LatitudeMeasure,
-                  TADA.LongitudeMeasure, OrganizationIdentifier, TADA.NearbySiteGroup) %>%
-    dplyr::distinct() 
-
-  icon.colors <- grDevices::rainbow(as.numeric(length(unique(.data$TADA.NearbySiteGroup)))) 
-
-  pal <- leaflet::colorFactor(palette = icon.colors,
-                     domain = .data$TADA.NearbySiteGroup)
-
+    dplyr::mutate(
+      LatitudeMeasure = as.numeric(LatitudeMeasure),
+      LongitudeMeasure = as.numeric(LongitudeMeasure)
+    ) %>%
+    dplyr::select(
+      LongitudeMeasure, LatitudeMeasure, TADA.MonitoringLocationIdentifier,
+      MonitoringLocationIdentifier, MonitoringLocationName, TADA.LatitudeMeasure,
+      TADA.LongitudeMeasure, OrganizationIdentifier, TADA.NearbySiteGroup
+    ) %>%
+    dplyr::distinct()
+
+  icon.colors <- grDevices::rainbow(as.numeric(length(unique(.data$TADA.NearbySiteGroup))))
+
+  pal <- leaflet::colorFactor(
+    palette = icon.colors,
+    domain = .data$TADA.NearbySiteGroup
+  )
+
   map <- leaflet::leaflet(.data) %>%
     leaflet::addProviderTiles("Esri.WorldTopoMap", group = "World topo", options = leaflet::providerTileOptions(updateWhenZooming = FALSE, updateWhenIdle = TRUE)) %>%
     leaflet.extras::addResetMapButton() # button to reset to initial zoom and lat/long
   if (nrow(.data) > 0) {
-    map <- map %>% leaflet::addCircleMarkers(~LongitudeMeasure,
-                                              ~LatitudeMeasure,
-                                              color = ~pal(TADA.NearbySiteGroup),
-                                              opacity = 1, 
-                                              fillColor = ~pal(TADA.NearbySiteGroup),
-                                              fillOpacity = 1,
-                                              radius = ifelse(dist_buffer > 200, 
-                                                              dist_buffer/10, 
-                                                              20),
-                                              weight = 1,
-                                              # label = ~as.character(TADA.MonitoringLocationIdentifier),
-                                              popup = paste0(
-                                                "Nearby Group Name: ", .data$TADA.MonitoringLocationIdentifier,
-                                                "<br> Nearby Site Group: ", .data$TADA.NearbySiteGroup,
-                                                "<br> Site ID: ", .data$MonitoringLocationIdentifier,
-                                                "<br> Site Name: ", .data$MonitoringLocationName,
-                                                "<br> Latitude: ", .data$LatitudeMeasure,
-                                                "<br> Longitude: ", .data$LongitudeMeasure
-                                              ),
-                                              data = .data,
-                                       clusterOptions = leaflet::markerClusterOptions(),
-    ) %>%
+    map <- map %>%
+      leaflet::addCircleMarkers(~LongitudeMeasure,
+        ~LatitudeMeasure,
+        color = ~ pal(TADA.NearbySiteGroup),
+        opacity = 1,
+        fillColor = ~ pal(TADA.NearbySiteGroup),
+        fillOpacity = 1,
+        radius = ifelse(dist_buffer > 200,
+          dist_buffer / 10,
+          20
+        ),
+        weight = 1,
+        # label = ~as.character(TADA.MonitoringLocationIdentifier),
+        popup = paste0(
+          "Nearby Group Name: ", .data$TADA.MonitoringLocationIdentifier,
+          "<br> Nearby Site Group: ", .data$TADA.NearbySiteGroup,
+          "<br> Site ID: ", .data$MonitoringLocationIdentifier,
+          "<br> Site Name: ", .data$MonitoringLocationName,
+          "<br> Latitude: ", .data$LatitudeMeasure,
+          "<br> Longitude: ", .data$LongitudeMeasure
+        ),
+        data = .data,
+        clusterOptions = leaflet::markerClusterOptions(),
+      ) %>%
       leaflet::addCircles(~LongitudeMeasure,
-                          ~LatitudeMeasure,
-                          color = ~pal(TADA.NearbySiteGroup),
-                          opacity = 0.1, 
-                          fillColor = ~pal(TADA.NearbySiteGroup),
-                          fillOpacity = 0.1,
-                          radius = dist_buffer,
-                          weight = 1)
+        ~LatitudeMeasure,
+        color = ~ pal(TADA.NearbySiteGroup),
+        opacity = 0.1,
+        fillColor = ~ pal(TADA.NearbySiteGroup),
+        fillOpacity = 0.1,
+        radius = dist_buffer,
+        weight = 1
+      )
   }
-  
+
   return(map)
 }