update mancofibdata and associated fib functions for simpler area sel…

…ection

R/anlz_fibmap.R

@@ -14,7 +14,7 @@
 #'
 #' All valid options for \code{areasel} for \code{fibdata} include \code{"Alafia River"}, \code{"Hillsborough River"}, \code{"Big Bend"}, \code{"Cockroach Bay"}, \code{"East Lake Outfall"}, \code{"Hillsborough Bay"}, \code{"Little Manatee"}, \code{"Lower Tampa Bay"}, \code{"McKay Bay"}, \code{"Middle Tampa Bay"}, \code{"Old Tampa Bay"}, \code{"Palm River"}, \code{"Tampa Bypass Canal"}, or \code{"Valrico Lake"}. One to any of the options can be used.
 #'
-#' Valid entries for \code{areasel} for \code{mancofibdata} include 'Big Slough', 'Bowlees Creek', 'Braden River', 'Bud Slough',  'Cedar Creek', 'Clay Gully', 'Cooper Creek', 'Curiosity Creek', 'Frog Creek', 'Gamble Creek', 'Gap Creek', 'Gates Creek', 'Gilley Creek', 'Hickory Hammock Creek', 'Lake Manatee', 'Little Manatee River', 'Lower Manatee River', 'Lower Tampa Bay', 'Manatee River Estuary', 'Mcmullen Creek', 'Mill Creek', 'Mud Lake Slough', 'Myakka River', 'Nonsense Creek', 'Palma Sola Bay', 'Piney Point Creek', 'Rattlesnake Slough', 'Sugarhouse Creek', 'Upper Manatee River', 'Ward Lake', or 'Williams Creek'. One to any of the options can be used.
+#' Valid entries for \code{areasel} for \code{mancofibdata} include \code{"Big Slough"}, \code{"Bowlees Creek"}, \code{"Braden River"}, \code{"Bud Slough"}, \code{"Clay Gully"}, \code{"Frog Creek"}, \code{"Gap Creek"}, \code{"Little Manatee River"}, \code{"Lower Tampa Bay"}, \code{"Manatee River"}, \code{"Mcmullen Creek"}, \code{"Mud Lake Slough"}, \code{"Myakka River"}, \code{"Palma Sola Bay"}, or \code{"Piney Point Creek"}. One to any of the options can be used.
 #'
 #' @return A \code{data.frame} if similar to \code{fibdata} or \code{mancofibdata} if \code{assf = FALSE} with additional columns describing station categories and optionally filtered by arguments passed to the function.  A \code{sf} object if \code{assf = TRUE} with additional columns for \code{\link{show_fibmap}}.
 #'
@@ -97,40 +97,41 @@ anlz_fibmap <- function(fibdata, yrsel = NULL, mosel = NULL, areasel = NULL, ass
       dplyr::filter(mo %in% mosel)
   }
 
-  # filter by area, epchc
-  if(!is.null(areasel) & isepchc){
-    areasls <- list(
-      `Alafia River` = c('Alafia River', 'Alafia River Tributary'),
-      `Hillsborough River` = c('Hillsborough River', 'Hillsborough River Tributary',  'Lake Thonotosassa',
-                       'Lake Thonotosassa Tributary', 'Lake Roberta'),
-      `Big Bend` = 'Big Bend',
-      `Cockroach Bay` = c('Cockroach Bay', 'Cockroach Bay Tributary'),
-      `East Lake Outfall` = 'East Lake Outfall',
-      `Hillsborough Bay` = c('Hillsborough Bay', 'Hillsborough Bay Tributary'),
-      `Little Manatee River` = c('Little Manatee River', 'Little Manatee River Tributary'),
-      `Lower Tampa Bay` = 'Lower Tampa Bay',
-      `McKay Bay` = c('McKay Bay', 'McKay Bay Tributary'),
-      `Middle Tampa Bay` = c('Middle Tampa Bay', 'Middle Tampa Bay Tributary'),
-      `Old Tampa Bay` = c('Old Tampa Bay', 'Old Tampa Bay Tributary'),
-      `Palm River` = c('Palm River', 'Palm River Tributary'),
-      `Tampa Bypass Canal` = c('Tampa Bypass Canal', 'Tampa Bypass Canal Tributary'),
-      `Valrico Lake` = 'Valrico Lake'
-    )
-    areasel <- match.arg(areasel, names(areasls), several.ok = TRUE)
-
-    out <- out %>%
-      dplyr::filter(area %in% unlist(areasls[areasel]))
-
-  }
+  # filter by area, epchc or manco
+  if(!is.null(areasel)){
+
+    if(isepchc)
+      areasls <- list(
+        `Alafia River` = c('Alafia River', 'Alafia River Tributary'),
+        `Hillsborough River` = c('Hillsborough River', 'Hillsborough River Tributary',  'Lake Thonotosassa',
+                         'Lake Thonotosassa Tributary', 'Lake Roberta'),
+        `Big Bend` = 'Big Bend',
+        `Cockroach Bay` = c('Cockroach Bay', 'Cockroach Bay Tributary'),
+        `East Lake Outfall` = 'East Lake Outfall',
+        `Hillsborough Bay` = c('Hillsborough Bay', 'Hillsborough Bay Tributary'),
+        `Little Manatee River` = c('Little Manatee River', 'Little Manatee River Tributary'),
+        `Lower Tampa Bay` = 'Lower Tampa Bay',
+        `McKay Bay` = c('McKay Bay', 'McKay Bay Tributary'),
+        `Middle Tampa Bay` = c('Middle Tampa Bay', 'Middle Tampa Bay Tributary'),
+        `Old Tampa Bay` = c('Old Tampa Bay', 'Old Tampa Bay Tributary'),
+        `Palm River` = c('Palm River', 'Palm River Tributary'),
+        `Tampa Bypass Canal` = c('Tampa Bypass Canal', 'Tampa Bypass Canal Tributary'),
+        `Valrico Lake` = 'Valrico Lake'
+      )
 
-  # filter by area, manatee county
-  if(!is.null(areasel) & ismanco){
-    areas <- sort(unique(mancofibdata$area))
+    if(ismanco){
+      areasls <- c("Big Slough", "Bowlees Creek", "Braden River", "Bud Slough",
+                   "Clay Gully", "Frog Creek", "Gap Creek", "Little Manatee River",
+                   "Lower Tampa Bay", "Manatee River", "Mcmullen Creek", "Mud Lake Slough",
+                   "Myakka River", "Palma Sola Bay", "Piney Point Creek")
+      names(areasls) <- areasls
+      areasls <- as.list(areasls)
+    }
 
-    areasel <- match.arg(areasel, areas, several.ok = TRUE)
+    areasel <- match.arg(areasel, names(areasls), several.ok = TRUE)
 
     out <- out %>%
-      dplyr::filter(area %in% areasel)
+      dplyr::filter(area %in% unlist(areasls[areasel]))
 
   }
 

R/read_formwqp.R

@@ -8,7 +8,7 @@
 #'
 #' @return A data frame containing formatted water quality and station metadata
 #'
-#' @details This function is used by \code{\link{read_importwqp}} to combine, format, and process data (\code{res}) and station metadata (\code{sta}) obtained from the Water Quality Portal for the selected county and data type. The resulting data frame includes the date, time, station identifier, latitude, longitude, variable name, value, unit, and quality flag.  Manatee County FIB data (21FLMANA_WQX) will also include an \code{area} column indicating the waterbody name as used by the USF Water Atlas.
+#' @details This function is used by \code{\link{read_importwqp}} to combine, format, and process data (\code{res}) and station metadata (\code{sta}) obtained from the Water Quality Portal for the selected county and data type. The resulting data frame includes the date, time, station identifier, latitude, longitude, variable name, value, unit, and quality flag.  Manatee County FIB data (21FLMANA_WQX) will also include an \code{area} column indicating the waterbody name as used by the USF Water Atlas, with some area aggregations.
 #'
 #' @concept read
 #'
@@ -194,13 +194,13 @@ read_formwqp <- function(res, sta, org, type, trace = F){
   if(type == 'fib' & org == '21FLMANA_WQX'){
 
     tomtch <- data.frame(
-      station = c("396", "BC1", "BC2", "BC41",
-        "BL01", "BL201", "BR1", "BR2", "BR3", "BU01A", "CC1", "CH1",
-        "D1", "D3", "ER1", "ER2", "FC1", "GA1", "GC1", "GC2", "GP", "LL1",
-        "LM3", "LM4", "LM5", "LM6", "MC1", "MC2", "MM", "MR1", "MR2",
-        "MS01", "MS02", "MY01", "MY02A", "MY04", "PP1", "SC1", "TS1",
-        "TS2", "TS3", "TS4", "TS5", "TS6", "TS7", "UM1", "UM2", "UM3",
-        "UM4", "WC1"),
+      station = c("396", "BC1", "BC2", "BC41", "BL01",
+        "BL201", "BR1", "BR2", "BR3", "BU01A", "CC1", "CH1", "D1", "D3",
+        "ER1", "ER2", "FC1", "GA1", "GC1", "GC2", "GP", "LL1", "LM3",
+        "LM4", "LM5", "LM6", "MC1", "MC2", "MM", "MR1", "MR2", "MS01",
+        "MS02", "MY01", "MY02A", "MY04", "PP1", "SC1", "TS1", "TS2",
+        "TS3", "TS4", "TS5", "TS6", "TS7", "UM1", "UM2", "UM3", "UM4",
+        "WC1"),
       area = c("Lower Tampa Bay", "Bowlees Creek", "Bowlees Creek",
         "Bowlees Creek", "Big Slough", "Big Slough", "Braden River",
         "Braden River", "Braden River", "Bud Slough", "Curiosity Creek",
@@ -213,10 +213,26 @@ read_formwqp <- function(res, sta, org, type, trace = F){
         "Myakka River", "Piney Point Creek", "Sugarhouse Creek", "Rattlesnake Slough",
         "Cedar Creek", "Cooper Creek", "Cooper Creek", "Hickory Hammock Creek",
         "Braden River", "Nonsense Creek", "Lower Manatee River", "Lake Manatee",
-        "Gilley Creek", "Upper Manatee River", "Williams Creek")
+        "Gilley Creek", "Upper Manatee River", "Williams Creek"),
+      areacmb = c("Lower Tampa Bay",
+        "Bowlees Creek", "Bowlees Creek", "Bowlees Creek", "Big Slough",
+        "Big Slough", "Braden River", "Braden River", "Braden River",
+        "Bud Slough", "Little Manatee River", "Palma Sola Bay", "Little Manatee River",
+        "Little Manatee River", "Braden River", "Braden River", "Frog Creek",
+        "Manatee River", "Manatee River", "Manatee River", "Gap Creek",
+        "Braden River", "Braden River", "Manatee River", "Manatee River",
+        "Manatee River", "Manatee River", "Manatee River", "Mcmullen Creek",
+        "Clay Gully", "Myakka River", "Mud Lake Slough", "Mud Lake Slough",
+        "Myakka River", "Myakka River", "Myakka River", "Piney Point Creek",
+        "Braden River", "Braden River", "Braden River", "Braden River",
+        "Braden River", "Braden River", "Braden River", "Braden River",
+        "Manatee River", "Manatee River", "Manatee River", "Manatee River",
+        "Braden River")
       )
 
-    out <- dplyr::left_join(out, tomtch, by = 'station', relationship = 'many-to-one')
+    out <- dplyr::left_join(out, tomtch, by = 'station', relationship = 'many-to-one') %>%
+      dplyr::select(-area) %>%
+      dplyr::rename(area = areacmb)
 
   }
 

R/show_fibmatmap.R

@@ -19,7 +19,7 @@
 #'
 #' If the input to \code{fibdata} is from EPCHC (from \code{\link{read_importfib}}), valid entries for \code{areasel} include 'Alafia River', 'Hillsborough River', 'Big Bend', 'Cockroach Bay', 'East Lake Outfall', 'Hillsborough Bay', 'Little Manatee River', 'Lower Tampa Bay', 'McKay Bay', 'Middle Tampa Bay', 'Old Tampa Bay', 'Palm River', 'Tampa Bypass Canal', and 'Valrico Lake'.  If the input data is not from EPCHC (from \code{\link{read_importentero}}), valid entries for \code{areasel} include 'OTB', 'HB', 'MTB', 'LTB', 'BCB', and 'MR'.
 #'
-#' Input from \code{\link{read_importwqp}} for Manatee County (21FLMANA_WQX) FIB data can also be used.  The function has not been tested for other organizations.  Valid entries for \code{areasel} include 'Big Slough', 'Bowlees Creek', 'Braden River', 'Bud Slough',  'Cedar Creek', 'Clay Gully', 'Cooper Creek', 'Curiosity Creek', 'Frog Creek', 'Gamble Creek', 'Gap Creek', 'Gates Creek', 'Gilley Creek', 'Hickory Hammock Creek', 'Lake Manatee', 'Little Manatee River', 'Lower Manatee River', 'Lower Tampa Bay', 'Manatee River Estuary', 'Mcmullen Creek', 'Mill Creek', 'Mud Lake Slough', 'Myakka River', 'Nonsense Creek', 'Palma Sola Bay', 'Piney Point Creek', 'Rattlesnake Slough', 'Sugarhouse Creek', 'Upper Manatee River', 'Ward Lake', or 'Williams Creek'
+#' Input from \code{\link{read_importwqp}} for Manatee County (21FLMANA_WQX) FIB data can also be used.  The function has not been tested for other organizations.  Valid entries for \code{areasel} include \code{"Big Slough"}, \code{"Bowlees Creek"}, \code{"Braden River"}, \code{"Bud Slough"}, \code{"Clay Gully"}, \code{"Frog Creek"}, \code{"Gap Creek"}, \code{"Little Manatee River"}, \code{"Lower Tampa Bay"}, \code{"Manatee River"}, \code{"Mcmullen Creek"}, \code{"Mud Lake Slough"}, \code{"Myakka River"}, \code{"Palma Sola Bay"}, or \code{"Piney Point Creek"}.
 #'
 #' Bay segment matrix categories can be shown if input data are from \code{\link{read_importentero}}).  Stations for these data were chosen specifically as downstream endpoints for each bay segment, whereas the other datasets are not appropriate for estimating bay segment outcomes.
 #'
@@ -116,13 +116,9 @@ show_fibmatmap <- function(fibdata, yrsel, areasel, indic, threshold = NULL,
 
     # check areas
     areas <- c("Big Slough", "Bowlees Creek", "Braden River", "Bud Slough",
-               "Cedar Creek", "Clay Gully", "Cooper Creek", "Curiosity Creek",
-               "Frog Creek", "Gamble Creek", "Gap Creek", "Gates Creek", "Gilley Creek",
-               "Hickory Hammock Creek", "Lake Manatee", "Little Manatee River",
-               "Lower Manatee River", "Lower Tampa Bay", "Manatee River Estuary",
-               "Mcmullen Creek", "Mill Creek", "Mud Lake Slough", "Myakka River",
-               "Nonsense Creek", "Palma Sola Bay", "Piney Point Creek", "Rattlesnake Slough",
-               "Sugarhouse Creek", "Upper Manatee River", "Ward Lake", "Williams Creek")
+               "Clay Gully", "Frog Creek", "Gap Creek", "Little Manatee River",
+               "Lower Tampa Bay", "Manatee River", "Mcmullen Creek", "Mud Lake Slough",
+               "Myakka River", "Palma Sola Bay", "Piney Point Creek")
 
     chk <- !areasel %in% areas
     if(any(chk)){