Merge branch 'rm_346' into shiny_review

DESCRIPTION

@@ -2,9 +2,10 @@ Package: TADA
 Type: Package
 Title: TADA (Tools for Automated Data Analysis) R Package
 Version: 0.0.1
-Organization: U.S. Environmental Protection Agency
 Authors@R: 
-  c(person(given = "Cristina",
+  c(person(given = "U.S. Environmental Protection Agency",
+           role = "aut"),
+    person(given = "Cristina",
            family = "Mullin",
            role = c("aut", "cre"),
            email = "[email protected]",
@@ -15,6 +16,9 @@ Authors@R:
     person(given = "Elise",
            family = "Hinman",
            role = "aut"), 
+    person(given = "Hillary",
+           family = "Marler",
+           role = "aut"), 
     person(given = "Kathleen",
            family = "Healy",
            role = "aut"), 
@@ -24,6 +28,9 @@ Authors@R:
     person(given = "Laura",
            family = "Decicco", 
            role = "ctb"),
+    person(given = "Renae",
+           family = "Myers",
+           role = "aut"), 
     person(given = "Brad",
            family = "Cooper", 
            role = "ctr"),

NAMESPACE

@@ -61,4 +61,6 @@ export(TADA_Stats)
 export(TADA_SubstituteDeprecatedChars)
 export(TADA_SummarizeColumn)
 export(TADA_TwoCharacteristicScatterplot)
+export(TADA_addPoints)
+export(TADA_addPolys)
 importFrom(magrittr,"%>%")

R/Figures.R

@@ -369,8 +369,8 @@ TADA_Histogram <- function(.data, id_cols = c("TADA.ComparableDataIdentifier"))
 #' @return A leaflet map that shows all sites in the data frame, where larger point sizes
 #' indicate more results collected at a site, and darker point colors indicate more
 #' characteristics measured at that site. Users can click on points on the map to see
-#' a pop-up window with exact counts for measurements, visits, and characteristics
-#' associated with each site.
+#' a pop-up window with exact counts for measurements (i.e. number of rows),
+#' visits (number of unique Activity ID's), and characteristics associated with each site.
 #'
 #' @export
 #'
@@ -395,12 +395,11 @@ TADA_OverviewMap <- function(.data) {
       return(leaflet::addLegend(map, colors = colorAdditions, labels = labelAdditions, opacity = opacity, title = "Measurements"))
     }
 
-
     sumdat <- .data %>%
       dplyr::group_by(MonitoringLocationIdentifier, MonitoringLocationName, TADA.LatitudeMeasure, TADA.LongitudeMeasure) %>%
       dplyr::summarise("Sample_Count" = length(unique(ResultIdentifier)), "Visit_Count" = length(unique(ActivityStartDate)), "Parameter_Count" = length(unique(TADA.CharacteristicName)), "Organization_Count" = length(unique(OrganizationIdentifier)))
 
-    pt_sizes <- round(quantile(sumdat$Sample_Count, probs = c(0.1, 0.25, 0.5, 0.75)), 0)
+    pt_sizes <- round(stats::quantile(sumdat$Sample_Count, probs = c(0.1, 0.25, 0.5, 0.75)), 0)
     pt_labels <- c(
       paste0("<=", pt_sizes[1]),
       paste0(">", pt_sizes[1]),
@@ -424,10 +423,25 @@ TADA_OverviewMap <- function(.data) {
       domain = sumdat$Parameter_Count
     )
 
+    # Tribal layers will load by default in the overview map, restricted by the bounding box of the current dataset
+    # They can be toggled on and off using a button (all layers work together and can't be turned on/off individually). 
+    # Colors and icons are as discussed previously (orange/tan colors and open triangle icons for points) but can be changed to match HMW if desired.
+    bbox <- sf::st_bbox(
+      c(
+        xmin = min(sumdat$TADA.LongitudeMeasure),
+        ymin = min(sumdat$TADA.LatitudeMeasure),
+        xmax = max(sumdat$TADA.LongitudeMeasure),
+        ymax = max(sumdat$TADA.LatitudeMeasure)
+      ),
+      crs = sf::st_crs(sumdat)
+    )
+    vbbox <- bbox %>%
+      as.vector()
+
     map <- leaflet::leaflet() %>%
       leaflet::addProviderTiles("Esri.WorldTopoMap", group = "World topo", options = leaflet::providerTileOptions(updateWhenZooming = FALSE, updateWhenIdle = TRUE)) %>%
       leaflet::clearShapes() %>% # get rid of whatever was there before if loading a second dataset
-      leaflet::fitBounds(lng1 = min(sumdat$TADA.LongitudeMeasure), lat1 = min(sumdat$TADA.LatitudeMeasure), lng2 = max(sumdat$TADA.LongitudeMeasure), lat2 = max(sumdat$TADA.LatitudeMeasure)) %>% # fit to bounds of data in tadat$raw
+      leaflet::fitBounds(lng1 = vbbox[1], lat1 = vbbox[2], lng2 = vbbox[3], lat2 = vbbox[4]) %>% # fit to bounds of data in tadat$raw
       leaflet.extras::addResetMapButton() %>% # button to reset to initial zoom and lat/long
       leaflet::addCircleMarkers(
         data = sumdat,
@@ -457,6 +471,17 @@ TADA_OverviewMap <- function(.data) {
         colors = "black",
         labels = site_legend$Sample_n, sizes = site_legend$Point_size * 2
       )
+    # TADA_addPolys and TADA_addPoints are in Utilities.R
+    map <- TADA_addPolys(map, AKAllotmentsUrl, "Tribes", "Alaska Allotments", bbox)
+    map <- TADA_addPolys(map, AmericanIndianUrl, "Tribes", "American Indian", bbox)
+    map <- TADA_addPolys(map, OffReservationUrl, "Tribes", "Off Reservation", bbox)
+    map <- TADA_addPolys(map, OKTribeUrl, "Tribes", "Oklahoma Tribe", bbox)
+    map <- TADA_addPoints(map, AKVillagesUrl, "Tribes", "Alaska Native Villages", bbox)
+    map <- TADA_addPoints(map, VATribeUrl, "Tribes", "Virginia Tribe", bbox)
+    map <- leaflet::addLayersControl(map,
+      overlayGroups = c("Tribes"),
+      options = leaflet::layersControlOptions(collapsed = FALSE)
+    )
     return(map)
   })
 }

R/RequiredCols.R

@@ -56,8 +56,8 @@ require.cols <- c(
   "TADA.ResultMeasure.MeasureUnitCode", # generated/required/replaces original
   "TADA.WQXResultUnitConversion", # generated, only added when transform = FALSE in TADA_ConvertResultUnits
   "TADA.WQXTargetUnit", # generated, only added when transform = FALSE in TADA_ConvertResultUnits
-  "Target.TADA.ResultMeasure.MeasureUnitCode", 
-  "Target.TADA.UnitConversionFactor", # generated when 
+  "Target.TADA.ResultMeasure.MeasureUnitCode",
+  "Target.TADA.UnitConversionFactor", # generated when
   "TADA.WQXUnitConversionFactor", # generated, only added when transform = FALSE in TADA_ConvertResultUnits
   "Target.TADA.UnitConversionCoefficient",
   "TADA.UnitConversionFactor", # generated, added from TADA harmonization template
@@ -307,7 +307,7 @@ TADA_OrderCols <- function(.data) {
 #'
 TADA_GetTemplate <- function() {
   data(Data_Nutrients_UT)
-  examplerow <- head(Data_Nutrients_UT, 1)
+  examplerow <- utils::head(Data_Nutrients_UT, 1)
   examplerow2 <- subset(examplerow, select = names(examplerow) %in% require.cols)
   writexl::write_xlsx(examplerow2, path = "TADATemplate.xlsx")
 }