update documentation for validate_coord_list

Author: RobLBaker

NEWS.md

@@ -1,10 +1,13 @@
+# QCkit v0.1.6
 2024-03-07
 * Update error warning in `check_te()` to not reference VPN since NPS no longer uses VPN.
+* add private function `.get_unit_bondaries()`: hits ArcGIS API to pull more precise park unit boundaries than `get_park_polgyon()`
+* add `validate_coord_list()` function that takes advantage of improved precision of `.get_unit_boundaries()` and is vectorized, enabling users to input multiple coordinate combinations and park units directly from a data frame.
 
 # QCkit v0.1.5
 2024-02-09
 * This version adds the DRR template, example files, and associated documentation to the QCkit package.
-* Bugfix in `get_custom_flag()`: it was counting both A (accepted) and AE (Accepted, estiamted) as Accepted. Fixed the regex such that it Accepted will include all cells that start with A followed by nothing or by any character except AE such that flags can have explanation codes added to them (e.g. A_jenkins if "Jenkins" flagged the data as accepted)
+* Bugfix in `get_custom_flag()`: it was counting both A (accepted) and AE (Accepted, estimated) as Accepted. Fixed the regex such that it Accepted will include all cells that start with A followed by nothing or by any character except AE such that flags can have explanation codes added to them (e.g. A_jenkins if "Jenkins" flagged the data as accepted)
 
 # QCkit v0.1.4
 2024-01-23

R/geography.R

@@ -1,11 +1,15 @@
-
 #' Test whether decimal GPS coordinates are inside a park unit
 #'
-#' This function can take a list of coordinates and park units as input. In addition to being vectorized, depending on the park borders, it can be a major improvement on `validate_coord()`. Known issues with this function include problems with overlapping unit boundaries. If two park unit boundaries overlap the function will through an error (e.g. Dry Tortugas National Park and Big Cypress National Preserve).
+#' This function can take a list of coordinates and park units as input. In
+#' adddition to being vectorized, depending on the park borders, it can be a
+#' major improvement on `validate_coord()`.
 #'
-#' @param lat numeric. An individual or vector of numeric values representing the decimal degree latitude of a coordinate
-#' @param lon numeric. An individual or vector of numeric values representing the decimal degree longitude of a coordinate
-#' @param park_unit String. Or list of strings each containing the four letter park unit designation
+#' @param lat numeric. An individual or vector of numeric values representing
+#' the decimal degree latitude of a coordinate
+#' @param lon numeric. An individual or vector of numeric values representing
+#' the decimal degree longitude of a coordinate
+#' @param park_unit String. Or list of strings each containing the four letter
+#' park unit designation
 #'
 #' @return logical
 #' @export
@@ -22,28 +26,35 @@
 #' df$test_GPS_coord <- x
 #' }
 validate_coord_list <- function(lat, lon, park_units) {
-  # get geography from NPS Rest Services
-  nps_unit <- .get_unit_boundary(park_units)
+  # get geography from ArcGIS Rest Services
+  park <- .get_unit_boundary(park_units)
 
+  #create a multipolygon sf object
+  valid_park <- sf::st_make_valid(park)
   # create sf dataframe from coordinates
   points_df <- data.frame(lon = lon, lat = lat)
-  points_sf <- sf::st_as_sf(points_df, coords = c("lon", "lat"), crs = 4326, na.fail = FALSE)
+  points <- sf::st_as_sf(points_df,
+                         coords = c("lon", "lat"),
+                         crs = 4326,
+                         na.fail = FALSE)
   # Test whether the coordinates provided are within the polygon spatial feature
-  results <- as.data.frame(sf::st_contains(nps_unit,
-                                         points_sf,
+  results <- as.data.frame(sf::st_covers(valid_park,
+                                         points,
                                          sparse = FALSE))
+  # Turn data frame into a list of logicals
+  colnames(results) <- park_units
+  rownames(results) <- unique(park_units)
   in_park <- NULL
-  for (i in 1:ncol(results)) {
-    if (sum(results[,i]) > 0) {
-      in_park <- append(in_park, TRUE)
-    } else {
-      in_park <- append(in_park, FALSE)
+  for (i in seq(ncol(results))) {
+    for (j in seq(nrow(results))) {
+      if (colnames(results)[i] == rownames(results)[j]) {
+        in_park <- append(in_park, results[j,i])
+      }
     }
   }
-  return(in_park)
+return(in_park)
 }
 
-
 #' Gets NPS unit boundaries from Arc GIS
 #'
 #' @param park_units String. Or list of strings.
@@ -64,14 +75,17 @@ validate_coord_list <- function(lat, lon, park_units) {
 
   for (locality in unique_localities) {
     # Request feature in WGS84 spatial reference (outSR=4326)
-    feature_service_path <- paste0('query?where=UNIT_CODE+%3D+%27', locality, '%27&outFields=*&returnGeometry=true&outSR=4326&f=pjson')
+    feature_service_path <- paste0(
+      "query?where=UNIT_CODE+%3D+%27",
+      locality,
+      "%27&outFields=*&returnGeometry=true&outSR=4326&f=pjson")
     feature_service_request <- paste(feature_service_url,
                                      feature_service_path,
                                      sep = "/")
     geo_json_feature <- jsonlite::fromJSON(feature_service_request)
 
     # Have to save to temp file
-    jsonFeature <- utils::download.file(feature_service_request,
+    json_feature <- utils::download.file(feature_service_request,
                                         temp_output,
                                         mode = "w",
                                         quiet = TRUE)
@@ -81,13 +95,11 @@ validate_coord_list <- function(lat, lon, park_units) {
 
     all_localities <- rbind(all_localities, feature_polygon)
   }
-  file.remove("temp.geojson")
+  suppressWarnings(file.remove("temp.geojson"))
   #featurePoly <- readOGR(dsn = tempOutput, layer = "OGRGeoJSON")
   return(all_localities)
 }
 
-
-
 #' Retrieve the polygon information for the park unit from NPS REST services
 #'
 #' @description `get_park_polygon()` retrieves a geoJSON string for a polygon of
@@ -139,7 +151,6 @@ validate_coord <- function(unit_code, lat, lon) {
 
   # Test whether the coordinates provided are within the polygon spatial feature
   result <- sf::st_covers(park, point, sparse = FALSE)[, 1]
-
   return(result)
 }