Merge pull request nationalparkservice#88 from RobLBaker/master

add function validate_coord_list

Author: RobLBaker

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: QCkit
 Type: Package
 Title: NPS Inventory and Monitoring Quality Control Toolkit
-Version: 0.1.5
+Version: 0.1.6
 Authors@R: c(
   person(given = "Robert",
            family = "Baker",
@@ -20,6 +20,9 @@ Authors@R: c(
            family = "Quevedo",
            role = "aut",
            comment = c(ORCID = "0000-0003-0129-981X")),
+  person(given = "Sarah",
+           family = "Kelson",
+           role = "ctb"),
   person(given = "Amy",
            family = "Sherman",
            role = "ctb",

NAMESPACE

@@ -21,9 +21,9 @@ export(long2UTM)
 export(order_cols)
 export(replace_blanks)
 export(te_check)
-export(test_coord)
 export(utm_to_ll)
 export(validate_coord)
+export(validate_coord_list)
 importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
 importFrom(stats,sd)

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

@@ -1,40 +1,58 @@
-
 #' Test whether decimal GPS coordinates are inside a park unit
 #'
-#' @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 containin the four-letter park unit designation
+#' 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_units String. Or list of strings each containing the four letter
+#' park unit designation
 #'
-#' @return dataframe
+#' @return logical
 #' @export
 #'
 #' @examples
 #' \dontrun{
-#' test_coord(105.555, -47.4332, "DRTO")
+#' x <- validate_coord_list(lat = 105.555, long = -47.4332, park_units = "DRTO")
+#'
+#' # or a dataframe with many coordinates and potentially many park units:
+#' x <- validate_coord_list(lat = df$decimalLatitutde,
+#'                 lon = df$decimalLongitude,
+#'                 park_units = df$park_units)
+#' # you can then merge it back in to the original dataframe:
+#' df$test_GPS_coord <- x
 #' }
-test_coord <- function(lat, lon, park_unit) {
-
-  # get geography from NPS Rest Services
-  park <- .get_unit_boundary(park_unit)
+validate_coord_list <- function(lat, lon, 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::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 <- sf::st_covers(park, points, sparse = FALSE)
-
-  # convert dataframe from wide to long format
-  results_long <- tidyr::gather(results)
-
-  # drop key column
-  results_long <- dplyr::select(results_long, -key)
-
-  # combine coordinates and results into a dataframe
-  result_df <- data.frame(lon = lon, lat = lat, in_polygon = results_long)
-
-
-  return(invisible(result_df))
+  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 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)
 }
 
 #' Gets NPS unit boundaries from Arc GIS
@@ -57,14 +75,17 @@ test_coord <- function(lat, lon, park_unit) {
 
   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)
@@ -74,14 +95,11 @@ test_coord <- function(lat, lon, park_unit) {
 
     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
@@ -133,7 +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)
 }
 

docs/404.html

@@ -5,5 +5,5 @@ articles:
   DRR_Purpose_and_Scope: DRR_Purpose_and_Scope.html
   Starting-a-DRR: Starting-a-DRR.html
   Using-the-DRR-Template: Using-the-DRR-Template.html
-last_built: 2024-03-21T19:40Z
+last_built: 2024-03-25T20:40Z