feat: updated to latest geodist, MazamaSpatialUtils

This revision also fixes issues with not being able to run
R CMD check --run-donttest by having mazama_initialize() install
the required datasets.

DESCRIPTION

@@ -1,35 +1,33 @@
 Type: Package
 Package: MazamaLocationUtils
-Version: 0.1.11
+Version: 0.1.12
 Title: Manage Spatial Metadata for Known Locations
 Authors@R: c(
     person("Jonathan", "Callahan", email="[email protected]", role=c("aut","cre")),
     person("Eli", "Grosman", email="[email protected]", role=c("aut"))
     )
 Author: Jonathan Callahan [aut, cre],
-    Eli Grosman [aut],
-    Oliver Fogelin [aut]
+    Eli Grosman [aut]
 Maintainer: Jonathan Callahan <[email protected]>
 Description: A suite of utility functions for discovering and managing metadata 
     associated with sets of spatially unique "known locations".
 License: GPL-3
 URL: https://github.com/MazamaScience/MazamaLocationUtils
 BugReports: https://github.com/MazamaScience/MazamaLocationUtils/issues
 Depends:
-    R (>= 3.1.0)
+    R (>= 3.5)
 Imports:
     digest,
     dplyr,
-    geodist,
+    geodist (>= 0.0.6.007),
     httr,
     jsonlite,
     lubridate,
     methods,
     magrittr,
     MazamaCoreUtils,
-    MazamaSpatialUtils,
+    MazamaSpatialUtils (>= 0.7),
     readr,
-    revgeo,
     rlang,
     stringr
 Suggests:

NEWS.md

@@ -1,3 +1,13 @@
+# MazamaLocationUtils 0.1.12
+
+* Updated `location_getSingleAddress_Photon()` to remove **revgeo** dependency.
+* Updated requirements to **geodist** 0.0.6.007 to handle errors finding longitude
+and latitude columns in the passed in tibble.
+* `geodist::geodist()` is now always called with `measure = "geodesic"` to avoid
+warning messages from `geodist()` about inaccuracies with `measure = "cheap"
+(the default).
+* `mazama_initialize()` now installs required datasets if they are missing.
+
 # MazamaLocationUtils 0.1.11
 
 * Added unit test for `table_findOverlappingLocations()`.

R/MazamaLocationUtils.R

@@ -96,10 +96,10 @@ coreMetadataNames <- c(
   "stateCode",                # from MazamaSpatialUtils::getStateCode()
   "county",                   # from MazamaSpatialUtils::getUSCounty()
   "timezone",                 # from MazamaSpatialUtils::getTimezone()
-  "houseNumber",              # from http://photon.komoot.de/
-  "street",                   # from http://photon.komoot.de/
-  "city",                     # from http://photon.komoot.de/
-  "zip"                       # from http://photon.komoot.de/
+  "houseNumber",              # from http://photon.komoot.io/
+  "street",                   # from http://photon.komoot.io/
+  "city",                     # from http://photon.komoot.io/
+  "zip"                       # from http://photon.komoot.io/
 )
 
 # ----- Internal Package State -------------------------------------------------

R/location_getSingleAddress_Photon.R

@@ -1,8 +1,22 @@
-
+#' @rdname location_getSingleAddress_Photon
+#' @export 
+#' @importFrom utils capture.output
+#' @importFrom jsonlite fromJSON
+#' @importFrom stringr str_detect str_sub str_subset
+#' 
 #' @title Get address data from the Photon API to OpenStreetMap
+#' 
+#' @param longitude Single longitude in decimal degrees E, Default: NULL
+#' @param latitude Single latitude in decimal degrees N, Default: NULL
+#' @param baseUrl Base URL for data queries.
+#' @param verbose Logical controlling the generation of progress messages.
+#' 
+#' @return List of address components.
+#' 
 #' @description The Photon API is used get address data associated with
 #' the \code{longitude} and \code{latitude}. The following list of data
 #' is returned:
+#' 
 #' \itemize{
 #' \item{\code{houseNumber}}
 #' \item{\code{street}}
@@ -13,16 +27,13 @@
 #' \item{\code{countryCode}}
 #' \item{\code{countryName}}
 #' }
+#' 
 #' The function makes an effort to convert both \code{state} and \code{country} 
 #' \code{Name} into \code{Code} with codes defaulting to \code{NA}. Both 
 #' \code{Name} and \code{Code} are returned so that improvements can be made in 
 #' the conversion algorithm.
-#' @param longitude Single longitude in decimal degrees E, Default: NULL
-#' @param latitude Single latitude in decimal degrees N, Default: NULL
-#' @param baseUrl Base URL for data queries.
-#' @param verbose Logical controlling the generation of progress messages.
-#' @return List of address components.
-#' @examples 
+#' 
+#' @examples
 #' \donttest{
 #' library(MazamaLocationUtils)
 #' 
@@ -36,12 +47,8 @@
 #' addressList <- location_getSingleAddress_Photon(lon, lat)
 #' str(addressList)
 #' }
-#' @references \url{http://photon.komoot.de}
-#' @rdname location_getSingleAddress_Photon
-#' @export 
-#' @importFrom utils capture.output
-#' @importFrom jsonlite fromJSON
-#' @importFrom stringr str_detect str_sub str_subset
+#' 
+#' @references \url{http://photon.komoot.io}
 #' 
 location_getSingleAddress_Photon <- function(
   longitude = NULL,

R/location_getSingleAddress_TexasAM.R

@@ -1,15 +1,21 @@
-
+#' @rdname location_getSingleAddress_TexasAM
+#' @export 
+#' 
 #' @title Get an address from a Texas A&M web service
-#' @description Texas A&M APIs are used to determine the address associated with
-#' the \code{longitude} and \code{latitude}.
+#' 
 #' @param longitude Single longitude in decimal degrees E, Default: NULL
 #' @param latitude Single latitude in decimal degrees N, Default: NULL
 #' @param verbose Logical controlling the generation of progress messages.
 #' @param apiKey Texas A&M Geocoding requires an API key. The first 2500 requests
 #' are free. Default: NULL
+#' 
 #' @return Numeric elevation value.
-#' @examples 
-#' \donttest{
+#' 
+#' @description Texas A&M APIs are used to determine the address associated with
+#' the \code{longitude} and \code{latitude}.
+#' 
+#' @examples
+#' \dontrun{
 #' library(MazamaLocationUtils)
 #' 
 #' # Set up standard directories and spatial data
@@ -23,9 +29,8 @@
 #' 
 #' location_getSingleAddress_TexasAM(longitude, latitude, apiKey)
 #' }
+#' 
 #' @references \url{https://geoservices.tamu.edu/Services/ReverseGeocoding/WebService/v04_01/HTTP.aspx}
-#' @rdname location_getSingleAddress_TexasAM
-#' @export 
 #' 
 location_getSingleAddress_TexasAM <- function(
   longitude = NULL,

R/location_getSingleElevation_USGS.R

@@ -1,12 +1,18 @@
-
+#' @rdname location_getSingleElevation_USGS
+#' @export 
+#' 
 #' @title Get elevation data from a USGS web service
-#' @description USGS APIs are used to determine the elevation associated with
-#' the \code{longitude} and \code{latitude}.
+#' 
 #' @param longitude Single longitude in decimal degrees E, Default: NULL
 #' @param latitude Single latitude in decimal degrees N, Default: NULL
 #' @param verbose Logical controlling the generation of progress messages.
+#' 
 #' @return Numeric elevation value.
-#' @examples 
+#' 
+#' @description USGS APIs are used to determine the elevation associated with
+#' the \code{longitude} and \code{latitude}.
+#' 
+#' @examples
 #' \donttest{
 #' library(MazamaLocationUtils)
 #' 
@@ -15,9 +21,8 @@
 #' lat <- 47.423333
 #' location_getSingleElevation_USGS(lon, lat)
 #' }
+#' 
 #' @references \url{https://nationalmap.gov/epqs/}
-#' @rdname location_getSingleElevation_USGS
-#' @export 
 #' 
 location_getSingleElevation_USGS <- function(
   longitude = NULL,

R/location_initialize.R

@@ -1,6 +1,23 @@
-
+#' @rdname location_initialize
+#' @export 
+#' @importFrom MazamaCoreUtils stopIfNull
+#' @importFrom MazamaSpatialUtils getCountryCode getStateCode getTimezone
+#' @importFrom dplyr tibble
+#' @importFrom stringr str_sub
+#' 
 #' @title  Create known location record with core metadata
 #' 
+#' @param longitude Single longitude in decimal degrees E, Default: NULL
+#' @param latitude Single latitude in decimal degrees N, Default: NULL
+#' @param stateDataset Name of spatial dataset to use for determining state
+#' @param elevationService Name of the elevation service to use for determining
+#' the elevation. Default: NULL. Accepted values: "usgs".
+#' @param addressService Name of the address service to use for determining
+#' the street address. Default: NULL Accepted values: "photon".
+#' @param verbose Logical controlling the generation of progress messages.
+#' 
+#' @return Tibble with a single new known location.
+#' 
 #' @description Creates a known location record with the following columns
 #' of core metadata:
 #' \itemize{
@@ -19,19 +36,6 @@
 #' \item{zip}
 #' }
 #' 
-#' @param longitude Single longitude in decimal degrees E, Default: NULL
-#' @param latitude Single latitude in decimal degrees N, Default: NULL
-#' @param stateDataset Name of spatial dataset to use for determining state
-#' @param elevationService Name of the elevation service to use for determining
-#' the elevation. Default: NULL. Accepted values: "usgs".
-#' @param addressService Name of the address service to use for determining
-#' the street address. Default: NULL Accepted values: "photon".
-#' @param verbose Logical controlling the generation of progress messages.
-#' 
-#' @return Tibble with a single new known location.
-#' 
-#' @rdname location_initialize
-#' 
 #' @examples
 #' \donttest{
 #' library(MazamaLocationUtils)
@@ -45,11 +49,7 @@
 #' lat <- 47.423333
 #' locationRecord <- location_initialize(lon, lat)
 #' }
-#' @export 
-#' @importFrom MazamaCoreUtils stopIfNull
-#' @importFrom MazamaSpatialUtils getCountryCode getStateCode getTimezone
-#' @importFrom dplyr tibble
-#' @importFrom stringr str_sub
+
 location_initialize <- function(
   longitude = NULL,
   latitude = NULL,

R/mazama_initialize.R

@@ -1,5 +1,15 @@
-
+#' @rdname mazama_initialize
+#' 
+#' @export 
+#' @importFrom MazamaSpatialUtils setSpatialDataDir loadSpatialData
+#' 
 #' @title Initialize with MazamaScience standard directories
+#' 
+#' @param spatialDataDir Directory where spatial datasets are found, 
+#' Default: "~/Data/Spatial"
+#' 
+#' @return No return value.
+#' 
 #' @description Convenience function to initialize spatial data. Wraps the 
 #' following setup lines:
 #' 
@@ -11,10 +21,7 @@
 #' MazamaSpatialUtils::loadSpatialData("NaturalEarthAdm1")
 #' MazamaSpatialUtils::loadSpatialData("USCensusCounties")
 #' }
-#' @param spatialDataDir Directory where spatial datasets are found, 
-#' Default: "~/Data/Spatial"
-#' @return No return value.
-#' @rdname mazama_initialize
+#' 
 #' @examples
 #' \donttest{
 #' library(MazamaLocationUtils)
@@ -23,17 +30,11 @@
 #' spatialDataDir <- tempdir() # typically "~/Data/Spatial"
 #' MazamaSpatialUtils::setSpatialDataDir(spatialDataDir)
 #' 
-#' # Install core spatial datasets (168 MB download)
-#' MazamaSpatialUtils::installSpatialData()
-#' 
 #' exists("NaturalEarthAdm1")
 #' mazama_initialize(spatialDataDir)
 #' exists("NaturalEarthAdm1")
 #' class(NaturalEarthAdm1)
 #' }
-#' @export 
-#' @importFrom MazamaSpatialUtils setSpatialDataDir loadSpatialData
-#' 
 mazama_initialize <- function(
   spatialDataDir = "~/Data/Spatial"
 ) {
@@ -48,6 +49,12 @@ mazama_initialize <- function(
     # Not initialized, so try to initialize
     result <- try({
       MazamaSpatialUtils::setSpatialDataDir(spatialDataDir)
+      # Install if not found
+      MazamaSpatialUtils::installSpatialData("EEZCountries")
+      MazamaSpatialUtils::installSpatialData("OSMTimezones")
+      MazamaSpatialUtils::installSpatialData("NaturalEarthAdm1")
+      MazamaSpatialUtils::installSpatialData("USCensusCounties")
+      # Now load
       MazamaSpatialUtils::loadSpatialData("EEZCountries")
       MazamaSpatialUtils::loadSpatialData("OSMTimezones")
       MazamaSpatialUtils::loadSpatialData("NaturalEarthAdm1")

R/table_addLocation.R

@@ -39,6 +39,8 @@
 #' locationTbl <- 
 #'   locationTbl %>%
 #'   table_addLocation(lon, lat, radius = 500)
+#'   
+#' dplyr::glimpse(locationTbl)
 #' }
 #' @seealso \link{table_addSingleLocation}
 #' @seealso \link{table_removeRecord}

R/table_addSingleLocation.R

@@ -26,7 +26,7 @@
 #' 
 #' # Set up standard directories and spatial data
 #' spatialDataDir <- tempdir() # typically "~/Data/Spatial"
-#' MazamaSpatialUtils::setSpatialDataDir(spatialDataDir)
+#' mazama_initialize(spatialDataDir)
 #' 
 #' locationTbl <- get(data("wa_monitors_500"))
 #' 

R/table_findOverlappingLocations.R

@@ -69,7 +69,7 @@ table_findOverlappingLocations <- function(
   # ----- Check for locations that are too close -------------------------------
 
   # Calculate distances between each location
-  distances <- geodist::geodist(tbl)
+  distances <- geodist::geodist(tbl, measure = "geodesic")
 
   # Get distances that are less than the given diameter
   # NOTE: the distance between a location and itself is always zero

R/table_getNearestLocation.R

@@ -1,13 +1,20 @@
-
+#' @rdname table_getNearestLocation
+#' @export
+#' @importFrom MazamaCoreUtils stopIfNull
+#' 
 #' @title Return known locations
-#' @description Returns a tibble of known locations from \code{locationTbl}, one 
-#' for each incoming location. If no known location is found for a particular
-#' incoming location, that record in the tibble will contain all \code{NA}.
+#' 
 #' @param locationTbl Tibble of known locations, Default: NULL
 #' @param longitude Vector of longitudes in decimal degrees E, Default: NULL
 #' @param latitude Vector of latitudes in decimal degrees N, Default: NULL
 #' @param radius Radius in meters, Default: NULL
+#' 
 #' @return Tibble of known locations.
+#' 
+#' @description Returns a tibble of known locations from \code{locationTbl}, one 
+#' for each incoming location. If no known location is found for a particular
+#' incoming location, that record in the tibble will contain all \code{NA}.
+#' 
 #' @examples
 #' library(MazamaLocationUtils)
 #' 
@@ -22,11 +29,7 @@
 #' 
 #' # Expanding the radius will find one
 #' table_getNearestLocation(locationTbl, lon, lat, radius = 5000) %>% str()
-#' @rdname table_getNearestLocation
-#' @export
-#' @importFrom MazamaCoreUtils stopIfNull
-#' @importFrom geodist geodist
-#' @importFrom rlang .data
+
 table_getNearestLocation <- function(
   locationTbl = NULL,
   longitude = NULL,

R/table_initializeExisting.R

@@ -254,7 +254,7 @@ table_initializeExisting <- function(
   # ----- Check for locations that are too close -------------------------------
 
   # Calculate distances between each location
-  distances <- geodist::geodist(locationTbl)
+  distances <- geodist::geodist(locationTbl, measure = "geodesic")
 
   # Get distances that are less than the given diameter
   # NOTE: the distance between a location and itself is always zero