Introduction to MazamaSpatialUtils

Background

The MazamaSpatialUtils package was created by MazamaScience to regularize our work with spatial data. The sp and sf packages have made it much easier to work with spatial data found in shapefiles. Many sources of shapefile data are available and can be used to make beautiful maps in R. Unfortunately, the data attached to these datasets, even when fairly complete, often lacks standardized identifiers such as the ISO 3166-1 alpha-2 encodings for countries. Maddeningly, even when these ISO codes are used, the dataframe column in which they are stored does not have a standardized name. It may be called ISO or ISO2 or alpha or COUNTRY or any of a dozen other names we have seen.

While many mapping packages provide ‘natural’ naming of countries, those who wish to develop operational, GIS-like systems need something that is both standardized and language-independent. The ISO 3166-1 alpha-2 encodings have emerged as the de facto standard for this sort of work. In similar fashion, ISO 3166-2 alpha-2 encodings are available for the next administrative level down – state/province/oblast, etc. For time zones, the de facto standard is the set of Olson time zones used in all UNIX systems.

The main goal of this package is to create an internally standardized set of spatial data that we can use in various projects. Along with three built-in datasets, this package provides convert~() functions for other spatial datasets that we currently use. These convert functions all follow the same recipe:

download spatial data in shapefile format into a standard directory
convert shapefile data into a sf simple features data frame
clean up any topological errors
modify the dataframe so that it adheres to package internal standards

Other datasets can be added following the same procedure.

The ‘package internal standards’ are very simple.

Every spatial dataset must contain the following columns:

polygonID – unique identifier for each polygon
countryCode – country at centroid of polygon (ISO 3166-1 alpha-2)

Spatial datasets with time zone data must contain the following column:

timezone – Olson time zone

Spatial datasets at scales smaller than the nation-state should contain the following column:

stateCode – ‘state’ at centroid of polygon (ISO 3166-2 alpha-2)

If other columns contain these data, those columns must be renamed or duplicated with the internally standardized name. This simple level of consistency makes it possible to generate maps for any data that is ISO encoded. It also makes it possible to create functions that return the country, state or time zone associated with a set of locations.

Functionality

The core functionality for which this package was developed is determining spatial information associated with a set of locations.

Current functionality includes the following:

getCountry~(longitude, latitude, ...) – returns names, ISO codes and other country-level data at specified locations
getState~(longitude, latitude, ...) – returns names, ISO codes and other state-level at specified locations
getUSCounty~(longitude, latitude, ...) – returns names and other county-level data at specified locations
getTimezones(longitude, latitude, ...) – returns Olson time zones and other data at specified locations
getHUC~(longitude, latitude, ...) – returns USGS Hydrologic Unit Codes and other data at specified locations

A generic getSpatialData(longitude, latitude, ...) returns a dataframe whose rows are associated with specified locations. This function can be used with newly converted simple features data frames.

For those working with geo-located data, the ability to enhance location metadata with this information can be extremely helpful.

Standard Datasets and Setup

When using MazamaSpatialUtils, always run setSpatialDataDir(<spatial_data_directory>) first. This sets the directory where spatial data will be installed and loaded from. This can be a directory on a user’s personal computer or perhaps a remotely mounted disk if huge spatial datasets are going to be used.

MazamaSpatialUtils has three built-in spatial datasets:

SimpleCountries – country outlines
SimpleCountriesEEZ – country outlines including Exclusive Economic Zones over water
SimpleTimezones – time zones

Version 0.8 of the package is built around the three built-in datasets and several other core datasets that may be installed including:

20 MB EEZCountries – country boundaries including Exclusive Economic Zones
X 5 MB EEZCountries – US EPA region boundaries
X 6 MB GACC – Geographic Area Coordination Center (GACC) boundaries
14 MB NaturalEarthAdm1 – state/province/oblast level boundaries
X 8 MB NWSFireZones – “NWS weather forecast zones
X 53 MB TerrestrialEcoregions – terrestrial eco-regions
3 MB TMWorldBorders – high resolution country level boundaries
X 7 MB USCensus116thCongress – US congressional districts
X 34 MB USCensusCBSA – US Core Based Statistical Areas
12 MB USCensusCounties – US county level boundaries
X 3 MB USCensusStates – US state level boundaries
X 1 MB USIndianLands – US tribal boundaries
X 9 MB WeatherZones – NWS public weather forecast zones
X 16 MB WorldTimezones – time zones

Install these one at a time with:

setSpatialDataDir('~/Data/Spatial_0.8')
installSpatialData("<datasetName>")

Once datasets have been installed, loadSpatialData() can be used load datasets found in the SpatialDataDir that match a particular pattern, e.g:

loadSpatialData('USCensusStates')
loadSpatialData('USCensusCounties')

Additional watershed data from the Watershed Boundary Dataset are quite large and may be installed in the same way:

X 40 MB WBDHU2.rda – USGS level 2 watersheds
X 127 MB WBDHU4.rda – USGS level 4 watersheds
X 157 MB WBDHU6.rda – USGS level 6 watersheds
X 337 MB WBDHU8.rda – USGS level 8 watersheds
X ??? MB WBDHU10.rda – USGS level 10 watersheds (not yet available)
X ??? Gb WBDHU12.rda – USGS level 12 watersheds (not yet available)

`getCountry()` and `getCountryCode()`

These two functions are used for assigning countries to one or many locations. getCountry() returns English country names and getCountryCode() returns the ISO-3166 two character country code. Both functions can be passed allData = TRUE which returns a dataframe with more information on the countries. You can also specify countryCodes = c(<codes>) to speedup searching by restricting the search to polygons associated within those countries.

These functions use the package-internal SimpleCountries dataset which can be used without loading any additional datasets.

In this example we’ll find the countries underneath a vector of points:

library(MazamaSpatialUtils)

longitude <- c(-122.3, -73.5, 21.1, 2.5)
latitude <- c(47.5, 40.75, 52.1, 48.5)

# Get countries/codes associated with locations
getCountry(longitude, latitude)

## [1] "United States" "United States" "Poland"        "France"

getCountryCode(longitude, latitude)

## [1] "US" "US" "PL" "FR"

# Review all available data
getCountry(longitude, latitude, allData = TRUE)

##   countryCode   countryName polygonID
## 1          US United States       113
## 2          US United States       113
## 3          PL        Poland       205
## 4          FR        France       167

`getState()` and `getStateCode()`

Similar to above, these functions return state names and ISO 3166 codes. They also take the same arguments. Adding the countryCodes argument is more important for getState() and getStateCode() because the NaturalEarthAdm1 dataset is fairly large. Lets use the same latitude and longitude variables as above and assign states to those locations.

These functions require installation of the large NaturalEarthAdm1 dataset which is not distributed with the package.

(The next block of code is not evaluated in the vignette.)

# Load states dataset if you haven't already
loadSpatialData('NaturalEarthAdm1')

# Get country codes associated with locations
countryCodes <- getCountryCode(longitude, latitude)

# Pass the countryCodes as an argument to speed everything up
getState(longitude, latitude, countryCodes = countryCodes)
getStateCode(longitude, latitude, countryCodes = countryCodes)

# This is a very detailed dataset so we'll grab a few important columns
states <- getState(longitude, latitude, allData = TRUE, countryCodes = countryCodes)
states[c('countryCode', 'stateCode', 'stateName')]

`getTimezone()`

Returns the Olsen time zone where the given points are located. Arguments are the same as the previous functions. allData = TRUE will return other useful information such as the UTC Offset.

These functions use the package-internal SimpleTimezones dataset which can be used without loading any additional datasets.

# Find the time zones the points are in
getTimezone(longitude, latitude)

## [1] "America/Los_Angeles" "America/New_York"    "Europe/Warsaw"      
## [4] "Europe/Paris"

# Get country codes associated with locations
countryCodes <- getCountryCode(longitude, latitude)

# Pass the countryCodes as an argument to potentially speed things up
getTimezone(longitude, latitude, countryCodes = countryCodes)

## [1] "America/Los_Angeles" "America/New_York"    "Europe/Warsaw"      
## [4] "Europe/Paris"

# Review all available data
getTimezone(longitude, latitude, allData = TRUE, countryCodes = countryCodes)

##              timezone countryCode countryCodes timezone_STD_abbreviation
## 1 America/Los_Angeles          US           US                       PST
## 2    America/New_York          US           US                       EST
## 3       Europe/Warsaw          PL           PL                       CET
## 4        Europe/Paris          FR       FR, MC                       CET
##   timezone_DST_abbreviation UTC_STD_offset UTC_DST_offset notes polygonID
## 1                       PDT             -8             -7             133
## 2                       EDT             -5             -4             152
## 3                      CEST              1              2             369
## 4                      CEST              1              2             348

`getUSCounty()`

Returns the US County which name pairs of coordinates fall in. The arguments are similar as above except that stateCodes=c() is used instead of countryCodes=c() since this dataset is US specific.

(The next block of code is not evaluated in the vignette.)

# Load counties dataset if you haven't already
loadSpatialData("USCensusCounties")

# New dataset of points only in the US
stateCodes <- getStateCode(longitude,latitude)

# Optionally pass the stateCodes as an argument to speed everything up
getUSCounty(longitude, latitude, stateCodes = stateCodes)
getUSCounty(longitude, latitude, allData = TRUE, stateCodes = stateCodes)

Timezone Map

While identifying the states, countries and time zones associated with a set of locations is important, we can also generate some quick eye candy with these datasets. Let’s color the time zones by the data variable ‘UTC_offset’

# Assign time zones polygons an index based on UTC_offset
colorIndices <- .bincode(SimpleTimezones$UTC_STD_offset, breaks = seq(-12.5,12.5,1))

# Color our time zones by UTC_offset

plot(SimpleTimezones$geometry, col = rainbow(25)[colorIndices])
title(line = 0, 'Timezone Offsets from UTC')

Working with ISO 3166-1 Encoded Data

On of the main reasons for ensuring that our spatial datasets use ISO encoding is that it makes it easy to generate plots with any datasets that use that encoding. Here is a slightly more involved example using Energy data from the British Petroleum Statistical Review that has been ISO-encoded.

library(sf)         # For spatial plotting

## Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE

# Read in ISO-encoded oil production and consumption data
prod <- read.csv(url('http://mazamascience.com/OilExport/BP_2016_oil_production_bbl.csv'),
                 skip = 6, stringsAsFactors = FALSE, na.strings = 'na')
cons <- read.csv(url('http://mazamascience.com/OilExport/BP_2016_oil_consumption_bbl.csv'),
                 skip = 6, stringsAsFactors = FALSE, na.strings = 'na')

# Only work with ISO-encoded columns of data
prodCountryCodes <- names(prod)[ stringr::str_length(names(prod)) == 2 ]
consCountryCodes <- names(cons)[ stringr::str_length(names(cons)) == 2 ]

# Use the last row (most recent data)
lastRow <- nrow(prod)
year <- prod$YEAR[lastRow]

# Neither dataframe contains all countries so create four categories based on the
# amount of information we have:  netExporters, netImporters, exportOnly, importOnly
sharedCountryCodes <- intersect(prodCountryCodes,consCountryCodes)
net <- prod[lastRow, sharedCountryCodes] - cons[lastRow, sharedCountryCodes]

# Find codes associated with each category
netExportCodes <- sharedCountryCodes[net > 0]
netImportCodes <- sharedCountryCodes[net <= 0]
exportOnlyCodes <- setdiff(prodCountryCodes,consCountryCodes)
importOnlyCodes <- setdiff(consCountryCodes,prodCountryCodes)

# Create a logical 'mask' associated with each category
netExportMask <- SimpleCountries$countryCode %in% netExportCodes
netImportMask <- SimpleCountries$countryCode %in% netImportCodes
onlyExportMask <- SimpleCountries$countryCode %in% exportOnlyCodes
onlyImportMask <- SimpleCountries$countryCode %in% importOnlyCodes

color_export = '#40CC90'
color_import = '#EE5555'
color_missing = 'gray90'

# Base plot (without Antarctica)
notAQ <- SimpleCountries$countryCode != 'AQ'
plot(SimpleCountries[notAQ,]$geometry, col = color_missing)

plot(SimpleCountries[netExportMask,]$geometry, col = color_export, add = TRUE)
plot(SimpleCountries[onlyExportMask,]$geometry, col = color_export, add = TRUE)
plot(SimpleCountries[netImportMask,]$geometry, col = color_import, add = TRUE)
plot(SimpleCountries[onlyImportMask,]$geometry, col = color_import, add = TRUE)

legend(
  'bottomleft',
  legend = c('Net Exporters','Net Importers'),
  fill = c(color_export,color_import)
)
title(line = 0, paste('World Crude Oil in', year))

Introduction to MazamaSpatialUtils

Mazama Science

Nov 04, 2022

Background

Functionality

Standard Datasets and Setup

`getCountry()` and `getCountryCode()`

`getState()` and `getStateCode()`

`getTimezone()`

`getUSCounty()`

Timezone Map

Working with ISO 3166-1 Encoded Data

Introduction to MazamaSpatialUtils

Mazama Science

Nov 04, 2022

Background

Functionality

Standard Datasets and Setup

getCountry() and getCountryCode()

getState() and getStateCode()

getTimezone()

getUSCounty()

Timezone Map

Working with ISO 3166-1 Encoded Data

`getCountry()` and `getCountryCode()`

`getState()` and `getStateCode()`

`getTimezone()`

`getUSCounty()`