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<CRANTaskView>
<name>Spatial</name>
<topic>Analysis of Spatial Data</topic>
<maintainer email="Roger.Bivand@nhh.no">Roger Bivand</maintainer>
<version>2021-06-03</version>
<info>
<p>Base R includes many functions that can be used for reading,
visualising, and analysing spatial data. The focus in this view is on
"geographical" spatial data, where observations can be identified
with geographical locations, and where additional information about
these locations may be retrieved if the location is recorded with
care.</p>
<p>Base R functions are complemented by contributed packages,
some of which are on CRAN, and others are still in development.
One location is <a href="https://github.com/">Github</a>. Some key packages
including <pkg>sf</pkg> and <pkg>stars</pkg> are grouped under
<a href="https://github.com/r-spatial">r-spatial</a>, others including
<pkg>raster</pkg> and <pkg>terra</pkg> under <a href="https://github.com/rspatial">rspatial</a>.
Maintenance of the <pkg>sp</pkg> is continuing here:
<github>edzer/sp</github>.</p>
<p>Another set of locations for the development and maintenance of packages on
<a href="https://R-Forge.R-project.org/">
R-Forge</a>, which lists "Spatial Data and Statistics" projects in its
<a href="https://R-Forge.R-project.org/softwaremap/trove_list.php">project
tree</a>. Information on R-spatial packages was until 2016 posted on the R-Forge rspatial project
<a href="https://rspatial.R-Forge.R-project.org/">website</a>, including
a visualisation gallery.</p>
<p>The contributed packages address two broad areas: moving spatial data
into and out of R, and analysing spatial data in R.</p>
<p>The <a href="https://stat.ethz.ch/mailman/listinfo/R-SIG-Geo/">
R-SIG-Geo</a> mailing-list is a good place to begin for obtaining help
and discussing questions about both accessing data, and analysing it.
The mailing list is a good place to search for information about
relevant courses. Further information about courses may be found
under the "Events" tab of <a href="http://r-spatial.org/">this blog</a>.
</p>
<p>There are a number of contributed tutorials and introductions;
a recent one is
<a href="https://cran.r-project.org/doc/contrib/intro-spatial-rl.pdf">
Introduction to visualising spatial data in R</a> by Robin Lovelace
and James Cheshire.</p>
<p>The packages in this
view can be roughly structured into the following topics. If you think
that some package is missing from the list, please fork the <a href="https://github.com/r-spatial/task_views">task view
repository</a> and provide a pull request in ctv format for the
ctv/Spatial.ctv file.
</p>
<h2 id="classes-for-spatial-data-and-metadata">Classes for spatial
data and metadata</h2>
<p>Because many of the packages importing and using spatial data have had
to include objects of storing data and functions for visualising it, an
initiative is in progress to construct shared classes and plotting
functions for spatial data.</p>
<p>Complementary initiatives are ongoing to support better handling of
geographic metadata in R.</p>
<p><strong>Spatial data - general</strong></p>
<ul>
<li>The <pkg>sp</pkg> package provides classes and methods for dealing with spatial data
and is discussed in a note in
<a href="http://CRAN.R-project.org/doc/Rnews/Rnews_2005-2.pdf">R
News</a>.</li>
<li><pkg>sf</pkg> is a newer package now on CRAN, and is being
actively developed here: <github>r-spatial/sf</github>,
providing Simple Features for R, in compliance with the
<a href="http://www.opengeospatial.org/standards/sfa">OGC Simple Feature</a> standard.
The development of the package is being supported by the
<a href="https://www.r-consortium.org/">R Consortium</a>.
It provides simple features access for vector data, and as such is a
modern implementation and standardization of parts of <pkg>sp</pkg>.
It is documented in an <a href="https://journal.r-project.org/archive/2018/RJ-2018-009/index.html">R Journal</a> article.</li>
<li><pkg>stars</pkg> is being actively developed here:
<github>rspatial/stars</github>, and supported by the
<a href="https://www.r-consortium.org/">R Consortium</a>; it
provides for spatiotemporal data in the form of dense arrays.</li>
<li><pkg>stplanr</pkg> provides a "SpatialLinesNetwork" class based
on objects defined in <pkg>sp</pkg> and <pkg>igraph</pkg> that can be
used for routing analysis within R. Another network package is
<pkg>shp2graph</pkg>.</li>
<li>The <pkg>spacetime</pkg> package extends the shared classes defined in <pkg>sp</pkg> for
spatio-temporal data (see <a href="http://www.jstatsoft.org/v51/i07">Spatio-Temporal Data in R</a>).</li>
<li> The <pkg>rcosmo</pkg> package provides simple access to spherical and HEALPix data. It extends
standard dataframes for HEALPix-type data.</li>
<li><pkg>inlmisc</pkg> has followed on from Grid2Polygons and converts a spatial object from class
SpatialGridDataFrame to SpatialPolygonsDataFrame among many other possibilities.</li>
<li><pkg>maptools</pkg> provides conversion functions between
<pkg>PBSmapping</pkg> and <pkg>spatstat</pkg> and <pkg>sp</pkg> classes,
in addition to <pkg>maps</pkg> databases and <pkg>sp</pkg> classes.</li>
</ul>
<p><strong>Raster data</strong></p>
<ul>
<li><pkg>raster</pkg> package is a major extension of <pkg>sp</pkg>spatial data
classes to virtualise access to large rasters, permitting large
objects to be analysed, and extending the analytical tools available
for both raster and vector data. Used with <pkg>rasterVis</pkg>, it
can also provide enhanced visualisation and interaction. </li>
<li><pkg>terra</pkg> is a re-implementation of <pkg>raster</pkg>
functionality, linking directly to PROJ, GDAL and GEOS, and introducing
new S4 classes for raster and vector data. See the
<a href="https://rspatial.org/terra/">manual and tutorials</a>
to get started. <pkg>terra</pkg> is very
similar to the <pkg>raster</pkg> package; but <pkg>terra</pkg> is
simpler, better, and faster. </li>
<li><pkg>stars</pkg> provides for spatiotemporal data in the form of dense arrays,
with space and time being array dimensions. Examples include socio-economic or
demographic data, environmental variables monitored at fixed stations, time series of
satellite images with multiple spectral bands, spatial simulations, and climate model
results.</li>
</ul>
<p><strong>Geographic metadata</strong></p>
<ul>
<li><pkg>geometa</pkg> provides classes and methods to write geographic
metadata following the ISO and OGC metadata standards (ISO 19115, 19110,
19119) and export it as XML (ISO 19139) for later publication into
metadata catalogues. Reverserly, geometa provides a way to read ISO 19139
metadata into R. The package extends <pkg>sf</pkg> to provide GML (ISO 19136)
representation of geometries. geometa is under active development on
<github>eblondel/geometa</github></li>
<li><pkg>ncdf4</pkg> provides read and write functions for handling metadata
(CF conventions) in the self-described NetXDF format.</li>
</ul>
<h2 id="reading-and-writing-spatial-data">Reading and writing spatial data</h2>
<p><strong>Reading and writing spatial data - <pkg>rgdal</pkg></strong></p>
<p>Maps may be vector-based or raster-based. The <pkg>rgdal</pkg> package provides
bindings to <a href="http://www.gdal.org/">GDAL (Geospatial Data Abstraction Library)</a>-supported raster
formats and <a href="http://www.gdal.org/ogr/">OGR</a>-supported
vector formats. It contains functions to write raster and vector files in supported formats. Formats
supported by GDAL/OGR include both OGC standard data formats (e.g. GeoJSON) and
proprietary formats (e.g. ESRI Shapefile).
The package also provides <a href="https://proj4.org/">PROJ.4</a> projection
support for vector objects
(<a href="http://spatialreference.org">this site</a> provides
searchable online PROJ.4 representations of projections).
Affine and similarity transformations on sp objects may be made
using functions in the <pkg>vec2dtransf</pkg> package.
The Windows and Mac OSX CRAN binaries of <pkg>rgdal</pkg>
include subsets of possible data source drivers; if others
are needed, use other conversion utilities, or install from source
against a version of GDAL with the required drivers.</p>
<p><strong> Reading and writing spatial data - data formats</strong></p>
<p>Other packages provide facilities to read and write spatial data, dealing
with open standard formats or proprietary formats.</p>
<p><em>OGC Standard Data formats</em></p>
<ul>
<li><em>Well-Known Text (WKT) / Well-Known Binary (WKB):</em> These standards are
part of the OGC Simple Feature specification. Both WKT/WKB formats are supported by <pkg>sf</pkg> package that
implements the whole OGC Simple Feature specification in R. Apart from the <pkg>sf</pkg> package, the <pkg>rgeos</pkg>
package provides functions for reading and writing well-known text (WKT) geometry.
Package <pkg>wkb</pkg> package provides functions for reading and writing well-known
binary (WKB) geometry.</li>
<li><em>GeoJSON:</em> An rOpenSci
<a href="http://ropensci.org/blog/blog/2016/11/22/geospatial-suite">
blog entry</a> described a GeoJSON-centred approach to reading GeoJSON
and WKT data. GeoJSON can be written and read using <pkg>rgdal</pkg>, and
WKT by <pkg>rgeos</pkg>. The entry lists <pkg>geojson</pkg>,
and <pkg>geojsonio</pkg>, among
others.</li>
<li><em>Geographic Markup Language (GML):</em>GML format can be read and writen with
<pkg>rgdal</pkg>. Additional GML native reader and writer is provided by <pkg>geometa</pkg>
model with bindings to the <pkg>sf</pkg> classes, for extension of geographic
metadata with GML data and metadata elements (GML 3.2.1 and 3.3) and interfacing OGC
web-services in <pkg>ows4R</pkg> package</li>
<li><em>NetCDF files:</em> <pkg>ncdf4</pkg> or <pkg>RNetCDF</pkg> may be used.</li>
</ul>
<p><em>Proprietary Data Formats</em></p>
<ul>
<li><em>ESRI formats:</em> <pkg>maps</pkg> (with <pkg>mapdata</pkg> and <pkg>mapproj</pkg>)
provides access to the same kinds of geographical databases as S.
<pkg>maptools</pkg> and <pkg>shapefiles</pkg>
read and write ESRI ArcGIS/ArcView shapefiles.</li>
<li><em>Others:</em> <pkg>maptools</pkg>
package provides helper functions for writing map polygon
files to be read by <em>WinBUGS</em>, <em>Mondrian</em>, and the tmap command
in <em>Stata</em>. The <pkg>gmt</pkg> package gives a simple interface between GMT
map-making software and R.</li>
</ul>
<p><strong>Reading and writing spatial data - GIS Software connectors</strong></p>
<ul>
<li><em>PostGIS:</em> The <pkg>rpostgis</pkg> package provides additional
functions to the <pkg>RPostgreSQL</pkg> package to interface R with
a 'PostGIS'-enabled database, as well as convenient wrappers to common
'PostgreSQL' queries. It is documented in an <a href="https://journal.r-project.org/archive/2018/RJ-2018-025/index.html">R Journal</a> article. <pkg>postGIStools</pkg> package provides functions
to convert geometry and 'hstore' data types from 'PostgreSQL' into standard
R objects, as well as to simplify the import of R data frames (including spatial
data frames) into 'PostgreSQL'. <pkg>sf</pkg> also provides an R interface to
Postgis, for both reading and writing, throuh GDAL.</li>
<li><em>GRASS:</em>Integration with version 7.* of the leading open source
GIS, GRASS, is provided in CRAN package <pkg>rgrass7</pkg>, using
<pkg>rgdal</pkg> for exchanging data.
For GRASS 6.*, use <pkg>spgrass6</pkg>.</li>
<li><em>SAGA:</em><pkg>RSAGA</pkg> is a similar shell-based wrapper for SAGA commands.</li>
<li><em>Quantum GIS (QGIS):</em>QGIS2 was supported by RQGIS.
QGIS3 is supported by <github>r-spatial/RQGIS3</github>, which
establishes an interface between R and QGIS, i.e. it allows
the user to access QGIS functionalities from the R console. It achieves
this by using the QGIS Python API.</li>
<li><em>ArcGIS:</em><pkg>RPyGeo</pkg> is a wrapper
for Python access to the ArcGIS GeoProcessor</li>
</ul>
<p><strong>Interfaces to Spatial Web-Services</strong></p>
<p>Some R packages focused on providing interfaces to web-services and web tools in support of
spatial data management. Here follows a first tentative (non-exhaustive) list:</p>
<ul>
<li><pkg>ows4R</pkg> is a new package that intends to provide an R interface
to OGC standard Web-Services. It is in active development at <github>eblondel/ows4R</github>
and currently support interfaces to the Web Feature Service (WFS) for vector data access,
with binding to the <pkg>sf</pkg> package, and the Catalogue Service (CSW) for geographic
metadata discovery and management (including transactions), with binding to the <pkg>geometa</pkg>
package.
</li>
<li><pkg>geosapi</pkg> is an R client for the <a href="http://geoserver.org">GeoServer</a> REST API,
an open source implementation used widely for serving spatial data.</li>
<li><pkg>geonapi</pkg> provides an interface to the <a href="https://geonetwork-opensource.org/">GeoNetwork</a>
legacy API, an opensource catalogue for managing geographic metadata.</li>
<li><pkg>rgee</pkg> ia an <a href="https://earthengine.google.com/">Earth Engine</a>
client library for R. All of the 'Earth Engine' API classes, modules,
and functions are made available. Additional functions implemented
include importing (exporting) of Earth Engine spatial objects,
extraction of time series, interactive map display, assets management
interface, and metadata display.</li>
</ul>
<p><strong>Specific geospatial data sources of interest</strong></p>
<ul>
<li><pkg>rnaturalearth</pkg> package facilitates interaction with
<a href="http://www.naturalearthdata.com/">Natural Earth</a> map data.
It includes functions to download a wealth of Natural Earth vector and raster data,
including cultural (e.g., country boundaries, airports, roads, railroads)
and physical (e.g., coastline, lakes, glaciates areas) datasets.</li>
<li>Modern country boundaries are
provided at 2 resolutions by <pkg>rworldmap</pkg> along with
functions to join and map tabular data referenced by country
names or codes. Chloropleth and bubble maps are supported and general
functions to work on user supplied maps (see <a href="http://journal.r-project.org/archive/2011-1/RJournal_2011-1_South.pdf">A New R package for Mapping Global Data</a>. Higher resolution country
borders are available from the linked package <pkg>rworldxtra</pkg>.
Historical country boundaries (1946-2012) can be obtained from the <pkg>cshapes</pkg>.</li>
<li><pkg>marmap</pkg> package is designed for downloading, plotting
and manipulating bathymetric and topographic data in R. It allows to
query the ETOPO1 bathymetry and topography database hosted by the
NOAA, use simple latitude-longitude-depth data in ascii format, and take
advantage of the advanced plotting tools available in R to build
publication-quality bathymetric maps (see the <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0073051">PLOS</a>
paper).</li>
<li><pkg>maptools</pkg> provides an interface to GSHHS shoreline databases.</li>
<li>The UScensus2000 suite of packages (<pkg>UScensus2000cdp</pkg>, <pkg>UScensus2000tract</pkg>) makes the
use of data from the 2000 US Census more convenient.</li>
<li>The <pkg>cancensus</pkg> package provides access to Statistics
Canada's Census data with the option to retrieve all data as
spatial data.</li>
<li>An important
data set, Guerry's "Moral Statistics of France", has been made
available in the <pkg>Guerry</pkg> package, which provides data
and maps and examples designed to contribute to the integration
of multivariate and spatial analysis.</li>
<li><pkg>rgbif</pkg> package is used to access Global
Biodiversity Information Facility (GBIF) occurence data</li>
<li><pkg>geonames</pkg> is an interface to
the <a href="http://www.geonames.org/">www.geonames.org</a> service.</li>
<li><pkg>OpenStreetMap</pkg> gives access to open street map raster images,
and <pkg>osmar</pkg> provides infrastructure to access OpenStreetMap
data from different sources, to work with the data in common R manner,
and to convert data into available infrastructure provided by
existing R packages.</li>
<li><pkg>tidycensus</pkg> provides access to US Census Bureau data in a tidy format,
including the option to bind the data spatially on import. </li>
<li><pkg>tigris</pkg> provides access to cartographic elements provided by the US
Census Bureau TIGER, including cartographic boundaries, roads, and water.</li>
<li><pkg>chilemapas</pkg> provides access to spatial data of political
and administrative divisions of Chile.</li>
<li><pkg>geobr</pkg> provides easy access to official spatial data
sets of Brazil for multiple geographies and years.</li>
<li><pkg>geouy</pkg> loads and process geographic information for
Uruguay.</li>
<li><pkg>RCzechia</pkg> downloads spatial boundary files of administrative
regions and other spatial objects of the Czech Republic.</li>
<li><pkg>rgugik</pkg> allows to search and retrieve data from Polish Head
Office of Geodesy and Cartography ("GUGiK").</li>
<li><pkg>giscoR</pkg> provides access to spatial elements provided by
GISCO - Eurostat, including boundary files of countries, NUTS regions,
municipalities and other spatial objects.</li>
<li><pkg>mapSpain</pkg> downloads spatial boundary files of
administrative regions and other spatial objects of Spain.</li>
<li><pkg>osmextract</pkg> matches, downloads, converts and reads OpenStreetMap
data extracts obtained from Geofabrik and other providers.</li>
</ul>
<h2 id="handling-spatial-data">Handling spatial data</h2>
<p>A number of packages dedicated to spatial data handling have been written
using sp classes.</p>
<p><strong>Data processing - general</strong></p>
<ul>
<li><pkg>rgdal</pkg> and <pkg>maptools</pkg>.
The <pkg>rgeos</pkg> package provides an interface to topology functions
for <pkg>sp</pkg> objects using <a href="http://trac.osgeo.org/geos/">GEOS</a>.</li>
<li><pkg>raster</pkg> package
introduces many GIS methods that now permit much to be done with
spatial data without having to use GIS in addition to R.</li>
<li>The <pkg>gdalUtils</pkg> package provides wrappers for the Geospatial
Data Abstraction Library (GDAL) Utilities.</li>
<li><pkg>gdistance</pkg>, provides functions to calculate
distances and routes on geographic grids. <pkg>geosphere</pkg>
permits computations of distance and area
to be carried out on spatial data in geographical coordinates.
<pkg>cshapes</pkg> package provides functions for calculating
distance matrices (see <a href="http://journal.r-project.org/archive/2010-1/RJournal_2010-1_Weidmann+Skrede~Gleditsch.pdf">Mapping and Measuring Country Shapes</a>).</li>
<li><pkg>spsurvey</pkg> provides a range of sampling functions.</li>
<li>The <pkg>trip</pkg> package extends sp
classes to permit the accessing and manipulating of spatial data for
animal tracking.</li>
<li><pkg>magclass</pkg> offers a data class for increased
interoperability working with spatial-temporal data together with
corresponding functions and methods (conversions, basic calculations
and basic data manipulation). The class distinguishes between spatial,
temporal and other dimensions to facilitate the development and
interoperability of tools build for it. Additional features are
name-based addressing of data and internal consistency checks (e.g.
checking for the right data order in calculations).</li>
<li><pkg>taRifx</pkg> is a collection of utility and
convenience functions, and some interesting spatial functions.</li>
<li>The <pkg>rcosmo</pkg> package offers various tools for geometric transformations,
computations, and statistical analysis of spherical data.</li>
<li>The <pkg>areal</pkg> package can be used to interpolate overlapping but incongruent polygons,
also known as areal weighted interpolation.</li>
<li>The <pkg>qualmap</pkg> package can be used to digitize qualitative GIS data.</li>
</ul>
<p><strong>Data processing - raster and imagery data</strong></p>
<ul>
<li>The <pkg>landsat</pkg> package with accompanying
<a href="http://www.jstatsoft.org/v43/i04">JSS paper</a> provides
tools for exploring and developing correction tools for remote
sensing data.</li>
</ul>
<p><strong>Data cleaning</strong></p>
<ul>
<li><pkg>cleangeo</pkg> may be used to
inspect spatial objects, facilitate handling and reporting of topology
errors and geometry validity issues. It may be used to reduce the likelihood
of having issues when doing spatial data processing.</li>
<li><pkg>lwgeom</pkg> may also be used to
facilitate handling and reporting of topology
errors and geometry validity issues.</li>
</ul>
<h2 id="visualizing-spatial-data">Visualizing spatial data</h2>
<p><strong>Base visualization packages</strong></p>
<ul>
<li>Packages such as <pkg>sp</pkg>, <pkg>sf</pkg>, <pkg>raster</pkg> and <pkg>rasterVis</pkg>
provide basic visualization methods through the generic plot function</li>
<li><pkg>RColorBrewer</pkg> provides very useful colour palettes that may
be modified or extended using the <code>colorRampPalette</code>
function provided with R.</li>
<li><pkg>viridis</pkg> also provides colour palettes designed with consideration
for colorblindness and printing in grayscale.</li>
<li><pkg>classInt</pkg> package provides
functions for choosing class intervals for thematic cartography.</li>
<li><pkg>rcosmo</pkg> package provides several tools to interactively
visualize HEALPix data, in particular, to plot data in
arbitrary spherical windows.</li>
</ul>
<p><strong>Thematic cartography packages</strong></p>
<ul>
<li><pkg>tmap</pkg> package provides a modern basis for thematic mapping
optionally using a Grammar of Graphics syntax. Because it has a custom
grid graphics platform, it obviates the need to fortify geometries to
use with ggplot2.</li>
<li><pkg>quickmapr</pkg>
provides a simple method to visualize 'sp' and 'raster' objects,
allows for basic zooming, panning, identifying, and labeling of
spatial objects, and does not require that the data be in geographic
coordinates.</li>
<li><pkg>cartography</pkg> package allows various
cartographic representations such as proportional symbols,
choropleth, typology, flows or discontinuities.</li>
<li>The <pkg>mapmisc</pkg>
package is a minimal, light-weight set of tools for producing nice
looking maps in R, with support for map projections.</li>
<li>Additional processing and mapping functions are available in <pkg>PBSmapping</pkg> package;
<pkg>PBSmodelling</pkg> provides modelling support. In addition, <pkg>GEOmap</pkg>
provides mapping facilities directed to meet the needs of geologists, and uses the
<pkg>geomapdata</pkg> package.</li>
</ul>
<p><strong>Packages based on web-mapping frameworks</strong></p>
<ul>
<li><pkg>mapview</pkg>, <pkg>leaflet</pkg> and <pkg>leafletR</pkg> packages provide methods to
view spatial objects interactively, usually on a web mapping base.</li>
<li><pkg>RgoogleMaps</pkg> package for accessing
Google Maps(TM) may be useful if the user wishes to place a map backdrop
behind other displays.</li>
<li>plotGoogleMaps package provides methods for the
visualisation of spatial and spatio-temporal objects in Google Maps in
a web browser.</li>
<li><pkg>plotKML</pkg> is a package providing methods for
the visualisation of spatial and spatio-temporal objects in Google
Earth.</li>
<li><pkg>ggmap</pkg> may be used for spatial visualisation with Google Maps
and OpenStreetMap;<pkg>ggsn</pkg> provides North arrows and scales for such maps.</li>
<li><pkg>mapedit</pkg> provides an R shiny widget based on <pkg>leaflet</pkg> for editing or creating sf geometries.</li>
</ul>
<p><strong>Building Cartograms</strong></p>
<ul>
<li>The <pkg>micromap</pkg> package provides linked micromaps using ggplot2.</li>
<li><pkg>recmap</pkg> package provides rectangular
cartograms with rectangle sizes reflecting for example population.</li>
<li><pkg>statebins</pkg> provides a simpler binning approach to US states.</li>
<li><pkg>cartogram</pkg> package allows for constructions of a
continuous area cartogram by a rubber sheet distortion algorithm,
non-contiguous Area Cartograms, and non-overlapping Circles Cartogram.</li>
<li><pkg>geogrid</pkg> package turns polygons into rectangular or
hexagonal cartograms.</li>
</ul>
<h2 id="analyzing-spatial-data">Analyzing spatial data</h2>
<p><strong>Point pattern analysis</strong></p>
<p>The <pkg>spatial</pkg>
package is a recommended package shipped with base R, and contains
several core functions, including an implementation of Khat
by its author, Prof. Ripley. In addition, <pkg>spatstat</pkg>
allows freedom in defining the region(s) of interest, and makes
extensions to marked processes and spatial covariates. Its
strengths are model-fitting and simulation, and it has a useful
<a href="http://www.spatstat.org/"> homepage</a>. It is the only
package that will enable the user to fit inhomogeneous point process
models with interpoint interactions.
The <pkg>spatgraphs</pkg>
package provides graphs, graph visualisation and graph based
summaries to be used with spatial point pattern analysis. The
<pkg>splancs</pkg> package also allows point data to be analysed
within a polygonal region of interest, and covers many methods,
including 2D kernel densities. The <pkg>smacpod</pkg> package provides
various statistical methods for analyzing case-control point data.
The methods available closely follow those in chapter 6 of Applied
Spatial Statistics for Public Health Data by Waller and Gotway
(2004).</p>
<p><pkg>ecespa</pkg> provides
wrappers, functions and data for spatial point pattern analysis,
used in the book on Spatial Ecology of the ECESPA/AEET. The
functions for binning points on grids in <pkg>ash</pkg> may
also be of interest. The ads package perform first-
and second-order multi-scale analyses derived from Ripley's
K-function. The <pkg>aspace</pkg> package is a collection of
functions for estimating centrographic statistics and computational
geometries from spatial point patterns.
The <pkg>dbmss</pkg> package allows
simple computation of a full set of spatial statistic functions of
distance, including classical ones (Ripley's K and others) and more
recent ones used by spatial economists (Duranton and Overman's Kd,
Marcon and Puech's M). It relies on spatstat for core
calculation.</p>
<p><strong>Geostatistics</strong></p>
<p>The <pkg>gstat</pkg> package
provides a wide range of functions for univariate and multivariate
geostatistics, also for larger datasets, while <pkg>geoR</pkg>
and geoRglm contain functions for model-based
geostatistics. Variogram diagnostics may be carried out with
<pkg>vardiag</pkg>. Automated interpolation using <pkg>gstat</pkg>
is available in <pkg>automap</pkg>. This family of packages is
supplemented by <pkg>intamap</pkg> with procedures for automated
interpolation. A similar wide range of
functions is to be found in the <pkg>fields</pkg> package. The
<pkg>spatial</pkg> package is shipped with base R, and contains
several core functions. The <pkg>spBayes</pkg> package fits Gaussian
univariate and multivariate models with MCMC. <pkg>ramps</pkg>
is a different Bayesian geostatistical modelling package.
The <pkg>geospt</pkg> package contains some geostatistical and radial
basis functions, including prediction and cross validation. Besides,
it includes functions for the design of optimal spatial sampling
networks based on geostatistical modelling. <pkg>spsann</pkg> is another
package to offer functions to optimize sample configurations, using
spatial simulated annealing. The <pkg>rcosmo</pkg> package offers various geostatistics
methods for spherical data: descriptive statistics, entropy based
methods, covariance-variogram methods, etc. Most of rcosmo features
were developed for Cosmic Microwave Background data, but they can
also be used for any spherical data. The <pkg>FRK</pkg> package is a tool for
spatial/spatio-temporal modelling and prediction with large datasets.
The approach, discussed in Cressie and Johannesson (2008), decomposes
the field, and hence the covariance function, using a fixed set of n
basis functions, where n is typically much smaller than the number of
data points (or polygons) m.</p>
<p>The <pkg>RandomFields</pkg> package provides functions for
the simulation and analysis of random fields, and variogram
model descriptions can be passed between <pkg>geoR</pkg>,
<pkg>gstat</pkg> and this package. <pkg>SpatialExtremes</pkg>
proposes several approaches for spatial extremes modelling
using <pkg>RandomFields</pkg>. In addition, <pkg>CompRandFld</pkg>,
<pkg>constrainedKriging</pkg> and <pkg>geospt</pkg> provide
alternative approaches to geostatistical modelling. The
<pkg>spTimer</pkg> package is able to fit, spatially predict and
temporally forecast large amounts of space-time data using [1]
Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive
(AR) Models, and [3] Bayesian Gaussian Predictive Processes (GPP)
based AR Models. The <pkg>rtop</pkg> package provides functions for
the geostatistical interpolation of data with irregular spatial
support such as runoff related data or data from administrative
units. The <pkg>georob</pkg> package provides functions for fitting
linear models with spatially correlated errors by robust and Gaussian
Restricted Maximum Likelihood and for computing robust and customary
point and block kriging predictions, along with utility functions for
cross-validation and for unbiased back-transformation of kriging
predictions of log-transformed data. The <pkg>SpatialTools</pkg>
package has an emphasis on kriging, and provides functions for
prediction and simulation. It is extended by <pkg>ExceedanceTools</pkg>,
which provides tools for constructing confidence regions for exceedance
regions and contour lines. The <pkg>gear</pkg> package implements
common geostatistical methods in a clean, straightforward, efficient
manner, and is said to be a quasi reboot of <pkg>SpatialTools</pkg>.
The <pkg>sperrorest</pkg> package implements spatial error estimation
and permutation-based spatial variable importance using different
spatial cross-validation and spatial block bootstrap methods.</p>
<p>The <pkg>sgeostat</pkg> package
is also available. Within the same general topical area are
the <pkg>deldir</pkg> and <pkg>tripack</pkg> packages for
triangulation and the <pkg>akima</pkg> package for spline
interpolation; the <pkg>MBA</pkg> package provides scattered
data interpolation with multilevel B-splines. In addition,
there are the <pkg>spatialCovariance</pkg> package, which
supports the computation of spatial covariance matrices
for data on rectangles, the <pkg>regress</pkg> package
building in part on <pkg>spatialCovariance</pkg>, and the
<pkg>tgp</pkg> package. The <pkg>Stem</pkg> package provides
for the estimation of the parameters of a spatio-temporal
model using the EM algorithm, and the estimation of the
parameter standard errors using a spatio-temporal parametric
bootstrap. <pkg>FieldSim</pkg> is another random fields
simulations package. The <pkg>SSN</pkg> is for geostatistical
modeling for data on stream networks, including models based on
in-stream distance. Models are created using moving average
constructions. Spatial linear models, including covariates, can be
fit with ML or REML. Mapping and other graphical functions are
included. The <pkg>ipdw</pkg> provides functions o interpolate
- georeferenced point data via Inverse Path Distance Weighting. Useful
- for coastal marine applications where barriers in the landscape
- preclude interpolation with Euclidean distances.
<pkg>RSurvey</pkg> may be used as a processing program for spatially
distributed data, and is capable of error corrections and data
visualisation.</p>
<p><strong>Disease mapping and areal data analysis</strong></p>
<p><pkg>DCluster</pkg> is a package for the detection of
spatial clusters of diseases. It extends and depends on the
<pkg>spdep</pkg> package, which provides basic functions for
building neighbour lists and spatial weights, tests for spatial
autocorrelation for areal data like Moran's I. Functions for
fitting spatial regression models, such as SAR and CAR models prior to
version 1.1-1 are now in <pkg>spatialreg</pkg>. These
models assume that the spatial dependence can be described by known
weights. In <pkg>spatialreg</pkg>, the <code>ME</code> and
<code>SpatialFiltering</code> functions provide Moran Eigenvector
model fitting, as do more modern functions in the <pkg>spmoran</pkg>
package. The <pkg>SpatialEpi</pkg> package provides implementations of
cluster detection and disease mapping functions, including Bayesian
cluster detection, and supports strata. The <pkg>smerc</pkg> package
provides statistical methods for the analysis of data areal data, with
a focus on cluster detection. The <pkg>diseasemapping</pkg>
package offers the formatting of population and case data, calculation
of Standardized Incidence Ratios, and fitting the BYM model using
INLA. Regionalisation of polygon
objects is provided by <pkg>AMOEBA</pkg>: a function to calculate
spatial clusters using the Getis-Ord local statistic. It searches
irregular clusters (ecotopes) on a map, and by <code>skater</code>
in <pkg>spdep</pkg>. The <pkg>seg</pkg> and <pkg>OasisR</pkg> packages
provide functions for measuring spatial segregation; <pkg>OasisR</pkg>
includes Monte Carlo simulations to test the indices.
The <pkg>spgwr</pkg> package contains an implementation of
geographically weighted regression methods for exploring possible
non-stationarity. The <pkg>gwrr</pkg> package fits geographically
weighted regression (GWR) models and has tools to diagnose and
remediate collinearity in the GWR models. Also fits geographically
weighted ridge regression (GWRR) and geographically weighted lasso
(GWL) models. The <pkg>GWmodel</pkg> package contains functions for
- computing geographically weighted (GW) models. Specifically, basic,
- robust, local ridge, heteroskedastic, mixed, multiscale, generalised
- and space-time GWR; GW summary statistics, GW PCA and GW discriminant analysis;
- associated tests and diagnostics; and options for a range of distance metrics.
The <pkg>lctools</pkg> package provides researchers and educators with easy-to-learn user
friendly tools for calculating key spatial statistics and to apply
simple as well as advanced methods of spatial analysis in real data.
These include: Local Pearson and Geographically Weighted Pearson
Correlation Coefficients, Spatial Inequality Measures (Gini, Spatial
Gini, LQ, Focal LQ), Spatial Autocorrelation (Global and Local
Moran's I), several Geographically Weighted Regression techniques and
other Spatial Analysis tools (other geographically weighted statistics).
This package also contains functions for measuring the significance of
each statistic calculated, mainly based on Monte Carlo simulations.
The <pkg>sparr</pkg> package provides another
approach to relative risks. The <pkg>CARBayes</pkg> package
implements Bayesian hierarchical spatial areal unit models. In
such models, the spatial correlation is modelled by a set of random
effects, which are assigned a conditional autoregressive (CAR) prior
distribution. Examples of the models included are the BYM model as
well as a recently developed localised spatial smoothing model.
The <pkg>spaMM</pkg> package fits spatial GLMMs,
using the Matern correlation function as the basic model for spatial
random effects. The <pkg>PReMiuM</pkg> package is for profile
regression, which is a Dirichlet process Bayesian clustering model;
it provides a spatial CAR term that can be included in the fixed
effects (which are global, ie. non-cluster specific, parameters)
to account for any spatial correlation in the residuals.
The spacom package provides tools to
construct and exploit spatially weighted context data, and further
allows combining the resulting spatially weighted context data with
individual-level predictor and outcome variables, for the purposes
of multilevel modelling.
The geospacom package generates
distance matrices from shape files and represents spatially weighted
multilevel analysis results. Spatial survival analysis is provided by
the <pkg>spBayesSurv</pkg> package: Bayesian
Modeling and Analysis of Spatially Correlated Survival Data.
The <pkg>spselect</pkg> package provides modelling functions based on
forward stepwise regression, incremental forward stagewise regression,
least angle regression (LARS), and lasso models for selecting the
spatial scale of covariates in regression models.
</p>
<p><strong>Spatial regression</strong></p>
<p>The choice of function for spatial regression will depend on the
support available. If the data are characterised by point support
and the spatial process is continuous, geostatistical methods may be
used, or functions in the <pkg>nlme</pkg> package. If the support
is areal, and the spatial process is not being treated as continuous,
functions provided in the <pkg>spatialreg</pkg> package may be used.
This package can also be seen as providing spatial econometrics
functions, and, as noted above, provides basic functions for
building neighbour lists and spatial weights, tests for spatial
autocorrelation for areal data like Moran's I, and functions for
fitting spatial regression models. <pkg>spdep</pkg> provides the full
range of
local indicators of spatial association, such as local Moran's I and
diagnostic tools for fitted linear models, including Lagrange
Multiplier tests. Spatial regression models that can be fitted using
maximum likelihood and Bayesian MCMC methods in <pkg>spatialreg</pkg>
include spatial lag models, spatial error models,
and spatial Durbin models. For larger data sets, sparse matrix
techniques can be used for maximum likelihood fits, while spatial
two-stage least squares and generalised method of moments estimators are
an alternative. When using GMM, <pkg>sphet</pkg> can be used to
accommodate both autocorrelation and heteroskedasticity.
The <pkg>splm</pkg> package provides methods for
fitting spatial panel data by maximum likelihood and GM. The two
small packages <pkg>S2sls</pkg> and <pkg>spanel</pkg> provide
alternative implementations without most of the facilities of
<pkg>splm</pkg>. The HSAR package provides Hierarchical
Spatial Autoregressive Models (HSAR), based on a Bayesian Markov Chain
Monte Carlo (MCMC) algorithm.
<pkg>spatialprobit</pkg> make possible Bayesian estimation of the
spatial autoregressive probit model (SAR probit model). The
ProbitSpatial package provides methods for fitting Binomial
spatial probit models to larger data sets; spatial autoregressive
(SAR) and spatial error (SEM) probit models are included. The
<pkg>starma</pkg> package provides functions to identify, estimate
and diagnose a Space-Time AutoRegressive Moving Average (STARMA)
model.</p>
<p><strong>Ecological analysis</strong></p>
<p>There are many packages for analysing ecological and environmental data. They include:</p>
<ul>
<li><pkg>ade4</pkg> for exploratory and Euclidean methods in the
environmental sciences, the adehabitat family of packages
for the analysis of habitat selection by animals
(<pkg>adehabitatHR</pkg>, <pkg>adehabitatHS</pkg>,
<pkg>adehabitatLT</pkg>, and <pkg>adehabitatMA</pkg>)</li>
<li><pkg>pastecs</pkg> for the
regulation, decomposition and analysis of space-time series</li>
<li><pkg>vegan</pkg> for ordination methods and other useful
functions for community and vegetation ecologists, and many
other functions in other contributed packages. One such is
<pkg>tripEstimation</pkg>, basing on the classes provided by
<pkg>trip</pkg>. <pkg>ncf</pkg> has entered CRAN recently, and
provides a range of spatial nonparametric covariance functions.</li>
<li>The <pkg>spind</pkg> package provides functions for spatial methods
based on generalized estimating equations (GEE) and wavelet-revised
methods (WRM), functions for scaling by wavelet multiresolution
regression (WMRR), conducting multi-model inference, and stepwise model
selection.</li>
<li>The <pkg>siplab</pkg> package is a platform for experimenting with
spatially explicit individual-based vegetation models.</li>
<li><pkg>ModelMap</pkg> builds on other packages to create models
using underlying GIS data.</li>
<li>The <pkg>SpatialPosition</pkg> computes
spatial position models: Stewart potentials, Reilly catchment areas,
Huff catchment areas. </li>
<li>The <pkg>Watersheds</pkg> package provides
methods for watersheds aggregation and spatial drainage network
analysis.</li>
<li><a href="http://www.leg.ufpr.br/Rcitrus/">Rcitrus</a> (off-CRAN package)
is for the spatial analysis of plant disease incidence.</li>
<li>The <pkg>ngspatial</pkg> package
provides tools for analyzing spatial data, especially non-Gaussian
areal data. It supports the sparse spatial generalized linear mixed
model of Hughes and Haran (2013) and the centered autologistic model
of Caragea and Kaiser (2009).</li>
<li><pkg>landscapemetrics</pkg> package calculates landscape metrics
for categorical landscape patterns. It can be used as a drop-in replacement for
<a href="https://www.umass.edu/landeco/research/fragstats/fragstats.html">FRAGSTATS</a>,
as it offers a reproducible workflow for landscape analysis in a single environment.
It also provides several visualization functions, e.g.
to show all labeled patches or the core area of all patches.</li>
</ul>
<p>The <a href="Environmetrics.html">Environmetrics</a> Task View contains
a much more complete survey of relevant functions and packages.</p>
</info>
<packagelist>
<pkg>ade4</pkg>
<pkg>adehabitatHR</pkg>
<pkg>adehabitatHS</pkg>
<pkg>adehabitatLT</pkg>
<pkg>adehabitatMA</pkg>
<pkg>akima</pkg>
<pkg>AMOEBA</pkg>
<pkg>areal</pkg>
<pkg>aspace</pkg>
<pkg>ash</pkg>
<pkg>automap</pkg>
<pkg>cancensus</pkg>
<pkg>CARBayes</pkg>
<pkg>cartogram</pkg>
<pkg>cartography</pkg>
<pkg>chilemapas</pkg>
<pkg priority="core">classInt</pkg>
<pkg>cleangeo</pkg>
<pkg>CompRandFld</pkg>
<pkg>constrainedKriging</pkg>
<pkg>cshapes</pkg>
<pkg>dbmss</pkg>
<pkg priority="core">DCluster</pkg>
<pkg priority="core">deldir</pkg>
<pkg>diseasemapping</pkg>
<pkg>ecespa</pkg>
<pkg>ExceedanceTools</pkg>
<pkg>fields</pkg>
<pkg>FieldSim</pkg>
<pkg>FRK</pkg>
<pkg>gdalUtils</pkg>
<pkg>gdistance</pkg>
<pkg>gear</pkg>
<pkg>geobr</pkg>
<pkg>geogrid</pkg>
<pkg>geojson</pkg>
<pkg>geojsonio</pkg>
<pkg>GEOmap</pkg>
<pkg>geomapdata</pkg>
<pkg>geometa</pkg>
<pkg>geonames</pkg>
<pkg>georob</pkg>
<pkg priority="core">geoR</pkg>
<pkg>geonapi</pkg>
<pkg>geosapi</pkg>
<pkg>geosphere</pkg>
<pkg>geospt</pkg>
<pkg>geouy</pkg>
<pkg>ggmap</pkg>
<pkg>ggsn</pkg>
<pkg>giscoR</pkg>
<pkg>gmt</pkg>
<pkg>inlmisc</pkg>
<pkg priority="core">gstat</pkg>
<pkg>Guerry</pkg>
<pkg>GWmodel</pkg>
<pkg>gwrr</pkg>
<pkg>igraph</pkg>
<pkg>intamap</pkg>
<pkg>ipdw</pkg>
<pkg>landsat</pkg>
<pkg>landscapemetrics</pkg>
<pkg>lctools</pkg>
<pkg>leaflet</pkg>
<pkg>leafletR</pkg>
<pkg>lwgeom</pkg>
<pkg>magclass</pkg>
<pkg>mapdata</pkg>
<pkg>mapedit</pkg>
<pkg>mapmisc</pkg>
<pkg>mapproj</pkg>
<pkg>mapSpain</pkg>
<pkg>maps</pkg>
<pkg priority="core">maptools</pkg>
<pkg>mapview</pkg>
<pkg>marmap</pkg>
<pkg>MBA</pkg>
<pkg>micromap</pkg>
<pkg>ModelMap</pkg>
<pkg>pastecs</pkg>
<pkg>ncdf4</pkg>
<pkg>ncf</pkg>
<pkg>ngspatial</pkg>
<pkg>nlme</pkg>
<pkg>OasisR</pkg>
<pkg>OpenStreetMap</pkg>
<pkg>osmar</pkg>
<pkg>osmextract</pkg>
<pkg>ows4R</pkg>
<pkg>PBSmapping</pkg>
<pkg>PBSmodelling</pkg>
<pkg>plotKML</pkg>
<pkg>postGIStools</pkg>
<pkg>PReMiuM</pkg>
<pkg>quickmapr</pkg>
<pkg>ramps</pkg>
<pkg priority="core">RandomFields</pkg>
<pkg priority="core">raster</pkg>
<pkg>rasterVis</pkg>
<pkg priority="core">RColorBrewer</pkg>
<pkg>rcosmo</pkg>
<pkg>RCzechia</pkg>
<pkg>recmap</pkg>
<pkg>regress</pkg>
<pkg>rgbif</pkg>
<pkg priority="core">rgdal</pkg>
<pkg>rgee</pkg>
<pkg priority="core">rgeos</pkg>
<pkg>RgoogleMaps</pkg>
<pkg>rgrass7</pkg>
<pkg>rgugik</pkg>
<pkg>rnaturalearth</pkg>
<pkg>RNetCDF</pkg>
<pkg>RPostgreSQL</pkg>
<pkg>rpostgis</pkg>
<pkg>RPyGeo</pkg>
<pkg>RSAGA</pkg>
<pkg>RSurvey</pkg>
<pkg>rtop</pkg>
<pkg>rworldmap</pkg>
<pkg>rworldxtra</pkg>
<pkg>S2sls</pkg>
<pkg>seg</pkg>
<pkg priority="core">sf</pkg>
<pkg>sgeostat</pkg>
<pkg>shapefiles</pkg>
<pkg>shp2graph</pkg>
<pkg priority="core">sp</pkg>
<pkg priority="core">spacetime</pkg>
<pkg>siplab</pkg>
<pkg>smacpod</pkg>
<pkg>smerc</pkg>
<pkg>spaMM</pkg>
<pkg>spanel</pkg>
<pkg>sparr</pkg>
<pkg>spatial</pkg>
<pkg>spatialCovariance</pkg>
<pkg>SpatialEpi</pkg>
<pkg>SpatialExtremes</pkg>
<pkg>SpatialPosition</pkg>
<pkg>spatgraphs</pkg>
<pkg>spatialprobit</pkg>
<pkg priority="core">spatialreg</pkg>
<pkg>SpatialTools</pkg>
<pkg priority="core">spatstat</pkg>
<pkg>spBayes</pkg>
<pkg>spBayesSurv</pkg>
<pkg priority="core">spdep</pkg>
<pkg>sperrorest</pkg>
<pkg>spgrass6</pkg>
<pkg>spgwr</pkg>
<pkg>sphet</pkg>
<pkg>spind</pkg>
<pkg priority="core">splancs</pkg>
<pkg>splm</pkg>
<pkg>spmoran</pkg>
<pkg>spsann</pkg>
<pkg>spselect</pkg>
<pkg>spsurvey</pkg>
<pkg>spTimer</pkg>
<pkg>SSN</pkg>
<pkg>starma</pkg>
<pkg>stars</pkg>
<pkg>statebins</pkg>
<pkg>Stem</pkg>
<pkg>stplanr</pkg>
<pkg>taRifx</pkg>
<pkg>terra</pkg>
<pkg>tgp</pkg>
<pkg>tidycensus</pkg>
<pkg>tigris</pkg>
<pkg>trip</pkg>
<pkg>tripEstimation</pkg>
<pkg>tripack</pkg>
<pkg>tmap</pkg>
<pkg>UScensus2000cdp</pkg>
<pkg>UScensus2000tract</pkg>
<pkg>vardiag</pkg>
<pkg>vec2dtransf</pkg>
<pkg>vegan</pkg>
<pkg>viridis</pkg>
<pkg>Watersheds</pkg>
<pkg>wkb</pkg>
<pkg>qualmap</pkg>
</packagelist>
<links>
<view>SpatioTemporal</view>
<view>Environmetrics</view>
<a href="https://stat.ethz.ch/mailman/listinfo/R-SIG-Geo/">R-SIG-Geo mailing list</a>
</links>
</CRANTaskView>