Cran Task Viewpauqte r Analis Espacila

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    CRAN Task View: Analysis of Spatial Data

    Maintainer: Roger Bivand

    Contact: Roger.Bivand at nhh.no

    Version: 2013-07-22

    Base R includes many functions that can be used for reading, visualising, and

    analysing spatial data. he focus in this vie! is on "geographical" spatial data,

    !here observations can be identified !ith geographical locations, and !here

    additional information about these locations may be retrieved if the location is

    recorded !ith care. Base R functions are complemented by contributed pac#ages,

    some of !hich are on $R%&, and others are still in development. 'ne active

    location is R-(orge , !hich lists ")patial *ata and )tatistics" pro+ects in

    itspro+ect tree . nformation on R-spatial pac#ages, especially sp!ill be posted

    on the R-(orge rspatial pro+ect !ebsite , including a visualisation gallery.

    he contributed pac#ages address t!o broad areas moving spatial data into and

    out of R, and analysing spatial data in R.

    he R-)-eo mailing-list is a good place to begin for obtaining help and

    discussing /uestions about both accessing data, and analysing it. he mailing list

    is a good place to search for information about relevant courses, and a list is

    hosted at the eo*a$enter .

    he pac#ages in this vie! can be roughly structured into the follo!ing topics. f

    you thin# that some pac#age is missing from the list, please let me #no!. lease

    also visit and contribute to the spatial data handling and spatial statisticspages on

    the R i#i.

    Classes for spatial data Because many of the pac#ages importing and

    using spatial data have had to include ob+ects of storing data and functions

    for visualising it, an initiative is in progress to construct shared classes and

    plotting functions for spatial data. he sppac#age has been published on

    $R%&. he sppac#age is discussed in a note in R &e!s . )ome other

    pac#ages have become dependent on these classes,including rgdaland maptools. (unctions provided by vec2dtransffor

    applying affine and similarity transformations on vector spatial data sp

    ob+ects. he rgeospac#age provides an interface to topology functions

    for spob+ects using 4') . rgeosis no! available for 5ac ')6 on

    $R%&. he rasterpac#age is a ma+or etension of spatial data classes to

    virtualise access to large rasters, permitting large ob+ects to be analysed,

    and etending the analytical tools available for both raster and vector data.

    http://r-forge.r-project.org/http://r-forge.r-project.org/softwaremap/trove_list.phphttp://cran.at.r-project.org/web/packages/sp/index.htmlhttp://rspatial.r-forge.r-project.org/https://stat.ethz.ch/mailman/listinfo/R-SIG-Geo/http://geodacenter.asu.edu/projects/rsphttp://rwiki.sciviews.org/doku.php?id=tips:spatial-datahttp://rwiki.sciviews.org/doku.php?id=tips:stats-spatialhttp://cran.at.r-project.org/web/packages/sp/index.htmlhttp://cran.at.r-project.org/web/packages/sp/index.htmlhttp://cran.r-project.org/doc/Rnews/Rnews_2005-2.pdfhttp://cran.at.r-project.org/web/packages/rgdal/index.htmlhttp://cran.at.r-project.org/web/packages/rgdal/index.htmlhttp://cran.at.r-project.org/web/packages/maptools/index.htmlhttp://cran.at.r-project.org/web/packages/vec2dtransf/index.htmlhttp://cran.at.r-project.org/web/packages/rgeos/index.htmlhttp://cran.at.r-project.org/web/packages/sp/index.htmlhttp://cran.at.r-project.org/web/packages/sp/index.htmlhttp://trac.osgeo.org/geos/http://cran.at.r-project.org/web/packages/rgeos/index.htmlhttp://cran.at.r-project.org/web/packages/raster/index.htmlhttp://r-forge.r-project.org/softwaremap/trove_list.phphttp://cran.at.r-project.org/web/packages/sp/index.htmlhttp://rspatial.r-forge.r-project.org/https://stat.ethz.ch/mailman/listinfo/R-SIG-Geo/http://geodacenter.asu.edu/projects/rsphttp://rwiki.sciviews.org/doku.php?id=tips:spatial-datahttp://rwiki.sciviews.org/doku.php?id=tips:stats-spatialhttp://cran.at.r-project.org/web/packages/sp/index.htmlhttp://cran.at.r-project.org/web/packages/sp/index.htmlhttp://cran.r-project.org/doc/Rnews/Rnews_2005-2.pdfhttp://cran.at.r-project.org/web/packages/rgdal/index.htmlhttp://cran.at.r-project.org/web/packages/maptools/index.htmlhttp://cran.at.r-project.org/web/packages/vec2dtransf/index.htmlhttp://cran.at.r-project.org/web/packages/rgeos/index.htmlhttp://cran.at.r-project.org/web/packages/sp/index.htmlhttp://trac.osgeo.org/geos/http://cran.at.r-project.org/web/packages/rgeos/index.htmlhttp://cran.at.r-project.org/web/packages/raster/index.htmlhttp://r-forge.r-project.org/
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    8sed !ith raster9is, it can also provide enhanced visualisation and

    interaction. he spatial.toolspac#age contains spatial functions meant to

    enhance the core functionality of the rasterpac#age, including a parallel

    processing engine for use !ith rasters. he micromappac#age provides

    lin#ed micromaps using ggplot2. he spacetimepac#age etends the

    shared classes defined in spfor spatio-temporal data.he rid2olygonsconverts a spatial ob+ect from class

    )patialrid*ata(rame to )patialolygons*ata(rame.

    %n alternative approach to some of these issues is implemented in

    the B)mappingpac#age: B)modellingprovides modelling support. n

    addition, 4'mapprovides mapping facilities directed to meet the needs

    of geologists, and uses the geomapdatapac#age.

    Handling spatial data % number of pac#ages have been !ritten using sp

    classes. he rasterpac#age introduces many ) methods that no! permitmuch to be done !ith spatial data !ithout having to use ) in addition to

    R. t may be complemented by gdistance, !hich provided calculation of

    distances and routes on geographic grids. geospherepermits computations

    of distance and area to be carried out on spatial data in geographical

    coordinates. he 5etadatapac#age collects and do!nloads a variety of

    open ) datasets that can be used to characteri;e the surface properties of

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    he landsatpac#age !ith accompanying ?)) paperprovides tools for

    eploring and developing correction tools for remote sensing

    data. taRifis a collection of utility and convenience functions, and some

    interesting spatial functions.

    Reading and writing spatial data - rgdal 5aps may be vector-based orraster-based. he rgdalpac#age provides bindings to *%< -supported

    raster formats and 'R -supported vector formats. t contains functions to

    !rite raster files in supported formats. he pac#age also

    provides R'?.@pro+ection support for vector ob+ects this siteprovides

    searchable online R'?.@ representations of pro+ections. he indo!s

    and 5ac ')6 $R%& binaries of rgdalinclude subsets of possible data

    source drivers: if others are needed, use other conversion utilities, or

    install from source against a version of *%< !ith the re/uired drivers.

    Reading and writing spatial data - other packages here are a number

    of other pac#ages for accessing vector data on

    $R%& maps!ith mapdataand mappro+ provides access to the same

    #inds of geographical databases as ) - R%rcnfoallo!s %rcnfo v.7 binary

    files and A.e00 files to be read, and maptoolsand shapefilesread and !rite

    %rc)=%rc9ie! shapefiles: for &et$*( files, ncdfmay be used.

    he maptoolspac#age also provides helper functions for !riting map

    polygon files to be read by inB8), 5ondrian, and the tmap command

    in )tata. t also provides interface functions

    bet!een B)mappingand spatstatand sp classes, in addition

    to mapsdatabases and sp classes. here is also an interface to ))

    shoreline databases. (or visualisation, the colour palettes provided in

    the R$olorBre!erpac#age are very useful, and may be modified or

    etended using the colorRampPalettefunction provided !ith R.

    he classntpac#age provides functions for choosing class intervals for

    thematic cartography. he gmtpac#age gives a simple interface bet!een

    5 map-ma#ing soft!are and R. geonamesis an interface to

    the !!!.geonames.org service. f the user !ishes to place a map

    bac#drop behind other displays, the the Rgoogle5apspac#age for

    accessing oogle 5aps5 may be useful. ggmapmay be used for

    spatial visualisation !ith oogle 5aps and 'pen)treet5ap.plotC5

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    program for spatially distributed data, and is capable of error corrections

    and data visualisation.

    ntegration !ith version D.A of the leading open source ), R%)), is

    provided in $R%& pac#age spgrassD, using rgdalfor echanging

    data. Ryeois a !rapper for ython access to the %rc) eorocessor,and R)%%is a similar shell-based !rapper for )%% commands.

    Point pattern analysis he spatialpac#age is a recommended pac#age

    shipped !ith base R, and contains several core functions, including an

    implementation of Chat by its author, rof. Ripley. n

    addition, spatstatallo!s freedom in defining the regions of interest, and

    ma#es etensions to mar#ed processes and spatial covariates. ts strengths

    are model-fitting and simulation, and it has a usefulhomepage . t is the

    only pac#age that !ill enable the user to fit inhomogeneous point process

    models !ith interpoint interactions. 5ar#edointrocessis anothercontemporary point pattern pac#age. hespatgraphspac#age provides

    graphs, graph visualisation and graph based summaries to be used !ith

    spatial point pattern analysis. he splancspac#age also allo!s point data

    to be analysed !ithin a polygonal region of interest, and covers many

    methods, including 2* #ernel densities.

    ecespaprovides !rappers, functions and data for spatial point pattern

    analysis, used in the boo# on )patial 4cology of the 4$4)%=%44. he

    functions for binning points on grids in ashmay also be of interest.

    he adspac#age perform first- and second-order multi-scale analysesderived from Ripley>s C-function. he aspacepac#age is a collection of

    functions for estimating centrographic statistcs and computational

    geometries from spatial point patterns. spatial#ernelprovides edge-

    corrected #ernel density estimation and binary #ernel regression estimation

    for multivariate spatial point process data.*)patcontains functions for

    spatial modelling for distance sampling data,

    and spatialsegregationprovides segregation measures for multitype spatial

    point patterns. rieg)mithuses the rieg-)mith method on 2 dimensional

    spatial data. he dbmsspac#age allo!s simple computation of a full set of

    spatial statistic functions of distance, including classical ones Ripley>s C

    and others and more recent ones used by spatial economists *uranton

    and 'verman>s Cd, 5arcon and uech>s 5. t relies on spatstat for core

    calculation.

    Geostatistics he gstatpac#age provides a !ide range of functions for

    univariate and multivariate geostatistics, also for larger datasets,

    http://cran.at.r-project.org/web/packages/spgrass6/index.htmlhttp://cran.at.r-project.org/web/packages/rgdal/index.htmlhttp://cran.at.r-project.org/web/packages/RPyGeo/index.htmlhttp://cran.at.r-project.org/web/packages/RSAGA/index.htmlhttp://cran.at.r-project.org/web/packages/spatial/index.htmlhttp://cran.at.r-project.org/web/packages/spatial/index.htmlhttp://cran.at.r-project.org/web/packages/spatstat/index.htmlhttp://www.spatstat.org/http://cran.at.r-project.org/web/packages/MarkedPointProcess/index.htmlhttp://cran.at.r-project.org/web/packages/spatgraphs/index.htmlhttp://cran.at.r-project.org/web/packages/splancs/index.htmlhttp://cran.at.r-project.org/web/packages/ecespa/index.htmlhttp://cran.at.r-project.org/web/packages/ash/index.htmlhttp://cran.at.r-project.org/web/packages/ads/index.htmlhttp://cran.at.r-project.org/web/packages/aspace/index.htmlhttp://cran.at.r-project.org/web/packages/spatialkernel/index.htmlhttp://cran.at.r-project.org/web/packages/DSpat/index.htmlhttp://cran.at.r-project.org/web/packages/spatialsegregation/index.htmlhttp://cran.at.r-project.org/web/packages/GriegSmith/index.htmlhttp://cran.at.r-project.org/web/packages/dbmss/index.htmlhttp://cran.at.r-project.org/web/packages/gstat/index.htmlhttp://cran.at.r-project.org/web/packages/gstat/index.htmlhttp://cran.at.r-project.org/web/packages/spgrass6/index.htmlhttp://cran.at.r-project.org/web/packages/rgdal/index.htmlhttp://cran.at.r-project.org/web/packages/RPyGeo/index.htmlhttp://cran.at.r-project.org/web/packages/RSAGA/index.htmlhttp://cran.at.r-project.org/web/packages/spatial/index.htmlhttp://cran.at.r-project.org/web/packages/spatstat/index.htmlhttp://www.spatstat.org/http://cran.at.r-project.org/web/packages/MarkedPointProcess/index.htmlhttp://cran.at.r-project.org/web/packages/spatgraphs/index.htmlhttp://cran.at.r-project.org/web/packages/splancs/index.htmlhttp://cran.at.r-project.org/web/packages/ecespa/index.htmlhttp://cran.at.r-project.org/web/packages/ash/index.htmlhttp://cran.at.r-project.org/web/packages/ads/index.htmlhttp://cran.at.r-project.org/web/packages/aspace/index.htmlhttp://cran.at.r-project.org/web/packages/spatialkernel/index.htmlhttp://cran.at.r-project.org/web/packages/DSpat/index.htmlhttp://cran.at.r-project.org/web/packages/spatialsegregation/index.htmlhttp://cran.at.r-project.org/web/packages/GriegSmith/index.htmlhttp://cran.at.r-project.org/web/packages/dbmss/index.htmlhttp://cran.at.r-project.org/web/packages/gstat/index.html
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    !hile geoRand geoRglmcontain functions for model-based geostatistics.

    9ariogram diagnostics may be carried out !ith vardiag. %utomated

    interpolation using gstatis available in automap. his family of pac#ages

    is supplemented by intamap!ith procedures for automated interpolation

    andpsgp, !hich implements pro+ected sparse aussian process #riging. %

    similar !ide range of functions is to be found in the fieldspac#age.he spatialpac#age is shipped !ith base R, and contains several core

    functions. he spBayespac#age fits aussian univariate and multivariate

    models !ith 5$5$. rampsis a different Bayesian geostatistical

    modelling pac#age. he geosptpac#age contains some geostatistical and

    radial basis functions, including prediction and cross validation. Besides, it

    includes functions for the design of optimal spatial sampling net!or#s

    based on geostatistical modelling.

    he Random(ieldspac#age provides functions for the simulation and

    analysis of random fields, and variogram model descriptions can be passed

    bet!een geoR, gstatand this pac#age. )patial4tremesproposes several

    approaches for spatial etremes modelling using Random(ields. n

    addition, $ompRand(ld, constrainedCrigingand geosptprovide

    alternative approaches to geostatistical modelling. hespimerpac#age is

    able to fit, spatially predict and temporally forecast large amounts of

    space-time data using E1F Bayesian aussian rocess 5odels, E2F

    Bayesian %uto-Regressive %R 5odels, and E3F Bayesian aussian

    redictive rocesses based %R 5odels. he rtoppac#age provides

    functions for the geostatistical interpolation of data !ith irregular spatial

    support such as runoff related data or data from administrative units.

    he georobpac#age provides functions for fitting linear models !ith

    spatially correlated errors by robust and aussian Restricted 5aimum

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    using the 45 algorithm, and the estimation of the parameter standard

    errors using a spatio-temporal parametric bootstrap. (ield)imis another

    random fields simulations pac#age. he ))&is for geostatistical modeling

    for data on stream net!or#s, including models based on in-stream

    distance. 5odels are created using moving average constructions. )patial

    linear models, including covariates, can be fit !ith 5< or R45s , and functions for fitting spatial regression models, such as )%R

    and $%R models. hese models assume that the spatial dependence can be

    described by #no!n !eights. he )patial4pipac#age provides

    implementations of cluster detection and disease mapping functions,

    including Bayesian cluster detection, and supports strata.

    he spg!rpac#age contains an implementation of geographically

    !eighted regression methods for eploring possible non-stationarity.

    he g!rrpac#age fits geographically !eighted regression R models

    and has tools to diagnose and remediate collinearity in the R models.

    %lso fits geographically !eighted ridge regression RR and

    geographically !eighted lasso

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    spatial process is not being treated as continuous, functions provided in

    the spdeppac#age may be used. his pac#age can also be seen as

    providing spatial econometrics functions, and, as noted above, provides

    basic functions for building neighbour lists and spatial !eights, tests for

    spatial autocorrelation for areal data li#e 5oran>s , and functions for

    fitting spatial regression models. t provides the full range of localindicators of spatial association, such as local 5oran>s and diagnostic

    tools for fitted linear models, including

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    include structure statistics, analyses based upon allele fre/uencies, and

    opulation raphs net!or# analysis of spatial conditional genetic

    covariance. his pac#age interfaces !ith raster and sp ob+ects directly. %n

    off-$R%& pac#age - Rcitrus - is for the spatial analysis of plant disease

    incidence. he enelandpac#age uses fieldsand Random(ieldsto ma#e

    use of both geographic and genetic informations to estimate the number ofpopulations in a dataset and delineate their spatial organisation.

    he ngspatialpac#age provides tools for analy;ing spatial data, especially

    non-aussian areal data. t supports the sparse spatial generali;ed linear

    mied model of ughes and aran 2013 and the centered autologistic

    model of $aragea and Caiser 200H. rlandscapeis a tool for generating

    data forests divided into management units for testing harvest scheduling

    models. t enables the user to create large amounts of sample forests !hile

    maintaining control over some spatial properties of the data, such as the

    degree and area distributions. he 4nvironmetrics as# 9ie! contains a

    much more complete survey of relevant functions and pac#ages.

    CRAN packages:

    ade@

    adehabitat

    adehabitatR

    adehabitat)

    adehabitat

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    constrainedCriging

    cshapes

    dbmss

    *$luster core

    deldir core

    *)pat

    ecespa

    fields

    (ield)im

    gdistance

    eneland

    4'map

    geomapdata

    geonames

    geoR core

    geoRglm

    georob

    geospacom

    geosphere

    geospt

    geospt

    eo6p

    ggmap

    glmmB8)

    gmt

    http://cran.at.r-project.org/web/packages/constrainedKriging/index.htmlhttp://cran.at.r-project.org/web/packages/cshapes/index.htmlhttp://cran.at.r-project.org/web/packages/dbmss/index.htmlhttp://cran.at.r-project.org/web/packages/DCluster/index.htmlhttp://cran.at.r-project.org/web/packages/deldir/index.htmlhttp://cran.at.r-project.org/web/packages/DSpat/index.htmlhttp://cran.at.r-project.org/web/packages/ecespa/index.htmlhttp://cran.at.r-project.org/web/packages/fields/index.htmlhttp://cran.at.r-project.org/web/packages/FieldSim/index.htmlhttp://cran.at.r-project.org/web/packages/gdistance/index.htmlhttp://cran.at.r-project.org/web/packages/Geneland/index.htmlhttp://cran.at.r-project.org/web/packages/GEOmap/index.htmlhttp://cran.at.r-project.org/web/packages/geomapdata/index.htmlhttp://cran.at.r-project.org/web/packages/geonames/index.htmlhttp://cran.at.r-project.org/web/packages/geoR/index.htmlhttp://cran.at.r-project.org/web/packages/geoRglm/index.htmlhttp://cran.at.r-project.org/web/packages/georob/index.htmlhttp://cran.at.r-project.org/web/packages/geospacom/index.htmlhttp://cran.at.r-project.org/web/packages/geosphere/index.htmlhttp://cran.at.r-project.org/web/packages/geospt/index.htmlhttp://cran.at.r-project.org/web/packages/geospt/index.htmlhttp://cran.at.r-project.org/web/packages/GeoXp/index.htmlhttp://cran.at.r-project.org/web/packages/ggmap/index.htmlhttp://cran.at.r-project.org/web/packages/glmmBUGS/index.htmlhttp://cran.at.r-project.org/web/packages/gmt/index.htmlhttp://cran.at.r-project.org/web/packages/constrainedKriging/index.htmlhttp://cran.at.r-project.org/web/packages/cshapes/index.htmlhttp://cran.at.r-project.org/web/packages/dbmss/index.htmlhttp://cran.at.r-project.org/web/packages/DCluster/index.htmlhttp://cran.at.r-project.org/web/packages/deldir/index.htmlhttp://cran.at.r-project.org/web/packages/DSpat/index.htmlhttp://cran.at.r-project.org/web/packages/ecespa/index.htmlhttp://cran.at.r-project.org/web/packages/fields/index.htmlhttp://cran.at.r-project.org/web/packages/FieldSim/index.htmlhttp://cran.at.r-project.org/web/packages/gdistance/index.htmlhttp://cran.at.r-project.org/web/packages/Geneland/index.htmlhttp://cran.at.r-project.org/web/packages/GEOmap/index.htmlhttp://cran.at.r-project.org/web/packages/geomapdata/index.htmlhttp://cran.at.r-project.org/web/packages/geonames/index.htmlhttp://cran.at.r-project.org/web/packages/geoR/index.htmlhttp://cran.at.r-project.org/web/packages/geoRglm/index.htmlhttp://cran.at.r-project.org/web/packages/georob/index.htmlhttp://cran.at.r-project.org/web/packages/geospacom/index.htmlhttp://cran.at.r-project.org/web/packages/geosphere/index.htmlhttp://cran.at.r-project.org/web/packages/geospt/index.htmlhttp://cran.at.r-project.org/web/packages/geospt/index.htmlhttp://cran.at.r-project.org/web/packages/GeoXp/index.htmlhttp://cran.at.r-project.org/web/packages/ggmap/index.htmlhttp://cran.at.r-project.org/web/packages/glmmBUGS/index.htmlhttp://cran.at.r-project.org/web/packages/gmt/index.html
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    rid2olygons

    rieg)mith

    gstat core

    gstudio

    uerry

    model

    g!rr

    hdeco

    intamap

    landsat

    mapdata

    mappro+

    maps

    maptools core

    5ar#edointrocess

    5B%

    5c)patial

    5etadata

    micromap

    5odel5ap

    ncdf

    ncf

    ngspatial

    nlme

    'pen)treet5ap

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  • 8/13/2019 Cran Task Viewpauqte r Analis Espacila

    11/13

    osmar

    pastecs

    B)mapping

    B)modelling

    plotC5