Progress in the R ecosystem for representing and handling spatial data
Tóm tắt
Twenty years have passed since Bivand and Gebhardt (J Geogr Syst 2(3):307–317, 2000.
https://doi.org/10.1007/PL00011460
) indicated that there was a good match between the then nascent open-source R programming language and environment and the needs of researchers analysing spatial data. Recalling the development of classes for spatial data presented in book form in Bivand et al. (Applied spatial data analysis with R. Springer, New York, 2008, Applied spatial data analysis with R, 2nd edn. Springer, New York, 2013), it is important to present the progress now occurring in representation of spatial data, and possible consequences for spatial data handling and the statistical analysis of spatial data. Beyond this, it is imperative to discuss the relationships between R-spatial software and the larger open-source geospatial software community on whose work R packages crucially depend.
Tài liệu tham khảo
Akima H, Gebhardt A (2020) akima: interpolation of irregularly and regularly spaced data. https://CRAN.R-project.org/package=akima, R package version 0.6-2.1
Appelhans T, Detsch F, Reudenbach C, Woellauer S (2020) mapview: interactive viewing of spatial data in R. https://CRAN.R-project.org/package=mapview, R package version 2.9.0
Baddeley A, Turner R (2005) spatstat: an R package for analyzing spatial point patterns. J Stat Softw 12(6):1–42
Baddeley A, Rubak E, Turner R (2015) Spatial point patterns: methodology and applications with R. Chapman and Hall, London
Baddeley A, Turner R, Rubak E (2020) spatstat: spatial point pattern analysis, model-fitting, simulation, tests. https://CRAN.R-project.org/package=spatstat, R package version 1.64-1
Bivand R (1998) Software and software design issues in the exploration of local dependence. The Statistician 47:499–508
Bivand R (2000) Using the R statistical data analysis language on GRASS 5.0 GIS database files. Comput Geosci 26(9):1043–1052
Bivand R (2002) Spatial econometrics functions in R: classes and methods. J Geogr Syst 4:405–421
Bivand R (2006) Implementing spatial data analysis software tools in R. Geogr Anal 38:23–40
Bivand R (2014) Geocomputation and open source software: components and software stacks. In: Abrahart RJ, See LM (eds) Geocomputation. CRC Press, Boca Raton, pp 329–355 (chap 14)
Bivand R (2020a) classInt: choose univariate class intervals. https://CRAN.R-project.org/package=classInt, R package version 0.4-3
Bivand R (2020b) spdep: spatial dependence: weighting schemes, statistics. https://CRAN.R-project.org/package=spdep, R package version 1.1-5
Bivand R, Gebhardt A (2000) Implementing functions for spatial statistical analysis using the R language. J Geogr Syst 2(3):307–317
Bivand R, Lewin-Koh N (2020) maptools: tools for handling spatial objects. https://CRAN.R-project.org/package=maptools, R package version 1.0-1
Bivand R, Piras G (2019) spatialreg: spatial regression analysis. https://CRAN.R-project.org/package=spatialreg, R package version 1.1-5
Bivand R, Rundel C (2020) rgeos: interface to geometry engine—open source (’GEOS’). https://CRAN.R-project.org/package=rgeos, R package version 0.5-3
Bivand R, Pebesma E, Gomez-Rubio V (2008) Applied spatial data analysis with R. Springer, New York
Bivand R, Pebesma E, Gomez-Rubio V (2013) Applied spatial data analysis with R, 2nd edn. Springer, New York
Bivand R, Keitt T, Rowlingson B (2020) rgdal: bindings for the ’geospatial’ data abstraction library. https://CRAN.R-project.org/package=rgdal, R package version 1.5-16
Brody H, Rip MR, Vinten-Johansen P, Paneth N, Rachman S (2000) Map-making and myth-making in Broad Street: the London cholera epidemic, 1854. Lancet 356:64–68
de Vries A (2014) Finding clusters of CRAN packages using igraph. https://blog.revolutionanalytics.com/2014/12/finding-clusters-of-cran-packages-using-igraph.html, Revolutions blog. Accessed 25 Aug 2020
Dunnington D, Pebesma E, Rubak E (2020) s2: spherical geometry operators using the S2 geometry library. https://CRAN.R-project.org/package=s2, r package version 1.0.2
Eddelbuettel D (2013) Seamless R and C++ integration with Rcpp. Springer, New York
Eddelbuettel D, Balamuta JJ (2018) Extending R with C++: a brief introduction to Rcpp. Am Stat 72(1):28–36. https://doi.org/10.1080/00031305.2017.1375990
Eddelbuettel D, François R, Allaire J, Ushey K, Kou Q, Russel N, Chambers J, Bates D (2011) Rcpp: seamless R and C++ integration. J Stat Softw 40(8):1–18
Eddelbuettel D, Francois R, Allaire J, Ushey K, Kou Q, Russell N, Bates D, Chambers J (2020) Rcpp: seamless R and C++ integration. https://CRAN.R-project.org/package=Rcpp, R package version 1.0.5
Evangelista PF, Beskow D (2018) Geospatial point density. R J 10(2):347–356. https://doi.org/10.32614/RJ-2018-061
Evers K, Knudsen T (2017) Transformation pipelines for PROJ.4. https://www.fig.net/resources/proceedings/fig_proceedings/fig2017/papers/iss6b/ISS6B_evers_knudsen_9156.pdf, fIG working week 2017 proceedings. Accessed 25 Aug 2020
Giraud T, Lambert N (2016) cartography: create and integrate maps in your R workflow. J Open Source Softw. https://doi.org/10.21105/joss.00054
Giraud T, Lambert N (2017) Reproducible cartography. In: Peterson M (ed) Advances in cartography and GIScience. ICACI 2017. Lecture notes in geoinformation and cartography. Springer, Cham, pp 173–183. https://doi.org/10.1007/978-3-319-57336-6_13
Giraud T, Lambert N (2020) cartography: thematic cartography. https://CRAN.R-project.org/package=cartography, R package version 2.4.1
Gómez-Rubio V (2011) RArcInfo: functions to import data from Arc/Info V7.x binary coverages. https://CRAN.R-project.org/package=RArcInfo, R package version 0.4-12
Gómez-Rubio V, López-Quílez A (2005) RArcInfo: using GIS data with R. Comput Geosci 31(8):1000–1006
Gómez-Rubio V, Ferrándiz-Ferragud J, Lopez-Quólez A (2005) Detecting clusters of disease with R. J Geogr Syst 7(2):189–206
Gómez-Rubio V, Ferrándiz-Ferragud J, López-Quílez A (2015) DCluster: functions for the detection of spatial clusters of diseases. https://CRAN.R-project.org/package=DCluster, R package version 0.2-7
Herring JR (2011) Opengis implementation standard for geographic information-simple feature access-part 1: common architecture. Open Geospatial Consortium Inc, Wayland, p 111
Hijmans RJ (2020a) terra: geographic data analysis and modeling. https://CRAN.R-project.org/package=raster, R package version 3.3-13
Hijmans RJ (2020b) terra: spatial data analysis. https://CRAN.R-project.org/package=terra, R package version 0.8-6
Hornik K (2020) stringsAsFactors. https://developer.r-project.org/Blog/public/2020/02/16/stringsasfactors/index.html. Accessed 25 Aug 2020
ISO (2004) ISO 19125-1:2004 geographic information—simple feature access—part 1: common architecture. https://www.iso.org/standard/40114.html, iSO 19125-1:2004. Accessed 25 Aug 2020
ISO (2019) ISO 19111:2019 Geographic information—referencing by coordinates. https://www.iso.org/standard/74039.html, ISO 19111:2019. Accessed 25 Aug 2020
Kalibera T (2019) Use of C++ in packages. https://developer.r-project.org/Blog/public/2019/03/28/use-of-c-in-packages/index.html, R blog. Accessed 25 Aug 2020
Kaluzny S, Vega S, Cardoso T, Shelly A (1998) S+SpatialStats. Springer, New York
Knudsen T, Evers K (2017) Transformation pipelines for PROJ.4. Geophysical research abstracts, vol 19, EGU2017-8050. https://meetingorganizer.copernicus.org/EGU2017/EGU2017-8050.pdf. Accessed 25 Aug 2020
Kralidis AT (2008) Geospatial open source and open standards convergences. In: Hall GB, Leahy M (eds) Open source approaches in spatial data handling. Springer, Berlin, pp 1–20
Lapa T, Ximenes R, Silva NN, Souza W, Albuquerque MdFM, Campozana G (2001) Vigilância da hanseníase em Olinda, Brasil, utilizando técnicas de análise espacial. Cadernos de Saúde Pública 17:1153–1162. https://doi.org/10.1590/S0102-311X2001000500016
Lovelace R, Ellison R (2018) stplanr: a package for transport planning. R J 10(2):7–23. https://doi.org/10.32614/RJ-2018-053
Lovelace R, Nowosad J, Muenchow J (2019) Geocomputation with R. CRC, Boca Raton
Lovelace R, Ellison R, Morgan M (2020) stplanr: sustainable transport planning. https://CRAN.R-project.org/package=stplanr, r package version 0.6.2
Majure JJ, Gebhardt A (2016) sgeostat: an object-oriented framework for geostatistical modeling in S+. https://CRAN.R-project.org/package=sgeostat, R package version 1.0-27
Meyer D, Dimitriadou E, Hornik K, Weingessel A, Leisch F (2019) e1071: misc functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien. https://CRAN.R-project.org/package=e1071, r package version 1.7-3
Neuwirth E (2014) RColorBrewer: ColorBrewer palettes. https://CRAN.R-project.org/package=RColorBrewer, R package version 1.1-2
Nowosad J (2019) ’CARTOColors’ palettes. https://nowosad.github.io/rcartocolor, R package version 2.0.0
Pebesma E (2012) spacetime: spatio-temporal data in R. J Stat Softw 51(7):1–30
Pebesma E (2018) Simple features for R: standardized support for spatial vector data. R J 10(1):439–446
Pebesma E (2020a) sf: simple features for R. https://CRAN.R-project.org/package=sf, R package version 0.9-5
Pebesma E (2020b) spacetime: classes and methods for spatio-temporal data. https://CRAN.R-project.org/package=spacetime, R package version 1.2-3
Pebesma E (2020c) stars: spatiotemporal arrays, raster and vector data cubes. https://CRAN.R-project.org/package=stars, R package version 0.4-3
Pebesma E, Bivand R (2005) Classes and methods for spatial data in R. R News 5(2):9–13
Pebesma E, Bivand R (2020) sp: classes and methods for spatial data. https://CRAN.R-project.org/package=sp, R package version 1.4-2
Pebesma E, Dunnington D (2020) In r-spatial, the Earth is no longer flat. https://www.r-spatial.org/r/2020/06/17/s2.html. Accessed 25 Aug 2020
Pebesma EJ, Wesseling CG (1998) Gstat, a program for geostatistical modelling, prediction and simulation. Comput Geosci 24:17–31
Pebesma E, Bivand R, Ribeiro P (2015) Software for spatial statistics. J Stat Softw 63(1):1–8. https://doi.org/10.18637/jss.v063.i01
Pebesma E, Mailund T, Hiebert J (2016) Measurement Units in R. R J 8(2):486–494. https://doi.org/10.32614/RJ-2016-061
Pebesma E, Mailund T, Kalinowski T (2020) units: measurement units for R vectors. https://CRAN.R-project.org/package=units, r package version 0.6-7
Renka RJ, Gebhardt A (2020) tripack: triangulation of irregularly spaced data. https://CRAN.R-project.org/package=tripack, R package version 1.3-9.1
Rowlingson B, Diggle PJ (1993) Splancs: spatial point pattern analysis code in S-Plus. Comput Geosci 19:627–655
Rowlingson B, Diggle P (2017) splancs: spatial and space-time point pattern analysis. https://CRAN.R-project.org/package=splancs, R package version 2.01-40
Sawicka K, Heuvelink GB, Walvoort DJ (2018) Spatial uncertainty propagation analysis with the spup R package. R J 10(2):180–199. https://doi.org/10.32614/RJ-2018-047
Tennekes M (2018) tmap: thematic maps in R. J Stat Softw 84(6):1–39
Tennekes M (2020) tmap: thematic maps. https://CRAN.R-project.org/package=tmap, R package version 3.1
Venables WN, Ripley BD (2002) Modern applied statistics with S, 4th edn. Springer, New York
Warmerdam F (2008) The geospatial data abstraction library. In: Hall GB, Leahy M (eds) Open source approaches in spatial data handling. Springer, Berlin, pp 87–104
Wickham H (2014) Tidy data. J Stat Softw 59(10):1–23. https://doi.org/10.18637/jss.v059.i10
Wickham H, Chang W, Henry L, Pedersen TL, Takahashi K, Wilke C, Woo K, Yutani H (2020) ggplot2: create elegant data visualisations using the grammar of graphics. https://CRAN.R-project.org/package=ggplot2, R package version 3.3.2