├── .gitignore ├── README.md └── geospatial-learning.Rproj /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Geospatial learning resources for biomedical applications 2 | Resources related to geospatial analysis in (mostly) R. Most are applicable to any context, but some are geared more for biomedical applications. 3 | 4 | - [R package resources](#r-package-resources) 5 | - [Spatial data visualization](#spatial-data-visualization) 6 | - [Spatial analysis](#spatial-analysis) 7 | - [Geocoding (offline)](#geocoding-offline) 8 | 9 | ## R package resources 10 | 11 | - [CRAN Task View: Analysis of Spatial Data](https://cran.r-project.org/web/views/Spatial.html) • Roger Bivand & Jakub Nowosad 12 | - [r-spatial.org](https://r-spatial.org/) • Edzer Pebesma, Marius Appel & Daniel Nüst: Website and blog for those interested in using R to analyse spatial or spatio-temporal data 13 | - [rspatial.org - Spatial Data Science with R — R Spatial](https://rspatial.org/): Materials that teach spatial data analysis and modeling with R using the `raster` and `terra` packages 14 | 15 | ## Spatial data visualization 16 | 17 | - Workshop (R/Medicine 2022): Using Public Data and Maps for Powerful Data Visualizations • Joy Payton 18 | - [Video](https://www.youtube.com/watch?v=iU1h5b3qp_Y) 19 | - [Slides](https://rpubs.com/pm0kjp/r_medicine_2022) 20 | - [Repo](https://github.com/pm0kjp/r-medicine-2022) 21 | - Talk (RStudio Conf 2022): Accelerating geospatial computing using Apache Arrow • Dewey Dunnington: 22 | - [Video](https://www.rstudio.com/conference/2022/talks/accelerating-geospatial-computing-using-apache/) 23 | - [Slides](https://github.com/rstudio/rstudio-conf/blob/master/2022/deweydunnington/Accelerating%20geospatial%20computing%20using%20Apache%20Arrow%20-%20Dewey%20Dunnington.pdf) 24 | - [Package (`geoarrow`)](https://paleolimbot.github.io/geoarrow/) 25 | - Course: Geospatial Workshop • The Carpentries 26 | - [Introduction to Geospatial Concepts](https://datacarpentry.org/organization-geospatial/) 27 | - [Introduction to Geospatial Raster and Vector Data with R](https://datacarpentry.org/r-raster-vector-geospatial/) 28 | - Course: GIS in R • Earth Lab 29 | - [Shapefile Structure](https://www.earthdatascience.org/courses/earth-analytics/spatial-data-r/shapefile-structure/) 30 | - [Coordinate Reference System (CRS) and Spatial Projection](https://www.earthdatascience.org/courses/earth-analytics/spatial-data-r/intro-to-coordinate-reference-systems/) 31 | - [Projected vs Geographic Coordinate Reference Systems](https://www.earthdatascience.org/courses/earth-analytics/spatial-data-r/geographic-vs-projected-coordinate-reference-systems-UTM/) 32 | - [Understand EPSG, WKT and other CRS definition styles](https://www.earthdatascience.org/courses/earth-analytics/spatial-data-r/understand-epsg-wkt-and-other-crs-definition-file-types/) 33 | - [How to Reproject Vector Data in Different CRS](https://www.earthdatascience.org/courses/earth-analytics/spatial-data-r/reproject-vector-data/) 34 | - [Making Interactive Maps with Leaflet Earth Lab • Earth Lab](https://www.earthdatascience.org/courses/earth-analytics/spatial-data-r/make-interactive-maps-with-leaflet-r/) 35 | - Course: Introduction to Spatial Data Science • Luc Anselin & Grant Morrison 36 | - [Spatial Data Handling](https://spatialanalysis.github.io/lab_tutorials/1_R_Spatial_Data_Handling.html) 37 | - [Basic Mapping](https://spatialanalysis.github.io/lab_tutorials/4_R_Mapping.html) 38 | - Tutorial: [Space - Data Visualization](https://datavizm20.classes.andrewheiss.com/example/12-example/) • Andrew Wheiss 39 | - Tutorial: [Mapping Environmental Exposures](https://education.arcus.chop.edu/mapping-environmental-exposures/) • CHOP Arcus Education 40 | - Tutorial: [How to use open vector file formats in R: GeoPackage & GeoJSON](https://inbo.github.io/tutorials/tutorials/spatial_standards_vector/) • Floris Vanderhaeghe 41 | - Tutorial: [Astonishingly easy mapping in R with mapview - InfoWorld](https://www.infoworld.com/article/3644848/astonishingly-easy-mapping-in-r-with-mapview.html) • Sharon Machlis (H/T [Sharon Machlis](https://twitter.com/sharon000/status/1565834900514668544?s=20&t=NXyKKyVqeWGqcBL8J3aCPA)) 42 | - Workshop notes: R Spatial Workshop - Center for Spatial Data Science • Angela Li 43 | - [Book of notes](https://spatialanalysis.github.io/workshop-notes/) 44 | - Book: Spatial Data Science • R Spatial 45 | - [Spatial data with terra](https://www.rspatial.org/terra/spatial/index.html) 46 | - Book: Spatial Analysis with R • Chia Jung, Yeh 47 | - [Shapefile](https://chiajung-yeh.github.io/Spatial-Analysis/basic-knowledge-on-gis.html#shapefile) 48 | - Book: Geospatial Health Data • Paula Moraga 49 | - [Coordinate reference systems](https://www.paulamoraga.com/book-geospatial/sec-intro.html) 50 | - [Shapefiles](https://www.paulamoraga.com/book-geospatial/sec-spatialdataandCRS.html#shapefiles) 51 | - [Making maps with ](https://www.paulamoraga.com/book-geospatial/sec-spatialdataandCRS.html#making-maps-with-r) 52 | - Book: Introduction to Spatial Data Programming with R • Michael Dorman 53 | - [Vector layers](https://geobgu.xyz/r/vector-layers.html) 54 | - Workshop (useR!2020): First steps in spatial handling and visualization • Sébastien Rochette, Dorris Scott & Jakub Nowosad 55 | - [Repo](https://github.com/statnmap/user2020_rspatial_tutorial) 56 | - [Video](https://www.youtube.com/watch?v=1Hp8MO82t4g) 57 | - Workshop: Creating maps in R (sp package) • Robin Lovelace 58 | - [Repo](https://github.com/Robinlovelace/Creating-maps-in-R) 59 | - Site: Designing accessible maps 60 | - [Maps & Geospatial: Accessibility Resources](https://guides.libraries.psu.edu/c.php?g=1246608&p=9122546) • Library Guides at Penn State University 61 | - Package: [Load US Census Boundary and Attribute Data as tidyverse and sf-Ready Data Frames • tidycensus](https://walker-data.com/tidycensus/) (H/T [Hansi Munasinghe](https://twitter.com/hansimunasinghe/status/1565968205876965377?s=20&t=y4IrbhPrbNWX-5b493eq3A)) 62 | - Tutorial(s): [Blog | Milos Popovic - personal website and blog](https://milospopovic.net/blog/) (H/T [Milos Popovic](https://twitter.com/milos_agathon/status/1565972400956653568?s=20&t=y4IrbhPrbNWX-5b493eq3A)) 63 | - Workshop: [Introduction to Geospatial Data in R - ResBaz 2021](https://figshare.com/articles/dataset/Introduction_to_Geospatial_Data_in_R_ResBaz_2021/17021726) • André Bellvé (H/T [André Bellvé](https://twitter.com/AndreBellve/status/1566993675305254915?s=20&t=9b-jNXJN6uRFcxXyxf-jdg)) 64 | 65 | ## Spatial analysis 66 | 67 | - Workshop (R/Medicine 2022): Analyzing Geospatial Data in R • Sherrie Xie 68 | - [Video](https://www.youtube.com/watch?v=DD7bXonh-_E) 69 | - [Slides (pptx)](https://github.com/sherriexie/SpatialAnalysisinR/raw/main/Analyzing%20geospatial%20data%20in%20R.pptx) 70 | - [Repo](https://github.com/sherriexie/SpatialAnalysisinR) 71 | - Book: [Geocomputation with R](https://geocompr.robinlovelace.net/) • Robin Lovelace, Jakub Nowosad & Jannes Muenchow (H/T [Kjetil Haukås](https://twitter.com/kjethauk/status/1565809648963403776?s=20&t=NXyKKyVqeWGqcBL8J3aCPA)) 72 | - Talk: Geocomputation with R’s guide to reproducible spatial data analysis • Jakub Nowosad 73 | - [Slides](https://jakubnowosad.com/ogh2022) 74 | - Talk (RStudio Conf 2018): Tidy spatial data analysis • Edzer Pebezma 75 | - [Video](https://www.rstudio.com/resources/rstudioconf-2018/tidy-spatial-data-analysis/) 76 | - [Slides](https://edzer.github.io/rstudio_conf/#1) 77 | - Webinar: [Introduction to Geospatial Analysis in R - ORNL DAAC](https://daac.ornl.gov/resources/tutorials/r-geospatial-webinar/) • Alison Boyer & Jessica Welch 78 | - [Video](https://www.youtube.com/watch?v=Ul5Ly0266fU) 79 | - [Slides](https://daac.ornl.gov/resources/tutorials/r-geospatial-webinar/Earthdata_R_Geospatial_webinar_Mar2019_v20190312.pdf) 80 | - [Repo](https://github.com/ornldaac/r-geospatial-webinar) 81 | - Workshop (RStudio Conf 2020): Modern Geospatial Data Analysis • Zev Ross 82 | - [Repo](https://github.com/rstudio-conf-2020/geospatial) 83 | - Book: Spatial data analysis • R Spatial 84 | - [Spatial autocorrelation](https://www.rspatial.org/terra/analysis/3-spauto.html) 85 | - [Spatial interpolation techniques](https://www.rspatial.org/terra/analysis/4-interpolation.html) 86 | - [Spatial distribution models](https://www.rspatial.org/terra/analysis/5-global_regression.html) 87 | - [Spatial regression models](https://www.rspatial.org/terra/analysis/7-spregression.html) 88 | - Book: Geospatial Health Data • Paula Moraga 89 | - [Spatial modeling of areal data](https://www.paulamoraga.com/book-geospatial/sec-arealdataexamplespatial.html) 90 | - [Spatio-temporal modeling of areal data](https://www.paulamoraga.com/book-geospatial/sec-arealdataexamplest.html) 91 | - [Geostatistical data](https://www.paulamoraga.com/book-geospatial/sec-geostatisticaldatatheory.html) 92 | - Book: Intro to GIS and Spatial Analysis • Manuel Gimond 93 | - [Point pattern analysis](https://mgimond.github.io/Spatial/chp11_0.html) 94 | - [Hypothesis testing](https://mgimond.github.io/Spatial/hypothesis-testing.html) 95 | - Course: [Applied Spatial Statistics in R](https://scholar.harvard.edu/zhukov/classes/applied-spatial-statistics-r) • Yuri Zhukov 96 | - Course: GIS in R • Earth Lab 97 | - [Shapefile Structure](https://www.earthdatascience.org/courses/earth-analytics/spatial-data-r/shapefile-structure/) 98 | - Tutorials: The Center for Spatial Data Science 99 | - [Univariate and bivariate analysis](https://spatialanalysis.github.io/lab_tutorials/2_R_EDA_1.html) 100 | - [Multivariate exploration](https://spatialanalysis.github.io/lab_tutorials/3_R_EDA_2.html) 101 | - [Rate mapping](https://spatialanalysis.github.io/lab_tutorials/Rate_mapping.html) 102 | - [Applications of spatial weights](https://spatialanalysis.github.io/lab_tutorials/Applications_of_Spatial_Weights.html) 103 | - [Dimension reduction methods](https://geodacenter.github.io/tutorials/pca_mds/pca_mds.html) 104 | - [Classic clustering methods](https://geodacenter.github.io/tutorials/classic_cluster/classic_cluster.html) 105 | - Workshop notes: R Spatial Workshop - Center for Spatial Data Science • Angela Li 106 | - [Book of notes](https://spatialanalysis.github.io/workshop-notes/) 107 | - Workshop: Introduction to Geographic Data Science • Francisco Rowe 108 | - [Website](https://fcorowe.github.io/intro-gds/) 109 | - [Repo](https://github.com/fcorowe/intro-gds) 110 | - Book: [Spatial Modelling for Data Scientists](https://gdsl-ul.github.io/san/) • Francisco Rowe & Dani Arribas-Bel 111 | - Book: [[An Introduction to Spatial Data Analysis and Statistics: A Course in R ](https://paezha.github.io/spatial-analysis-r/) • Antonio Paez (H/T [Antonio Paez](https://twitter.com/paezha/status/1565808944198680578?s=20&t=NXyKKyVqeWGqcBL8J3aCPA)) 112 | - Book: Public Policy Analytics: Code & Context for Data Science in Government • Ken Steif (H/T [Matt Harris](https://twitter.com/Md_Harris/status/1565820991485394944?s=20&t=NXyKKyVqeWGqcBL8J3aCPA)) 113 | - [Book site](https://urbanspatial.github.io/PublicPolicyAnalytics/index.html) 114 | - [Repo w/ data](https://github.com/urbanSpatial/Public-Policy-Analytics-Landing) 115 | - Book: [16 Geospatial | Big Book of R](https://www.bigbookofr.com/geospatial.html) • Oscar Baruffa (H/T [Oscar Baruffa](https://twitter.com/OscarBaruffa/status/1565947499923349504?s=20&t=y4IrbhPrbNWX-5b493eq3A)) 116 | - Book: [Bayesian inference with INLA](https://becarioprecario.bitbucket.io/inla-gitbook/index.html) • Virgilio Gómez-Rubio (H/T [Jose Luis Cañadas](https://twitter.com/joscani/status/1566023665095004161?s=20&t=y4IrbhPrbNWX-5b493eq3A)) 117 | - Course (OpenGeoHub Foundation): Analysing spatial data (ECS530 01) • Roger Bivand (H/T [@datamaps](https://twitter.com/datamaps/status/1566126046893809664?s=20&t=y4IrbhPrbNWX-5b493eq3A)) 118 | - [Video playlist](https://www.youtube.com/playlist?list=PLXUoTpMa_9s10NVk4dBQljNOaOXAOhcE0) 119 | - [Site](https://rsbivand.github.io/ECS530_h19/) 120 | 121 | ## Geocoding (offline) 122 | - Residential mobility[^1] 123 | - R programming language 124 | - Decentralized and reproducible geocoding and characterization of community and environmental exposures for multisite studies[^2] (H/T [Zev Ross](https://twitter.com/zevross)) 125 | - [Video](https://www.cctst.org/news/2019/04/decentralized-and-reproducible-geocoding_11.html) 126 | - DeGAUSS: Decentralized Geomarker Assessment for Multi-Site Studies[^3] 127 | - Tool & instructions: https://degauss.org/ 128 | - [Challenges and solutions for private and reproducible environmental exposure assessment at scale](https://www.niehs.nih.gov/news/events/pastmtg/2022/elsi/challenges_and_solutions_for_private_and_reproducible_environmental_exposure_assessment_at_scale_508.pdf) 129 | - OpenStreetMap data to PostgreSQL converter: [openstreetmap/osm2pgsql](https://github.com/openstreetmap/osm2pgsql) 130 | - [Geocoding Made Easy • tidygeocoder](https://jessecambon.github.io/tidygeocoder/index.html) 131 | - [Geocoding Services - Data Privacy • tidygeocoder](https://jessecambon.github.io/tidygeocoder/articles/geocoder_services.html#data-privacy) 132 | - ArcGIS software 133 | - [What is geocoding?—ArcMap | Documentation](https://desktop.arcgis.com/en/arcmap/latest/manage-data/geocoding/what-is-geocoding.htm) 134 | - [Geocode Addresses (Geocoding)—ArcGIS Pro | Documentation](https://pro.arcgis.com/en/pro-app/latest/tool-reference/geocoding/geocode-addresses.htm) 135 | - R + ArcGIS 136 | - [Leveraging ArcGIS World Geocoding Service in R](https://www.esri.com/arcgis-blog/products/arcgis-pro/analytics/leveraging-arcgis-world-geocoding-service-in-r/) 137 | - [R-ArcGIS/r-bridge: Bridge library to connect ArcGIS and R, including arcgisbinding R library.](https://github.com/R-ArcGIS/r-bridge) 138 | - [R-ArcGIS Bridge | Spatial Analysis in R & GIS for Spatiotemporal Data](https://www.esri.com/en-us/arcgis/products/r-arcgis-bridge/overview) 139 | - [R Notebooks in ArcGIS Pro for Spatial Data Science](https://www.esri.com/arcgis-blog/products/arcgis-pro/analytics/r-notebooks-in-arcgis-pro-for-spatial-data-science/) 140 | 141 | 142 | [^1]: J.R. Meeker, H. Burris, M.R. Boland, An algorithm to identify residential mobility from electronic health-record data, International Journal of Epidemiology. 50 (2021) 2048–2057. https://doi.org/10.1093/ije/dyab064. 143 | 144 | [^2]: C. Brokamp, C. Wolfe, T. Lingren, J. Harley, P. Ryan, Decentralized and reproducible geocoding and characterization of community and environmental exposures for multisite studies, J Am Med Inform Assoc. 25 (2018) 309–314. https://doi.org/10.1093/jamia/ocx128. 145 | 146 | [^3]: C. Brokamp, DeGAUSS: Decentralized Geomarker Assessment for Multi-Site Studies, JOSS. 3 (2018) 812. https://doi.org/10.21105/joss.00812. 147 | -------------------------------------------------------------------------------- /geospatial-learning.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: No 4 | SaveWorkspace: No 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | LineEndingConversion: Posix 18 | --------------------------------------------------------------------------------