class: center, middle  <!-- Do not forget to adapt the presentation title in the header! --> <!-- Adjust the presentation to the session. Focus on the challenges, this is not a coding tutorial. Note, to include figures, store the image in the `/docs/assets/images/yyyymmdd/` folder and use the jekyll base.url reference as done in this template or see https://jekyllrb.com/docs/liquid/tags/#links. using the scale attribute , you can adjust the image size. --> <!-- Adjust the day, month --> # 26 JANUARY 2026 ## INBO coding club <!-- Adjust the room number and name --> Herman Teirlinck Building 01.05 - Isala Van Diest --- class: left, top # Reminders 1. Did we confirm the room reservation on the _roomie_? 2. Did we start the recording? --- class: left, top # INBO Coding Club is 8 years old! 🎉 First coding club session: 23 January 2018 🥳 Thanks to all the participants and contributors over the years! Do you want hex stickers? Just take one!  --- class: center, middle <!-- Create a new badge using Inkscape based on the assets/images/coding_club_badges.svg file -->  Long title: __"spatial data in R with sf"__ --- class: left, top # The sf package  The [sf homepage](https://r-spatial.github.io/sf/) is the best place to start your "spatial" voyage. --- class: left, top # The sf package sf stays for: _[simple features](https://en.wikipedia.org/wiki/Simple_Features)_, a scary way to express "geographic features", where feature is a scary term to refer to an abstraction of real world phenomena with geometrical properties such as lat/lon (or x-y). --- class: left, top ## I use sp. Why do you bother me with sf? - Short answer: because Thierry says so :-) - Long answer: sp is not actively maintained anymore. It relied on retired packages (rgdal, rgeos, maptools) and now uses sf as backend instead. So, why not use sf directly?  --- class: left, top ## I use sp. Why do you bother me with sf? sf is not only the present and the future, but also the recent past! This [sp-sf migration table](https://github.com/r-spatial/sf/wiki/Migrating) will help you refactoring your code.  --- class: left, top Install the package: ```r install.packages("sf") ``` Load the package: ```r library(sf) ``` --- class: left, top # Spatial coordinates Two types of spatial coordinates: - **projected** (or Cartesian) coordinates: refer to points on a flat space. The coordinates are the distance along the x and y axis - **unprojected** or **geographic** coordinates: refer to angles (latitude, longitude) pointing to locations on a sphere (or ellipsoid) No geospatial data without specifying the **Coordinate Reference System** (CRS) you work with! And what is a [(map) projection](https://en.wikipedia.org/wiki/Map_projection)? A way to visualize a surface of a sphere on a flat space.  <small> "R Spatial", Edzer Pebesma, R Foundation. UseR! 2021: Jul 5, 2021, 15:30 UTC, https://edzer.github.io/UseR2021/#11 </small> --- class: left, top # Projections A lot of projections exist. Each one has its own purpose. Check this [projection reference](http://www.radicalcartography.net/?projectionref) page by Bill Rankin, 2006 containing (almost) all the projections available in ArcGIS. Example 1: [**Lambert Azimuthal Equal Area**](https://en.wikipedia.org/wiki/Lambert_azimuthal_equal-area_projection), used by the [European Environment Agency](https://www.eea.europa.eu/) (EEA) to provide standard grids of Europe. Parameters: latitude of origin 52° N, longitude of origin 10° E  --- class: left, top # Projections Example 2: [Lambert coordinate systems](https://nl.wikipedia.org/wiki/Lambertco%C3%B6rdinaten), used by the [Belgian National Geographic Institute](https://ngi.be/) (NGI) to provide standard grids of Belgium. The most important is the Lambert72 (LB72), which has been the most used grid in Flanders/Belgium for over 50 years. Parameters: latitude of origin 49° 18′ 0″ N, longitude of origin 2° 18′ 0″ E. Did you know that Flemish Authority is [moving towards the Lambert2008 projection](https://www.vlaanderen.be/digitaal-vlaanderen/van-lambert72-naar-lambert2008)? --- class: left, top # Projections: it can get crazy! What does your [favorite map projection say](https://xkcd.com/977/) about you?  <small> The Peirce quincuncial projection is the conformal map projection from the sphere to an unfolded square dihedron, developed by Charles Sanders Peirce in 1877. __Source__: Wikipedia contributors. (2025, November 3). Peirce quincuncial projection. In Wikipedia, The Free Encyclopedia. Retrieved 08:48, January 23, 2026, from [link](https://en.wikipedia.org/w/index.php?title=Peirce_quincuncial_projection&oldid=1320267734)  --- class: left, top # Projections Some INBOers collected the map projection cards of [Daniel Huffman](https://somethingaboutmaps.com/). I am one of them :-) Why? - Short answer: they are cool. - Long answer: they are a perfect example of diversity and change of perspective while looking at things. [“We must constantly look at things in a different way.”](https://www.youtube.com/watch?v=XtYRC00IoUs), said Mr. Keating in the film _Dead Poets Society_ (1989).  --- class: left, top # Projections: CRS & EPSG codes A common way to specify the CRS is by providing the EPSG (numeric) code or identifier. EPSG stands for European Petroleum Survey Group*, an organization that maintained a geodetic parameter database with standard codes, the EPSG codes, for coordinate systems, datums, spheroids, units and such alike. There are a lot of EPSG codes! Full list: https://spatialreference.org/  <small> In 2005, the International Association of Oil & Gas Producers (IOGP) absorbed the European Petroleum Survey Group (1986–2005) into its structure as **IOGP Geodesy Subcommittee**. The Geodesy subcommittee kept the name of the EPSG Registry to avoid confusion. Source: chapter "The dilemma thickens" of https://www.spatialsource.com.au/gda2020-and-overcoming-the-web-mercator-dilemma/. </small> --- class: center, top <br> sf [cheatsheet](https://github.com/inbo/coding-club/blob/master/cheat_sheets/20211026_cheat_sheet_sf.pdf) See also this very nice [article with some examples](https://r-spatial.github.io/sf/articles/sf2.html) and the excellent books: [Spatial Data Science With Applications in R](https://r-spatial.org/book/)\* and [geocomputation with R](https://r.geocompx.org/)\*\*. <small> \* Pebesma, E.; Bivand, R. (2023). Spatial Data Science: With Applications in R (1st ed.). 314 pages. Chapman and Hall/CRC, Boca Raton. https://doi.org/10.1201/9780429459016 \*\* Lovelace, R., Nowosad, J., & Muenchow, J. (2025). Geocomputation with R (Second). CRC Press. </small> --- class: left, top ## How to get started? Check the [Each session setup](https://inbo.github.io/coding-club/gettingstarted.html#each-session-setup) to get started. ## First time coding club? Check the [First time setup](https://inbo.github.io/coding-club/gettingstarted.html#first-time-setup) section to setup. --- class: left, top  --- class: center, top # Share your code during the coding session <!-- Create a new hackmd file and replace this link (twice!) --> Go to https://hackmd.io/acJrz9VVS9e1Mp_ED7pZeQ?both and start by adding your name in section "Participants". <iframe src="https://hackmd.io/acJrz9VVS9e1Mp_ED7pZeQ?edit" height="400px" width="800px"></iframe> --- class: left, top # Download data and code You can download the material of today: - automatically via `inborutils::setup_codingclub_session()`* - manually** from GitHub foders [coding-club/data/20260126](https://github.com/inbo/coding-club/blob/main/data/20260126) and [coding-club/src/20260126](https://github.com/inbo/coding-club/blob/main/src/20260126) <br> <small> \* You can use the date in "YYYYMMDD" format to download the coding club material of a specific day, e.g. run `setup_codingclub_session("20230228")` to download the coding club material of February, 28 2023. If date is omitted, i.e. `setup_codingclub_session()`, the date of today is used. For all options, check the [tutorial online](https://inbo.github.io/tutorials/tutorials/r_setup_codingclub_session/).</small> <br> <small> \*\* Check the getting started instructions on [how to download a single file](https://inbo.github.io/coding-club/gettingstarted.html#each-session-setup).</small> --- class: left, top # Data description 1 Today we will work with these datasets: - [`20260126_occurrences_raccoon_be.txt`](https://github.com/inbo/coding-club/blob/main/data/20260126/20260126_occurrences_raccoon_be.txt) contains GBIF occurrences* of raccoon, _Procyon lotor_, in Belgium from 2000 up to 2025. - [`20260126_species_cube_raccoon_be.csv`](https://github.com/inbo/coding-club/blob/main/data/20260126/20260126_species_cube_raccoon_be.csv) contains the species occurrence cube** of raccoon (_Procyon lotor_) in Belgium from 2015 up to 2025, using the EEA 10kmx10km grid. - [`20260126_communesgemeente-belgium.zip`](https://github.com/inbo/coding-club/blob/main/data/20260126/20260126_communesgemeente-belgium.zip) contains the shapefile with the municipalities of Belgium\*\*\*. The coode to unzip is provided. <small> __\* __ Derived from GBIF.org (06 January 2026) GBIF Occurrence Download https://doi.org/10.15468/dl.juf58a <br> __\*\* __ Derived from GBIF.org (23 January 2026) GBIF Occurrence Download https://doi.org/10.15468/dl.bhc3h3 <br> __\*\*\* __ Source: https://data.gov.be/nl/datasets/httpswwwodwbbeexploredatasetcommunesgemeente-belgium. </small> --- class: left, top # Data description 2 Today we will work with these datasets: - [`20260126_protected_areas_be.gpkg`](https://github.com/inbo/coding-club/blob/main/data/20260126/20260126_protected_areas_be.gpkg) contains the Natura2000 protected areas of Belgium\*. - [`20260126_eea_grid_be.zip`](https://github.com/inbo/coding-club/blob/main/data/20260126/20260126_eea_grid_be.zip) contains the EEA 10kmx10km reference grid covering Belgium\*\*. The code to unzip is provided. <small> __\* __ Derived from a geopackage with all European Natura2000 areas: https://www.eea.europa.eu/en/datahub/datahubitem-view/6fc8ad2d-195d-40f4-bdec-576e7d1268e4. <br> __\*\* __ Source: European Environment Agency (2013), CC-BY 4.0. EEA reference grid for Belgium (10km), May 2013. https://sdi.eea.europa.eu/catalogue/srv/api/records/a25da98d-0df0-420a-bc27-1c486376c72bf </small> --- class: left, top # Scripts description Today we will work with this R script: - [`20260126_challenges.R`](https://github.com/inbo/coding-club/blob/main/src/20260126/20260126_challenges.R): code to start with the challenges. --- class: left, top # Species occurrence cubes The "cubes" are a relative new data output format from GBIF, [conceived](https://doi.org/10.1101/2020.03.23.983601) by us at INBO during TrIAS project, and then [formalised](https://docs.b-cubed.eu/guides/occurrence-cube/) and realised by GBIF (in collaboration with us) during the [B-Cubed project](http://b-cubed.eu/). Read [more](https://www.gbif.org/occurrence-cubes) about it or come to the Open Science Cafe about the B-Cubed project (Feb 24th) or to the Open Science Workshop about how to create and use species occurrence cubes ( March 31th).  --- class: left, top # Load libraries If needed, install them first (`install.packages("package_name")`). ```r library(tidyverse) library(sf) ``` We don't cover visualization of spatial data today, but if you want to easily inspect the spatial objects on a map, install and load the [mapview R package](https://r-spatial.github.io/mapview/). Use `mapview()` function to visualize your sf objects: ```r library(mapview) # one object mapview(my_sf_object) # 2 objects mapview(my_sf_object1) + mapview(my_sf_object2) ``` --- background-image: url(/assets/images/background_challenge_1.png) class: left, top # Challenge 1 Starting from the code provided in `20260126_challenges.R`: 1. Create a geospatial data frame called `occs` starting from `occs_df`. Use the columns `decimalLongitude` and `decimalLatitude` to specify the coordinates. Note that GBIF data are stored using [WGS 84](https://epsg.io/4326) (CRS = 4326). 3. Which **layers** does the geospatial file `20260126_protected_areas_be.gpkg` contain? What differences can you see between the first and the other layers? 4. **Read** the layer `NaturaSite_polygon`: call it `pa`. 5. **Read** the other layers as well. Call them `pa_bioregion` and `pa_habitats`. Are these spatial data.frames? 6. **Read** the shapefile with the municipalities of Belgium (see `municipalities_folder` variable): call it `municipalities`. 7. **Read** the EEA 10kmx10km grid (see `eea_grid_folder` variable): call it `eea_grid`. 8. Get the **CRS** of `occs`, `pa`, `municipalities` and `eea_grid`. Do they have the same CRS? 9. Extract the protected areas of type (`SITETYPE`) A as `pa_a`. Hint: do it as you would do with a standard data.frame. The motto of the sf package is "Spatial data, simplified" for a reason! --- background-image: url(/assets/images/background_challenge_2.png) class: left, top # Challenge 2 1. Create `occs_3035` by **transform**ing `occs` to CRS with [EPSG code 3035](https://epsg.io/3035) (called also ETRS89-extended / LAEA Europe). 2. **Write** a geopackage called `pa_occs_3035.gpkg` with two layers: first layer called `NaturaSite` and containing the protected areas (`pa`) and a second layer called `raccoon_occs`, containing `occs_3035`. Hint: check https://r-spatial.github.io/sf/articles/sf2.html#using-st_write. 3. Transform also `municipalities` to the CRS with EPSG code 3035. Call them `municipalities_3035`. 4. Find the **centroids** of `municipalities_3035`. Call it `municipalities_3035_centroids`. --- background-image: url(/assets/images/background_challenge_3.png) class: left, top # Challenge 3 - Manipulating spatial objects 1. Let's work with `cube`. How can you make a sf data frame of it? Call the new sf data frame `cube_sf`. Hint: `eea_grid` and `cube` both have a column called `CELLCODE`. 2. For each municipality in `municipalities_3035`, get the number of protected areas intersecting it. You can add it as a new column `n_pa` to `municipalities_3035`. 3. Are there municipalities without any protected areas? Extract them as `no_pa_municipalities_3035`. Hint: do it as you would do with a standard data.frame. 4. Get the 10 largest municipalities among no_pa_municipalities_3035. Hint: measure the **area**. 5. Get the number of raccoon occurrences per municipality. Add it as a new column `n_occs` to `municipalities_3035`. 6. Get the 10 municipalities with the highest number of raccoon occurrences. Hint: do it as you would do with a standard data.frame. 7. Add a column `protected_area_m2` to `municipalities_3035`, containing the total area of protected areas per municipality. You can eventually show it on a map using `mapview(municipalities_3035, zcol = "protected_area_m2")`. 8. Add a column `protected_percentage` to `municipalities_3035`, containing the percentage of municipality area that is protected. Which municipality has the highest percentage of protected area? --- class: left, top # The package of the month: qgisprocess Do you know that "our" Floris Vanderhaeghe is the maintainer of [qgisprocess](https://r-spatial.github.io/qgisprocess/), a package to provide an R interface to the popular and open source desktop geographic information system (GIS) program [QGIS](https://qgis.org/en/site/). qgisprocess has a [cheat sheet](https://r-spatial.github.io/qgisprocess/articles/cheatsheet_en.html) too! Floris also wrote some [slides](https://florisvdh.github.io/foss4g-2023-qgisprocess) presenting the package at the [FOSS4G 2023](https://2023.foss4g.org/) conference. The package was also the topic of the INBO coding club of December, 2023. See the [slides](https://inbo.github.io/coding-club/sessions/20231214_qgisprocess.html) and the edited [video recording](https://vimeo.com/900825991?share=copy).  --- class: left, top ## Resources - Comprehensive [solutions](https://github.com/inbo/coding-club/blob/main/src/20260126/20260126_challenges_solutions.R) are available on GitHub. You can opt to download the solutions automatically by using `inborutils::setup_codingclub_session("20260126")`. - The edited [video recording](https://vimeo.com/1159566109) is available on our [vimeo channel](https://vimeo.com/user/8605285/folder/1978815). - sf [homepage](https://r-spatial.github.io/sf/): the best place to start your "spatial" voyage. - sf [cheatsheet](https://github.com/inbo/coding-club/blob/master/cheat_sheets/20211026_cheat_sheet_sf.pdf) - See also this very nice [article with some examples](https://r-spatial.github.io/sf/articles/sf2.html) - Keynote "R spatial" of Edzer Pebesma at the useR! 2021 conference: [video](https://www.youtube.com/watch?v=cK08bxUJn5A) and [slides](https://edzer.github.io/UseR2021/#1). Very interesting to learn the principles and basics of spatial data in R - Everything what Edzer Pebesma says or write, actually :-) - Excellent online books: [Spatial Data Science With Applications in R](https://r-spatial.org/book/) and [geocomputation with R](https://r.geocompx.org/). Printed versions available. - [mapview homepage](https://r-spatial.github.io/mapview/) to visualize spatial data. - [Daniel Huffman](https://somethingaboutmaps.com/) website, with cartographic material (not necessarily in R). - [qgisprocess](https://r-spatial.github.io/qgisprocess/) package to provide an R interface to the popular and open source desktop geographic information system (GIS) program QGIS. Maintained by our INBO colleague, Floris Vanderhaeghe. - The [species occurrence cubes](https://www.gbif.org/occurrence-cubes), aggregated format for GBIF occurrences, output of the [B-Cubed project](http://b-cubed.eu/). --- class: center, middle  <!-- Adjust the room and date --> Room: 00.48 - Keldermans - <br> Date: __25/02/2026__, van 10:00 tot 12:30<br> Subject: to be decided <br> (registration announced via DG_useR@inbo.be)