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` 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 MARCH 2020 ## INBO coding club <!-- Adjust the room number and name --> Online<br> My living room --- class: center, left  <p>No, not this time!</p> --- class: center, middle <!-- Create a new badge using Inkscape based on the assets/images/coding_club_badges.svg file -->  --- class: left, middle Install the package: ```r install.packages("sf") ``` Load the package: ```r library(sf) ``` --- class: left, middle After coding club 2019-02-26: https://github.com/rstudio/cheatsheets/issues/74 <br>  --- class: left, middle Not only, thanks to that coding club @ryangarnett learned a lot about git and GitHub!<br>  <br>Open science: it's good for you, it's good for everyone. --- class: center, middle <br> [`sf` cheatsheet](https://github.com/inbo/coding-club/blob/master/cheat_sheets/20200326_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 book [geocomputation with R](https://geocompr.robinlovelace.net/). --- class: center, middle ### 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, middle  <br> No yellow sticky notes online :-( We use hackmd (see next slide) but basic principle doesn't change. --- class: center, middle ### Share your code during the coding session! <!-- Create a new hackmd file and replace this link (twice!) --> Go to https://hackmd.io/Xx5FJXrWQV-Pn79ZxdDQBg?both <iframe src="https://hackmd.io/Xx5FJXrWQV-Pn79ZxdDQBg?both" height="400px" width="800px"></iframe> --- class: left, middle # Download data and code Today we will use an R script and some datasets. Download* the R script in `src ` and datasets in `data`. - R script: [20200326/20200326_challenges.R](https://github.com/inbo/coding-club/blob/master/src/20200326/20200326_challenges.R) - Dataset of butterfly observations in Belgium [20200326/20200326_butterflies.txt](https://github.com/inbo/coding-club/blob/master/data/20200326/20200326_butterflies.txt) - the reference grid of Belgium at 10km resolution: [`20200326/20200326_utm10_bel.gpkg`](https://github.com/inbo/coding-club/blob/master/data/20200326/20200326_utm10_bel.gpkg). Source: [European Environment Agency](https://www.eea.europa.eu/data-and-maps/data/eea-reference-grids-2) - the Belgian municipalities: [20200326/20200326_Belgian_municipalities.geojson](https://github.com/inbo/coding-club/blob/master/data/20200326/20200326_Belgian_municipalities.geojson) - the Flemish protected areas: [`20200326/20200326_protected_areas.gpkg`](https://github.com/inbo/coding-club/blob/master/data/20200326/20200326_protected_areas.gpkg). Source:[geopunt](https://www.geopunt.be/catalogus/datasetfolder/a84a87f5-5607-4019-a8db-9d52a827786b) <small>* __Note__: check the getting started instructions on [how to download a single file](https://inbo.github.io/coding-club/gettingstarted.html#each-session-setup)</small> --- background-image: url(/assets/images/background_challenge_1.png) class: left, middle # Challenge 1 1. Run 20200326/20200326_challenges.R and create a spatial data.frame, `spatial_butterfly_df`, from `butterfly_df` with: `crs =4326`, the **C**oordinate **R**eference **S**ystem used by the author of the dataset 2. A `sf` data.frame is tidyverse compatible! Create `spatial_atalanta_df` with only the observations of `Atalanta` butterflies 2. Read the Belgian reference grid 3. Read the Belgian municipalities 3. Compare the CRS of occurrences, grids and municipalities <p> --- class: left, middle ### CRS No geospatial data without specifying the Coordinate Reference System you work with!<br> Why? Because we need to project a sphere on a flat map! The typical Mercator projection stretches at the Poles: .<br> For more strange effects of the mercator projection see this [video](https://youtu.be/KUF_Ckv8HbE) from [tutorial](https://www.earthdatascience.org/courses/earth-analytics/spatial-data-r/intro-to-coordinate-reference-systems/). --- class: left, middle ### CRS by EPSG codes A common way to specify the CRS is by providing the EPSG code. EPSG stands for European Petroleum Survey Group and is an organization that maintains 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/  --- background-image: url(/assets/images/background_challenge_2.png) class: left, middle # Challenge 2 1. For each observation of Atalanta find the 10x10km cell it belongs to. Hint: an `intersection` is needed... 2. How many observations in each cell of the grid? 3. For each observation of Atalanta find the municipality it belongs to. 4. How many observations in each municipality? <p> --- background-image: url(/assets/images/background_challenge_3.png) class: left, middle # Challenge 3 1. Get information on the layers of the Flemish protected area. How are they called? 2. Read the layer `ps_hbtrl` of the Flemish protected areas as `hab_flanders`. Does it have a EPSG code? If not, *transform* to EPSG code 31370 ( [geopunt source](https://www.geopunt.be/catalogus/datasetfolder/a84a87f5-5607-4019-a8db-9d52a827786b)) 3. Overlap protected areas and municipalities 4. In which municipalities is *Kalmthoutse Heide* located? 5. And the *Voerstreek*? <p> --- class: left, middle # Bonus challenge Some extra exercises... 1. Via `st_read()` you can also read shape files! Go to the zipped shape file of Flemish protected areas: [`20190226/20190226_ps_hbtrl.zip`](https://github.com/inbo/coding-club/blob/master/data/20190226/20190226_ps_hbtrl.zip). Download it in your `data` folder and extract in subfolder `data/20190226/20190226_ps_hbtrl`. Check the names of the layers and read the layer `ps_hbtrl` as in challenge 3 2. Calculate centroids of the municipalities 3. Calculate distance of Atalanta observations to the centroids of the municipalities --- class: left, middle # Resources - [Geocomputation with R](https://geocompr.robinlovelace.net/) - [Spatial Data Science](https://keen-swartz-3146c4.netlify.com/) - [How to use open vector file formats in R](https://inbo.github.io/tutorials/tutorials/spatial_standards_vector/) - [`sf` cheatsheet](https://github.com/inbo/coding-club/blob/master/cheat_sheets/20200326/20200326_cheat_sheet_sf.pdf) - [`sf` article with some examples](https://r-spatial.github.io/sf/articles/sf2.html) --- class: center, middle <!-- Always try to include some type of reviewing (can be short and entertaining). Remove this slide if no reviewing is included -->  --- class: center, middle  <!-- Adjust the room and date --> Room: Herman Teirlinck - 01.05 - Isala Van Diest<br> Date: 28/04/2020, van 10:00 tot 12:00<br> (registration announced via DG_useR@inbo.be)