Damiano Oldoni
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# INBO CODING CLUB 25 October 2022 Welcome! ## Share your code snippet If you want to share your code snippet, copy paste your snippet within a section of three backticks (```): As an **example**: ``` library(tidyverse) ``` (*you can copy paste this example and add your code further down*) ## Yellow sticky notes No yellow sticky notes online. Put your name + " | " and add a "*" each time you solve a challenge (see below). ## Participants Name | Challenges --- | --- Damiano Oldoni | Anja Leyman |** Lynn Pallemaerts | ** Emma Cartuyvels| Thomas Scheppers | Hans Van Calster | Marijke Thoonen | Teun Everts | Adriaan Seynaeve | Amber Mertens |** Raïsa Carmen | Zoé Hermans An Leyssen | Wouter Depaepe | Leen Govaere Natalie Beenaerts Wim Kuypers Heleen Deroo Helee ## Challenge 1 Raisa: ``` # Create a geospatial data.frame called spatial_ludwigia_df starting from ludwigia_df. Note that GBIF data are stored using WGS 84. Hint: find first which numeric code is associated with WGS84 coordinate reference system and use the cheatsheet. spatial_ludwigia_df <- st_as_sf(ludwigia_df, coords = c("decimalLongitude", "decimalLatitude"), crs = "EPSG:4326") # 2. How many layers does the geospatial file `20221025_protected_areas.gpkg` # contain? lyrs <- sf::st_layers("./data/20221025/20221025_protected_areas.gpkg") length(lyrs$name) # 3. Import the layer `ps_hbtrl`: call it `prot_areas` prot_areas <- st_read("./data/20221025/20221025_protected_areas.gpkg", layer = lyrs$name[1]) # 4. What is the CRS declared by user? Does it coincide with the real Geographic # Coordinate Reference System (GEOCRS)? st_crs(prot_areas) # 5. Do `prot_areas` and `spatial_ludwigia_df` have the same CRS? st_crs(prot_areas) == st_crs(spatial_ludwigia_df) # 6. Read the Belgian provinces rds file as `be_provinces_sp` (the code is # given!). What is the class of this variable? From which package? How to # transform it to a sf object? be_provinces_sp <- read_rds( file = "./data/20221025/20221025_be_provinces_sp.rds" ) summary(be_provinces_sp ) typeof(be_provinces_sp) be_provinces_sf <- st_as_sf(be_provinces_sp) st_crs(prot_areas) == st_crs(be_provinces_sf) # 7. Extract the Flemish provinces. provinces_flanders <- be_provinces_sf %>% filter(TX_RGN_DESCR_NL == "Vlaams Gewest") ``` Hans ``` library(tidyverse) library(sf) ludwigia_df <- read_tsv("./data/20221025/20221025_ludwigia_grandiflora.txt") spatial_ludwigia_df <- ludwigia_df %>% st_as_sf(coords = c("decimalLongitude", "decimalLatitude"), crs = 4326) gpkg_file <- file.path("data/20221025/20221025_protected_areas.gpkg") # 1. Transform both `prot_areas` and `spatial_ludwigia_df` to [European # Terrestrial Reference System 1989](https://epsg.io/3035) (EPSG: 3035), the # coordinate reference system used at EU level View(spatial_ludwigia_df) View(prot_areas) # 2. How many layers does the geospatial file `20221025_protected_areas.gpkg` # contain? st_layers(gpkg_file) length(st_layers(gpkg_file)$name) # 3. Import the layer `ps_hbtrl`: call it `prot_areas` prot_areas <- read_sf(gpkg_file, layer = "ps_hbtrl") plot(st_geometry(prot_areas)) # 4. What is the CRS declared by user? Does it coincide with the real Geographic # Coordinate Reference System (GEOCRS)? prot_areas # 5. Do `prot_areas` and `spatial_ludwigia_df` have the same CRS? waldo::compare( st_crs(prot_areas), st_crs(spatial_ludwigia_df)) st_crs(prot_areas) == st_crs(spatial_ludwigia_df) # 6. Read the Belgian provinces rds file as `be_provinces_sp` (the code is # given!). What is the class of this variable? From which package? How to # transform it to a sf object? be_provinces_sp <- read_rds( file = "./data/20221025/20221025_be_provinces_sp.rds" ) class(be_provinces_sp) be_provinces_sf <- st_as_sf(be_provinces_sp) # 7. Extract the Flemish provinces. be_prov_fla <- be_provinces_sf %>% filter(TX_RGN_DESCR_NL == "Vlaams Gewest") plot(st_geometry(be_prov_fla)) ``` Lynn: ``` # 1. Create a geospatial data.frame called spatial_ludwigia_df starting from # ludwigia_df. Note that GBIF data are stored using WGS 84. Hint: find first # which numeric code is associated with WGS84 coordinate reference system and # use the cheatsheet. ludwigia_df <- read_tsv("./data/20221025/20221025_ludwigia_grandiflora.txt") spatial_ludwigia_df <- st_as_sf(ludwigia_df, coords = c("decimalLongitude", "decimalLatitude"), crs = 4326) # 2. How many layers does the geospatial file 20221025_protected_areas.gpkg # contain? st_layers("./data/20221025/20221025_protected_areas.gpkg") # maar dit toont maar de eerste layer # 3. Import the layer ps_hbtrl: call it prot_areas prot_areas <- st_read("./data/20221025/20221025_protected_areas.gpkg", layer = "ps_hbtrl") # 4. What is the CRS declared by user? Does it coincide with the real Geographic # Coordinate Reference System (GEOCRS)? prot_areas st_crs(prot_areas) # 5. Do prot_areas and spatial_ludwigia_df have the same CRS? st_crs(spatial_ludwigia_df) == st_crs(prot_areas) # 6. Read the Belgian provinces rds file as `be_provinces_sp` (the code is # given!). What is the class of this variable? From which package? How to # transform it to a sf object? be_provinces_sp <- read_rds("./data/20221025/20221025_be_provinces_sp.rds") class(be_provinces_sp) st_crs(be_provinces_sp) be_provinces_sp <- st_as_sf(be_provinces_sp, crs = 6326) # 7. Extract the Flemish provinces. fl_provinces_sp <- be_provinces_sp %>% filter(CD_RGN_REFNIS == 2000 ) ``` ## Challenge 2 Lynn: ``` # 1. Transform both `prot_areas` and `spatial_ludwigia_df` to [European # Terrestrial Reference System 1989](https://epsg.io/3035), the coordinate # reference system used at EU level ludwigia_3035 <- st_transform(spatial_ludwigia_df, crs = 3035) prot_areas_3035 <- st_transform(prot_areas, crs = 3035) # 2. Write the transformed data as a geopackage file called # `prot_areas_and_ludwigia_3035.gpkg` with two layers: the first called # `prot_areas`, containing the protected areas, the second layer, # `ludwigia_obs`, containing the observations of water primrose st_write(prot_areas_3035, layer = "prot_areas", "./data/20221025/prot_areas_and_ludwigia_3035.gpkg", append = F) st_write(ludwigia_3035, layer = "ludwigia_obs", "./data/20221025/prot_areas_and_ludwigia_3035.gpkg", append = T) # 3. Due to spatial uncertainty (gridded data, GPS uncertainty, etc.) GBIF # observations should not be idealized as points in space, but as circles. # Create such circles using the values stored in column # `coordinateUncertaintyInMeters` of `spatial_ludwigia_df_3035` st_write(prot_areas_3035, layer = "prot_areas", "./data/20221025/prot_areas_and_ludwigia_3035.gpkg", append = F) st_write(ludwigia_3035, layer = "ludwigia_obs", "./data/20221025/prot_areas_and_ludwigia_3035.gpkg", append = T) ``` Hans: ```` # 1. Transform both `prot_areas` and `spatial_ludwigia_df` to [European # Terrestrial Reference System 1989](https://epsg.io/3035), the coordinate # reference system used at EU level prot_areas <- st_transform(prot_areas, crs = 3035) spatial_ludwigia_df <- st_transform(spatial_ludwigia_df, crs = 3035) # 2. Write the transformed data as a geopackage file called # `prot_areas_and_ludwigia_3035.gpkg` with two layers: the first called # `prot_areas`, containing the protected areas, the second layer, # `ludwigia_obs`, containing the observations of water primrose st_write(prot_areas, "prot_areas_and_ludwigia_3035.gpkg", layer = "prot_areas") st_write(spatial_ludwigia_df, "prot_areas_and_ludwigia_3035.gpkg", layer = "ludwigia_obs") st_layers("prot_areas_and_ludwigia_3035.gpkg") # 3. Due to spatial uncertainty (gridded data, GPS uncertainty, etc.) GBIF # observations should not be idealized as points in space, but as circles. # Create such circles using the values store in column # `coordinateUncertaintyInMeters` of `spatial_ludwigia_df_3035` spatial_ludwigia_df %>% st_buffer(dist = .$coordinateUncertaintyInMeters) ```` ## Challenge 3 Hans: ``` # Using data in CRS 3035: # 1. Find which observations, as points, are _contained_ in each protected area? st_contains(x = prot_areas, y = spatial_ludwigia_df) # You can use `st_intersects()` as well: same result. However, st_contains gives # more the idea of what you are doing # 2. But we should better check which observations, as circles (!), _intersect_ # each protected area. How to do it? st_intersects(prot_areas, spatial_ludwigia_buffer) # 3. So, how many observations in the protected area called `"Demervallei"`? st_join(spatial_ludwigia_buffer, prot_areas, left = FALSE) %>% filter(NAAM == "Demervallei") %>% count(NAAM) # 4. Sometimes it's interesting to calculate the centroid of a polygon, e.g. for # visualizations. Easy by using sf function `st_centroids()`. However, you get # an error while calculating the centroids of `prot_areas`. What does it mean? How to solve the problem? st_centroid(prot_areas) ``` ``` # Using data in CRS 3035: # 1. Find which observations, as points, are _contained_ in each protected area? prot_area_ob <- st_contains(x = prot_areas_etrs, y = spatial_ludwigia_df_etrs) # You can use `st_intersects()` as well: same result. However, st_contains gives # more the idea of what you are doing prot_area_ob2 <- st_intersects(y = prot_areas_etrs, x = spatial_ludwigia_df_etrs) #the other way around works >< contains prot_area_ob3 <- st_intersects(x = prot_areas_etrs, y = spatial_ludwigia_df_etrs) #the same as before # 2. But we should better check which observations, as circles (!), _intersect_ # each protected area. How to do it? prot_area_ob4 <- st_intersects(x = prot_areas_etrs, y = circles) # 3. So, how many observations in the protected area called `"Demervallei"`? demervallei <- which(prot_areas$NAAM == "Demervallei") length(prot_area_ob4[[demervallei]]) # 4. Sometimes it's interesting to calculate the centroid of a polygon, e.g. for # visualizations. Easy by using sf function `st_centroids()`. However, you get # an error while calculating the centroids of `prot_areas`. What does it mean? How to solve the problem? st_centroid(st_make_valid(prot_areas)) ``` ## Bonus challenge

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