# INBO CODING CLUB

31 August 2023

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 |
Pieter Huybrechts | ***
Rhea Maesele |
Dirk Maes |
Nele Mullens |
Adriaan Seynaeve |

## Challenge 1

### Pieter

# 1 Vector data (continuous variable)
natura2000 <- sf::st_read("./data/20230831/20230831_protected_areas.gpkg")


pajottenland_municipalities <- st_read("./data/20230831/20230831_Pajottenland_municipalities.gpkg")

natura2000 %>% 
  ggplot(aes(fill = Shape_area)) +
  geom_sf() +
  scale_fill_viridis_c()

pajottenland_municipalities %>% 
  ggplot(aes(fill = Shape_Area)) +
  geom_sf() +
  scale_fill_viridis_b()`

# 2. Raster data (continous variable)
nitrogen <- terra::rast("./data/20230831/20230831_nitrogen.tif")

nitrogen

ggplot() +
  tidyterra::geom_spatraster(data = nitrogen, show.legend = TRUE)

terra::plot(nitrogen,
            range = c(0,47),
            col = hcl.colors(n = 100, palette = "Blue-Red 3"),
            legend = TRUE)

# 3. Raster data (categorical values)
terra::plot(lu_nara_2016,
            col = legend_land_use$color,
            type = "classes",
            levels = legend_land_use$land_use,
            box = FALSE,
            main = "Land is used"
            )

## Challenge 2

### Pieter

## Challenge 2 - static maps

natura2000 <- sf::st_read("./data/20230831/20230831_protected_areas.gpkg")
natura2000_osm <- get_tiles(natura2000, crop = TRUE, zoom = 8)
plot_tiles(natura2000_osm)
plot(natura2000$geom, add = TRUE)
mtext(text = get_credit("OpenStreetMap"), 
      side = 1, line = -1, adj = 1, cex = .9, 
      font = 3)

svg("20230831_great_old_plot.svg") # save the plot we are about to create
natura2000_esri <- get_tiles(natura2000, provider = "Esri.NatGeoWorldMap", crop = TRUE, zoom = 9)
plot_tiles(natura2000_esri)
plot(natura2000$geom, add = TRUE)
mtext(text = get_credit("Esri.NatGeoWorldMap"), 
      side = 1, line = -1, adj = 1, cex = .9, 
      font = 3)
dev.off() # close graphics device, (which we opened by `svg()`)
## see also png() bmp() pdf(), ggplot2::ggsave() is more fun.

## INTERMEZZO

## Challenge 3

### Pieter

# read data.frame with number of moths species for each UTM1km cell (`TAG`
# identifier)
n_moths <- readr::read_csv("./data/20230831/20230831_n_moths.txt")
n_moths

# read the geospatial file containing the UTM1km cells of Pajottenland
utm1_pajottenland <- sf::st_read(
  "./data/20230831/20230831_utm1km_Pajottenland.gpkg"
)

# Join data
n_moths <- utm1_pajottenland %>%
  dplyr::left_join(n_moths, by = "TAG")

n_moths

# 1 + 2
mapview(
  n_moths,
  color = "red",
  alpha.regions = 0.8,
  col.regions = RColorBrewer::brewer.pal(9, name = "Spectral"),
  alpha = 0.2,
  map.types = "OpenStreetMap",
  legend = TRUE,
  zcol = "n",
  layer.name = "number of moth species"
)

# 3
mapview(
  pajottenland_municipalities,
  layer.name = "municipality",
  map.types = "OpenStreetMap",
  alpha.regions = 0,
  lwd = 1,
  legend = FALSE,
 
)

# 4

mapview(
  list(n_moths, pajottenland_municipalities),
  layer.name = list("number of moth species", "municipality"),
  legend = list(TRUE, FALSE),
  alpha.regions = list(0.2, 0),
  alpha = list(0.8, NULL),
  zcol = list("n", NULL),
  color = list("red","black"),
  map.types = "OpenStreetMap",
  lwd = list(2, 1)
  )


# 5
img <- "https://raw.githubusercontent.com/inbo/coding-club/master/docs/assets/images/coding_club_logo.svg"
mapview(
  list(n_moths, pajottenland_municipalities),
  layer.name = list("number of moth species", "municipality"),
  legend = list(TRUE, FALSE),
  alpha.regions = list(0.2, 0),
  alpha = list(0.8, NULL),
  zcol = list("n", NULL),
  color = list("red","black"),
  map.types = "OpenStreetMap",
  lwd = list(2, 1)
) %>% 
  leafem::addLogo(img, url = "https://inbo.github.io/coding-club/")

### Dirk, example using your own colour palette

colpal <- colorRampPalette(c("white", "grey", "red", "darkgreen"))

map_n_moths <- mapview(n_moths,
                       zcol = "n",
                       legend = TRUE,
                       color = "pink",
                       col.regions = colpal,
                       map.types = "OpenStreetMap",
                       alpha = 50)
map_n_moths

### How to save leaflet maps as html?

saveWidget(map, filename = "filename.html")

## Bonus challenge 1

## Bonus challenge 2