# INBO CODING CLUB

28 November 2024

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 | ***
Emma Cartuyvels| **
Pieter Huybrechts | **
Dirk Maes | **
Falk Mielke | ***
Rhea Maesele | *
Sanne Govaert | ***
Anja Leyman |
Jonas Bertels |
Britt Lonneville | **
Cyrielle Delvenne |
Adriaan Seynaeve |
Arc'hantael Labriere |
Bert Van Hecke | **

## Challenge 1

### Damiano's solution (example)

Copy paste this section to show your solutions.

# dummy code
print("This is how to insert code.")

### Pieter's solution

I used a different palette, I hear it's more colour blind friendly: https://doi.org/10.1371/journal.pone.0199239

library(ggplot2)
library(ggrepel)

ias_in_pa <- sf::st_read(
  dsn = "./data/20241128/20241128_ias_union_concern_Natura2000_B.gpkg"
)

ias_in_pa |>
  ggplot() +
  geom_sf(colour = "black") +
  aes(fill = n_ias) +
  # geom_sf_label_(aes(label = SITECODE), size = 2) +
  geom_label_repel(
    aes(label = SITECODE, geometry = geom),
    stat = "sf_coordinates",
    size = 2,
    max.time = 9,
    max.iter = 50000,
    colour = "snow"
  ) +
  # scale_fill_viridis_c() +
  paletteer::scale_fill_paletteer_c("viridis::cividis") +
  theme_minimal() +
  theme(legend.position = "bottom") +
  labs(
    title = "Invasive Alien Species of union concern in Natura2000 protected areas",
    fill = "Number of IAS"
  )


### Falk's attempt

# https://ggplot2.tidyverse.org/reference/ggsf.html
ias_in_pa %>%
  ggplot(aes(fill = n_ias)) +
  geom_sf(color = "black") +
  # geom_sf_label(aes(label = SITECODE), size = 8, fontface = "bold") +
  # geom_sf_text(aes(label = SITECODE), size = 4, fontface = "bold") +
  geom_text_repel(aes(label = SITECODE, geometry = geom), stat = "sf_coordinates", size = 8, fontface = "bold") +
  scale_fill_viridis_c() +
  theme(legend.position = "none")

### Dirk's attempt (categorising the number of species), needs some more cleaning!

ias_in_pa <- ias_in_pa %>%
  mutate(n_ias2 = case_when(
    n_ias <10 ~ "<10",
    n_ias >= 10 & n_ias < 15 ~ "10 - 15",
    n_ias >= 15 & n_ias < 20 ~ "15 - 20",
    n_ias >= 20 & n_ias < 25 ~ "20 - 25",
    n_ias >= 25              ~ ">25"
  ))
head(ias_in_pa)

ias_in_pa$n_ias2 <- factor(ias_in_pa$n_ias2,
                                 levels = c("<10",
                                            "10 - 15",
                                            "15 - 20",
                                            "20 - 25",
                                            ">25"))

p <- ggplot(ias_in_pa,
            aes(fill = n_ias2),
            colour = "black") +
  scale_fill_manual(values = c(viridis::inferno(5))) +
  geom_sf() +
  geom_label_repel(aes(label = SITECODE,
                       geometry = geom),
                   colour = "lightgreen",
                   size = 5,
                   fontface = "bold",
                  stat = "sf_coordinates",
                  max.overlaps = 38) +
  theme_minimal() +
  theme(legend.position = "bottom") +
  labs(
    title = "Invasive Alien Species of union concern in Natura2000 protected areas",
    fill = "Number of IAS"
  )
p

### Emma's solution

ggplot(ias_in_pa) +
  geom_sf(aes(fill = n_ias), color = "black") +
  scale_fill_viridis_c() +
  geom_label_repel(aes(label = SITECODE, geometry = geom),
                  stat = "sf_coordinates",
                  size = 2,
                  fontface = "bold",
                  max.overlaps = 15)

### Sanne's solution

ias_in_pa %>%
  ggplot() +
  geom_sf(aes(fill = n_ias), color = "black") +
  # geom_sf_label(aes(label = SITECODE, size = 2), color = "black") +
  geom_text_repel(
    aes(label = SITECODE, geometry = geom),
    stat = "sf_coordinates",
    size = 2
  ) +
  scale_fill_viridis_c()

### Rhea's solution

#1. How to plot the Natura2000 areas with ggplot? 
#Fill the areas based on the number of alien species of Union concern, n_ias. 
#This kind of map is known as choropleth map. 
#Hint: see documentation of the geom_sf function or the general hint below.
ggplot(ias_in_pa) + geom_sf(aes(fill = n_ias))

#2. Add the site code (SITECODE column) as labels. 
#Show them in black, with fontsize 2 and bold style.
ggplot(ias_in_pa) + geom_sf(aes(fill = n_ias)) +
  geom_sf_label(aes(label = SITECODE), color = "black", size = 2, fontface = "bold")

#3. A pure ggplot question: how to set the color of the borders of the Natura2000 areas 
#to black?
ggplot(ias_in_pa) + geom_sf(aes(fill = n_ias), color = "black") +
  geom_sf_label(aes(label = SITECODE), color = "black", size = 2, fontface = "bold")
#within geom_sf, but outside 'aes()', set color = "black" to set the color of the borders as another color than the 'fill'
  
#4. A pure ggplot question: Scale the color using the continuous viridis palette. 
#Hint: see documentation of the scale_fill_viridis family of functions.
ggplot(ias_in_pa) + geom_sf(aes(fill = n_ias)) +
  geom_sf_label(aes(label = SITECODE), color = "black", size = 2, fontface = "bold") +
  scale_fill_viridis_c()

#5. How to avoid overlapping labels? Hint: see the general hint below.
#General hint: Follow the first part of this good tutorial from R CHARTS!
ggplot(ias_in_pa) + geom_sf(aes(fill = n_ias)) +
  scale_fill_viridis_c() +
  geom_text_repel(
    aes(label = SITECODE, geometry = geom),
    stat = "sf_coordinates",
    size = 2,
    fontface = "bold")

### Arc'hantael's attempt:
ias_in_pa %>%
ggplot() +
geom_sf(color = "black") +
aes(fill = n_ias) +
geom_sf_text(aes(label = SITECODE), size = 2, fontface = "bold") +
scale_fill_viridis_c() +
labs(fill = "Number of IAS")

## Challenge 2

### Emma's solution

ias_in_pa_sample |>
  ggplot() +
  annotation_map_tile(type = "cartolight",
                      zoomin = 0,
                      cachedir = "./data/20241128") +
  geom_sf(aes(fill = n_ias), color = "black") +
  scale_fill_viridis_c() +
  geom_label_repel(aes(label = SITECODE, geometry = geom),
                   stat = "sf_coordinates",
                   size = 2,
                   fontface = "bold",
                   max.overlaps = 15) +
  annotation_north_arrow(location = "bl", which_north = "grid") +
  labs(x = NULL, y = NULL)

### Pieter's solution

ias_in_pa_sample <- ias_in_pa[1:10,]

ias_in_pa_sample %>%
  ggplot() +
  scale_fill_viridis_c() +
  ggspatial::annotation_map_tile(
    type = "cartolight",
    zoom = 10,
    cachedir = tempdir()
  ) +
  geom_sf(aes(fill = n_ias)) +
  ggspatial::annotation_north_arrow(
    location = "tr",
    which_north = "true",
    style = ggspatial::north_arrow_fancy_orienteering()) +
  ggspatial::annotation_scale(location = "br")


### Falk's Attempt

# more map types: https://paleolimbot.github.io/rosm/
ias_in_pa %>%
  ggplot(aes(fill = n_ias)) +
  annotation_map_tile(
    type = "hotstyle",
    zoomin = 0,
    cachedir = "./.tiles/"
  ) +
  geom_sf(color = "black") +
  geom_text_repel(aes(label = SITECODE, geometry = geom), stat = "sf_coordinates", size = 4, fontface = "bold") +
  scale_fill_viridis_c() +
  annotation_north_arrow(location = "tr", which_north = "true") +
  annotation_scale(location = "bl") +
  theme_bw() +
  theme(legend.position = "none")

### Sanne's solution

ias_in_pa_sample %>%  
  ggplot() +
  annotation_map_tile(
    type = "thunderforestlandscape",
    zoomin = 0, 
    cachedir = "./data/20241128"
    ) +
  geom_sf(color = "black") +
  aes(fill = n_ias) +
  scale_fill_viridis_c() +
  geom_label_repel(
    aes(label = SITECODE, geometry = geom),
    stat = "sf_coordinates",
    size = 2
  ) +
  annotation_north_arrow(location = "tl", which_north = "grid")

## Challenge 3

### Falk's attempt

# https://r-spatial.github.io/mapview/articles/mapview_02-advanced.html
# c("SITECODE", "SITENAME", "n_ias")
m1 <- mapview(
  ias_in_pa,
  zcol = "n_ias",
  popup = popupTable(ias_in_pa), # does not work
  layer.name = "Alien species of Union concern",
  color = "gray90",
  alpha.regions = 0.8,
  alpha.lines = 0.1,
  map.types = c("OpenStreetMap", "CartoDB.DarkMatter"),
  legend = TRUE
  )
# m1

m2 <- vl_mun %>% 
  mapview(
  layer.name = "municipalities",
  color = "black",
  alpha.regions = 0.0,
  alpha.lines = 1.0,
  map.types = c("OpenStreetMap", "CartoDB.DarkMatter"),
  legend = TRUE
  )

m2 + m1
# ~~adding mouse coords did not work for me :`(~~
# https://r-spatial.github.io/mapview/articles/mapview_06-add.html
# actually it did work by `library("leafem")`

### Pieter's solution

mv_ias <- ias_in_pa %>% 
  mapview::mapview(
    zcol = "n_ias",
    color = "grey20",
    map.types = "OpenStreetMap",
    alpha.regions = 0.8,
    alpha = 0.1,
    layer.name = "Alien species of Union concern",
    popup = leafpop::popupTable(
      ias_in_pa,
      zcol = c("SITECODE", "SITENAME", "n_ias")
    )
  )

mapview::mapview(flanders,
                 # map = mv_ias,
                 layer.name = "municipalities",
                 alpha.regions = 0,
                 legend = FALSE,
                 lwd = 1,
                 map.types = "OpenStreetMap") + mv_ias

### Emma's solution

mapview(flanders,
        layer.name = "municipality",
        map.types = "OpenStreetMap",
        color = "black",
        legend = FALSE,
        alpha.regions = 0,
        lwd = 1) +
  mapview(ias_in_pa,
          zcol = "n_ias",
          legend = TRUE,
          color = "grey30",
          map.types = "OpenStreetMap",
          alpha.regions = 0.8,
          alpha = 0.1,
          layer.name = "Alien species of Union concern",
          popup = popupTable(ias_in_pa,
                             zcol = c("SITECODE",
                                      "SITENAME",
                                      "n_ias")))

### Robin's solution

map1  <- mapview(ias_in_pa_sample, 
        zcol = "n_ias",   
        color.palette = viridis,  
        legend = TRUE,   
        alpha = 0.7,     
        color.palette = viridis::viridis,  
        lwd = 1.5,       
        contour = TRUE,  
        contour.color = "gray30",  
        layer.name = "Alien species of Union concern",
        popup = popupTable(ias_in_pa_sample, zcol = c("SITECODE", "SITENAME", "n_ias")),  
        label = TRUE)    

map2 <- mapview(flanders, 
        legend = TRUE,   
        alpha = 0.7,     
        alpha.regions = 0,
        color.palette = viridis::viridis,  
        lwd = 1,       
        contour = TRUE,  
        contour.color = "black",  
        layer.name = "Municipalities",
        label = TRUE)    

combined_map <- map2 + map1
combined_map

### Sanne's solution

mapview(
  flanders,
  layer.name = "Municipalities",
  color = "black",
  matypes = "OpenStreetMap",
  legend = FALSE,
  alpha = 1,
  alpha.regions = 0,
  label = FALSE
) +
  mapview(
    ias_in_pa,
    zcol = "n_ias",
    legend = "TRUE",
    alpha.regions = 0.8,
    layer.name = "Alien species of Union concern",
    maptypes = "OpenStreetMap",
    color = "gray30",
    alpha = 0.1,
    popup = popupTable(
      ias_in_pa,
      zcol = c("SITECODE", "SITENAME", "n_ias")
    )
  )