# INBO CODING CLUB

26 August 2025

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 star ("*") each time you solve a challenge (see below).

## Participants

Name | Challenges
--- | ---
Damiano Oldoni | ***
Emma Cartuyvels |
Pieter Huybrechts | **
Rhea Maesele |
Florian Van Hecke |
Anne-Lie Van Praet |
Hanna Jaspaert |
Tosca Vanroy |
Stien Mertens |**
Falk Mielke |
Toon Westra |*

## General

### Mapview and the Pipe

library("sf")
library("mapview")

mapview(franconia) # does work -> reference

franconia %>%
  mapview() # does not work

franconia |>
  mapview() # DOES work

franconia %>%
  mapView() # does not work

franconia %>%
  mapView(x = .) # does not work

franconia %>%
  mapview(x = .) # does not work


view_map <- function (.data, ...) {
  mapview(x = .data, ...)
}

franconia %>%
  view_map # does not work

franconia |>
  view_map() # does not work

### Cleanup Suggestion *(Falk)*

FYI you can clean up all the character columns at once:

n_giant_hogweed %>%
  mutate(
    across(
      where(is.character), 
      function(col) stringr::str_extract(col, "(?<=\\[').*(?='\\])")
    ) 
  )
# modified from https://forum.posit.co/t/extract-text-between-brakets/43448/6

## 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

## 1.1 ####
mapview(n_giant_hogweed,
        legend = TRUE,
        zcol = "n",
        color = "white"
        )

## 1.2 ####
mapview(n_giant_hogweed,
        legend = TRUE,
        zcol = "n",
        color = "white",
        layer.name = "Number of giant hogweed occurrences",
        alpha = 0.5,
        alpha.regions = 0.8,
        col.regions = heat.colors,
        popup = popupTable(n_giant_hogweed,
                           zcol = c("n",
                                    "mun_name_nl",
                                    "mun_name_fr")
                           ),

)

## 1.3 ####
hogweed_map <- mapview(n_giant_hogweed,
        legend = TRUE,
        zcol = "n",
        color = "white",
        layer.name = "Number of giant hogweed occurrences",
        alpha = 0.5,
        alpha.regions = 0.8,
        col.regions = heat.colors,
        popup = popupTable(n_giant_hogweed,
                           zcol = c("n",
                                    "mun_name_nl",
                                    "mun_name_fr")
        ),
        map.types = "OpenStreetMap.Mapnik"
)
hogweed_map
## 1.4 ####
giant_hogweed <- readr::read_tsv(
  "data/20250826/20250826_giant_hogweed_fl_bxl.tsv",
  na = ""
  ) %>%
  sf::st_as_sf(
    coords = c("decimalLongitude", "decimalLatitude"),
    crs = 4326
  )

hogweed_occ_map <-
  hogweed_map + mapview(giant_hogweed,
                      col.regions = "gray80",
                      cex = 5,
                      layer.name = "Giant hogweed occurrences"
                      )

hogweed_occ_map
## 1.5 ####

hogweed_occ_map %>% leafem::addMouseCoordinates()

## 1.6 ####

hogweed_occ_map %>%
  leafem::addMouseCoordinates() %>%
  mapshot(url = file.path("data", "20250826", "hogweed.html"))

### Emma's solution

## 1.1 ####
m <- mapview(n_giant_hogweed,
        zcol = "n",
        legend = TRUE,
        color = "white")
m

## 1.2 ####
m <- mapview(n_giant_hogweed,
        zcol = "n",
        layer.name = "Number of giant hogweed occurrences",
        legend = TRUE,
        color = "white",
        alpha.regions = 0.8,
        alpha = 0.5,
        popup = popupTable(n_giant_hogweed,
                           zcol = c("mun_name_nl", "mun_name_fr", "n")))
m

## 1.3 ####
m <- mapview(n_giant_hogweed,
        zcol = "n",
        layer.name = "Number of giant hogweed occurrences",
        legend = TRUE,
        color = "white",
        alpha.regions = 0.8,
        alpha = 0.5,
        map.types = "OpenStreetMap",
        popup = popupTable(n_giant_hogweed,
                           zcol = c("mun_name_nl", "mun_name_fr", "n")))
m

## 1.4 ####
giant_hogweed <- readr::read_tsv(
  "data/20250826/20250826_giant_hogweed_fl_bxl.tsv",
  na = ""
  ) %>%
  sf::st_as_sf(
    coords = c("decimalLongitude", "decimalLatitude"),
    crs = 4326
  )

m + mapview(giant_hogweed,
            layer.name = "Giant hogweed occurrences",
            color = "grey80",
            col.regions = "grey80",
            cex = 5)


## 1.5 ####
leafem::addMouseCoordinates(m + mapview(giant_hogweed,
                                        layer.name = "Giant hogweed occurrences",
                                        color = "grey80",
                                        col.regions = "grey80",
                                        cex = 5))


mapshot(leafem::addMouseCoordinates(m + mapview(giant_hogweed,
                                                layer.name = "Giant hogweed occurrences",
                                                color = "grey80",
                                                col.regions = "grey80",
                                                cex = 5)),
        url = "map.html")

### Hanna's solution

## 1.1 ####
mapview(n_giant_hogweed, zcol = "n", legend = TRUE, color = "white", alpha = 0.8, lwd = 0.5, layer.name = "Number of giant hogweed occurrences", popup = leafpop::popupTable(n_giant_hogweed, c("mun_name_nl", "n", "mun_name_fr")))

## 1.2 ####
mapview(n_giant_hogweed, zcol = "n", legend = TRUE, color = "white", alpha = 0.8, lwd = 0.5, layer.name = "Number of giant hogweed occurrences", popup = leafpop::popupTable(n_giant_hogweed, c("mun_name_nl", "n", "mun_name_fr")))

## 1.3 ####
mapview(n_giant_hogweed, zcol = "n", legend = TRUE, color = "white", alpha = 0.8, lwd = 0.5, layer.name = "Number of giant hogweed occurrences", popup = leafpop::popupTable(n_giant_hogweed, c("mun_name_nl", "n", "mun_name_fr")), map.types = "OpenStreetMap")


## 1.4 ####
giant_hogweed <- readr::read_tsv(
  "data/20250826/20250826_giant_hogweed_fl_bxl.tsv",
  na = ""
  ) %>%
  sf::st_as_sf(
    coords = c("decimalLongitude", "decimalLatitude"),
    crs = 4326
  )

mapview(n_giant_hogweed, zcol = "n", legend = TRUE, color = "white", alpha = 0.8, lwd = 0.5, layer.name = "Number of giant hogweed occurrences", popup = leafpop::popupTable(n_giant_hogweed, c("mun_name_nl", "n", "mun_name_fr")), map.types = "OpenStreetMap")+
mapview(giant_hogweed, color = "grey80", cex = 5, layer.name = "Giant hogweed occurrences")


## 1.5 ####
m <- mapview(n_giant_hogweed, zcol = "n", legend = TRUE, color = "white", alpha = 0.8, lwd = 0.5, layer.name = "Number of giant hogweed occurrences", popup = leafpop::popupTable(n_giant_hogweed, c("mun_name_nl", "n", "mun_name_fr")), map.types = "OpenStreetMap")+
mapview(giant_hogweed, color = "grey80", cex = 5, layer.name = "Giant hogweed occurrences")

map <- leafem::addMouseCoordinates(m)

## 1.6 ####
# save as HTML
mapshot(m, url = "output/20250826_giant_hogweed_map.html")

### Falk's mapview pipe issue odyssee

Thinking too complicated: there is a `year` column.

- I should be able to aggregate over `year` / sum up `n` because otherwise I do not know how the number in the map is produced.

# glimpse(n_giant_hogweed)

# n_giant_hogweed %>%
#   count(mun_code) %>%
#   arrange(desc(n))

aggregated_hogweed <- n_giant_hogweed %>%
  summarise(
    n = sum(n),
    across(geom, st_union),
    .by = mun_code
  ) %>%
  sf::st_as_sf() %>%
  sf::st_cast("MULTIPOLYGON")

# does NOT work
aggregated_hogweed %>% 
  mapview(
    color = "white", lwd = 1,
    zcol = "n"
  )

I initially got the error:

[...]
Caused by error in `dyn.load()`:
! unable to load shared object '/data/R/library/s2/libs/s2.so':
  libabsl_flags_internal.so.2501.0.0: cannot open shared object file: No such file or directory

found [this](https://github.com/r-spatial/sf/issues/1977) sf issue

- would rather not use `sf_use_s2(FALSE)` because I do not know which other features it disables
- `install.packages("s2")` and reload did the job.

now I can aggregate; seems there is only one row per municipality

- but: cannot plot map any more.
- Geometry type changed. Casting the geometry yields visually identical objects:

> n_giant_hogweed
Simple feature collection with 319 features and 28 fields
Geometry type: MULTIPOLYGON
Dimension:     XY
Bounding box:  xmin: 2.541 ymin: 50.69 xmax: 5.911 ymax: 51.51
Geodetic CRS:  WGS 84

> aggregated_hogweed
Simple feature collection with 319 features and 2 fields
Geometry type: MULTIPOLYGON
Dimension:     XY
Bounding box:  xmin: 2.541 ymin: 50.69 xmax: 5.911 ymax: 51.51
Geodetic CRS:  WGS 84

identical(
  n_giant_hogweed %>% select(mun_code, n),
  aggregated_hogweed
  ) # NOT identical

# waldo::compare(
#   n_giant_hogweed %>% select(mun_code, n),
#   aggregated_hogweed
#   )
# -> nothing of relevance

Solution:
the objects were fine; turned out it was the PIPE!

# does NOT work
aggregated_hogweed %>% 
  mapview(
    color = "white", lwd = 1,
    zcol = "n"
  )
  
  
# DOES work
mapview(
  aggregated_hogweed
  color = "white", lwd = 1,
  zcol = "n"
)

# # (by the way, this was already wrong:)
# n_giant_hogweed %>%
#   mapview()

Thank you, Emma!

Post coding club addition: the problem actually is a bug in mapview while dealing with the pipe: see https://github.com/r-spatial/mapview/issues/348

Still to be fixed by package authors.

## Challenge 2

### Solution Stijn

n_giant_hogweed_bxl <- n_giant_hogweed %>%
dplyr::filter(reg_name_nl == "['Brussels Hoofdstedelijk Gewest']")

g2 <- ggplot(data = n_giant_hogweed_bxl) +
geom_sf(aes(fill=n),colour="red") +
scale_fill_viridis_c(option = "C") +
geom_sf_text(
aes(label = mun_name_nl),
size = 2,
fontface = "bold",
color = "gray50",
check_overlap = TRUE
)
g2

### Pieter's solution

# Get n_giant_hogweed for Brussels only
n_giant_hogweed_bxl <- n_giant_hogweed %>%
  dplyr::filter(reg_name_nl == "['Brussels Hoofdstedelijk Gewest']")

## 2.1 ####

n_giant_hogweed_bxl %>%
  ggplot() +
  geom_sf()
## 2.2 ####
n_giant_hogweed_bxl %>%
  ggplot(aes(fill = n,
             color = "red4")) +
  geom_sf()

## 2.3 ####
n_giant_hogweed_bxl %>%
  ggplot() +
  geom_sf(aes(fill = n,
              color = "red4")) +
  geom_sf_label(aes(label = stringr::str_extract(mun_name_nl, "[a-zA-Z\\-]+")),
                size = 2,
                colour = "grey50",
                fontface = "bold",
                fill = "white"
  )

## 2.4 ####
n_giant_hogweed_bxl %>%
  ggplot(aes(fill = n)) +
  scale_fill_viridis_c() +
  geom_sf()

## 2.5 ####

n_giant_hogweed_bxl %>%
  ggplot() +
  geom_sf(aes(fill = n,
              color = "red4")) +
  geom_label_repel(
    aes(label = stringr::str_extract(mun_name_nl, "[a-zA-Z\\-]+"),
        geometry = geom,
        size = 2,
        fontface = "bold"),
    stat = "sf_coordinates"
    )

### Emma's solution

## 2.1 ####
ggplot(data = n_giant_hogweed_bxl) +
  geom_sf()

## 2.2 ####
ggplot(data = n_giant_hogweed_bxl) +
  geom_sf(color = "red", aes(fill = n))

## 2.3 ####
ggplot(data = n_giant_hogweed_bxl) +
  geom_sf(color = "red", aes(fill = n)) +
  geom_sf_text(aes(label = mun_name_nl),
               color = "gray50",
               size = 2,
               fontface = "bold")

## 2.4 ####
ggplot(data = n_giant_hogweed_bxl) +
  geom_sf(color = "red", aes(fill = n)) +
  geom_sf_text(aes(label = mun_name_nl),
               color = "gray50",
               size = 2,
               fontface = "bold") +
  scale_colour_viridis_c()

## 2.5 ####
ggplot(data = n_giant_hogweed_bxl) +
  geom_sf(color = "red", aes(fill = n)) +
  geom_text_repel(aes(label = mun_name_nl, geometry = geom),
                  stat = "sf_coordinates",
                  color = "gray50",
                  size = 2,
                  fontface = "bold") +
  scale_colour_viridis_c()

### Note on `geom_sf()` and CRS *(Falk)*

hogweed_31370 <- n_giant_hogweed_bxl %>%
  sf::st_transform(31370)
print(sf::st_crs(hogweed_31370))
hogweed_31370 %>% 
  ggplot() + geom_sf()
# shows axis labels in degrees

## Challenge 3

### Solution Stijn

g3 <- ggplot(data = n_giant_hogweed_bxl) +
  annotation_map_tile(zoomin = -1, cachedir = "./data/20250826/") +
  geom_sf(aes(fill=n),colour="red") +
  scale_fill_viridis_c(option = "C") +
  geom_sf_text(
    aes(label = mun_name_nl),
    size = 2,
    fontface = "bold",
    color = "gray50",
    check_overlap = TRUE
  ) +
  annotation_scale(location = "bl", width_hint = 0.5) +
  annotation_north_arrow(location = "tl", which_north = "true",
                         style = north_arrow_fancy_orienteering)
g3

### Pieter's solution

## 3.1 -> 3.3 ####
my_tempdir <- withr::local_tempdir(pattern = "coding_club", tmpdir = tempdir())
n_giant_hogweed_bxl %>%
  ggplot() +
  annotation_map_tile(
    type = "osm",
    zoomin = 0,
    cachedir = my_tempdir
  ) +
  annotation_north_arrow(location = "tl", which_north = "true") +
  geom_sf(aes(fill = n))

## 3.4 ####
n_giant_hogweed_bxl %>%
  ggplot() +
  annotation_map_tile(
    type = "cartolight",
    zoomin = 0,
    cachedir = my_tempdir
  ) +
  annotation_north_arrow(location = "tl", which_north = "true") +
  geom_sf(aes(fill = n))

### Emma's solution

## 3.1 ####
ggplot(data = n_giant_hogweed_bxl) +
  annotation_map_tile(zoomin = 0) +
  geom_sf(color = "red", aes(fill = n)) +
  geom_text_repel(aes(label = mun_name_nl, geometry = geom),
                  stat = "sf_coordinates",
                  color = "gray50",
                  size = 2,
                  fontface = "bold") +
  scale_colour_viridis_c()


## 3.2 ####
ggplot(data = n_giant_hogweed_bxl) +
  annotation_map_tile(zoomin = 0, cachedir = "./data/20250826") +
  geom_sf(color = "red", aes(fill = n)) +
  geom_text_repel(aes(label = mun_name_nl, geometry = geom),
                  stat = "sf_coordinates",
                  color = "gray50",
                  size = 2,
                  fontface = "bold") +
  scale_colour_viridis_c()

## 3.3 ####
ggplot(data = n_giant_hogweed_bxl) +
  annotation_map_tile(zoomin = 0, cachedir = "./data/20250826") +
  geom_sf(color = "red", aes(fill = n)) +
  geom_text_repel(aes(label = mun_name_nl, geometry = geom),
                  stat = "sf_coordinates",
                  color = "gray50",
                  size = 2,
                  fontface = "bold") +
  scale_colour_viridis_c() +
  annotation_scale(location = "bl") +
  annotation_north_arrow(location = "tl",
                         style = north_arrow_fancy_orienteering,
                         which_north = "true")


## 3.4 ####
ggplot(data = n_giant_hogweed_bxl) +
  annotation_map_tile(type = "cartolight",
                      zoomin = 0,
                      cachedir = "./data/20250826") +
  geom_sf(color = "red", aes(fill = n)) +
  geom_text_repel(aes(label = mun_name_nl, geometry = geom),
                  stat = "sf_coordinates",
                  color = "gray50",
                  size = 2,
                  fontface = "bold") +
  scale_colour_viridis_c() +
  annotation_scale(location = "bl") +
  annotation_north_arrow(location = "tl",
                         style = north_arrow_fancy_orienteering,
                         which_north = "true")