assignment_2_Feedback_Otter_mortality.qmd

---
title: "Otter mortality in Vestland"
format: 
  html:
    self-contained: true
    code-tools: 
      source: true
---

<!-- This assignment builds upon one of the tasks in the map-making datalab. -->

<!-- Landa and Guidos [(2020)](https://doi.org/10.1111/csp2.208) explore causes of otter (_Lutra lutra_) mortality in Hordaland Fylke, where otter recently re-established after being extirpated by hunting. This paper (based on a Master's thesis) includes data up to 2018. -->

<!-- File ExcelExport_7972978_Page_1a.xlsx contains data on otter sightings in Vestland (the file was downloaded from https://artsobservasjoner.no/ and edited slightly to remove an invalid character). -->

<!-- Import the data and make a publication quality figure showing otter deaths from 2019 to the present. -->

<!-- Relevant columns are "East Coord",	"North Coord", "Start Date", and "activity".  -->
<!-- The coordinates UTM coordinates (UTM zone 33N, EPSG code 25833). -->

<!-- Relevant activities are "Roadkill", "Drowned in fishing net", and "Found dead". -->


```{r}
#| label: setup
#| message: false
library(tidyverse)
library(ggspatial)
library(conflicted) # always a good idea to use conflicted
library(here) # help find the data file

conflicts_prefer(dplyr::filter)
```

```{r}
#| label: import-data
#| message: false
otter <- readxl::read_excel(here("data/ExcelExport_7972978_Page_1a.xlsx"), skip = 2, sheet = "Export")|> # find the data rectangle with skip
  janitor::clean_names() |> # sanitise column names
  mutate(year = year(start_date)) # using lubridate

dead_otter <- otter |> # filter required rows
  filter(  # filter new deaths
    year > 2018,
    activity %in% c("Roadkill", "Drowned in fishing net", "Found dead"))

```

# First try

```{r}
#| label: make-first-map
norway <- rnaturalearth::ne_countries(scale = 10, returnclass = "sf", country = "Norway")
ggplot() +
  geom_sf(data = norway) +
  geom_spatial_point(
    data = dead_otter, 
    mapping = aes(x = east_coord,  y = north_coord, colour = activity), 
    crs = 25833) +
  coord_sf(xlim = c(4.5, 8), ylim = c(59.5, 62.2)) +
  labs(x = "Longitude", y = "Latitude")
```


```{r}
#| eval: false
# alternative approach
# make data into sf object 
# no advantage in this case. Useful if you need to do GIS analyses first

dead_otter_sf <- sf::st_as_sf(dead_otter, 
                              coords = c("east_coord", "north_coord"), 
                              crs = 25833)

ggplot() +
  geom_sf(data = norway) +
  geom_sf(data = dead_otter_sf, mapping = aes(colour = activity)) +
  coord_sf(xlim = c(4.5, 8), ylim = c(59.5, 62.2)) +
  labs(x = "Longitude", y = "Latitude", colour = "Cause of death")
```
issues with first map

- unhelpful theme
- Colours not colourblind friendly
  - change palette
  - use shape
  - make larger?
- too many x-axis labels
- do we really need latitude & longitude?
- Is being dead an "activity"?

```{r}
#| label: make-second-map
theme_set(theme_bw()) # set default theme
norway <- rnaturalearth::ne_countries(scale = 10, returnclass = "sf", country = "Norway")
ggplot() +
  geom_sf(data = norway) +
  geom_spatial_point(
    data = dead_otter, 
    mapping = aes(x = east_coord,  y = north_coord, colour = activity, shape = activity), 
    crs = 25833, 
    size = 3) +
  coord_sf(xlim = c(4.5, 8), ylim = c(59.5, 62.2)) +
  labs(colour = "Cause of death", shape = "Cause of death") +
  scale_x_continuous(breaks = 4:10) + # only use integers on x axis
  scale_color_viridis_d() +
  theme(axis.title = element_blank()) # remove axis labels
```
Getting better. Would improve with

- scalebar
- geographic context
- sufficient resolution
- colours washed out - use symbols with outline

```{r}
#| label: make-better-map
#| message: false

norway <- sf::st_read("data/fylker2021.json") |> # higher resolution map
  mutate(vestland = Fylkesnavn == "Vestland")

vestland <- ggplot() +
  geom_sf(data = norway, mapping = aes(fill = vestland), show.legend = FALSE) +
 scale_fill_manual(values = c("FALSE" = "grey90", "TRUE" = "grey80")) +
  ggnewscale::new_scale_fill() + # allow points to have fill
  geom_spatial_point(
    data = dead_otter, 
    mapping = aes(x = east_coord,  y = north_coord, fill = activity, shape = activity), # using fill because using shapes > 20 
    size = 3,
    crs = 25833) +
  scale_fill_viridis_d() +
  scale_shape_manual(values = c(21, 23, 24)) +
  scale_x_continuous(breaks = 4:10) + # only use integers on x axis
  coord_sf(xlim = c(4.5, 10), ylim = c(59.5, 62.2), crs = 4326) +
  labs(fill = "Cause of death", shape = "Cause of death") +
  annotation_scale(location = "br") +
  theme(
    axis.title = element_blank(),
    legend.position = c(0.99, 0.2), # move legend
    legend.justification = c(1, 0)
    )

inset_map <- ggplot() +
  geom_sf(data = norway, mapping = aes(fill = vestland), show.legend = FALSE) +
  scale_fill_manual(values = c("FALSE" = "grey90", "TRUE" = "grey60")) +
  theme(axis.text = element_blank(), 
        axis.ticks = element_blank(), 
         plot.margin = margin())
  
vestland +
  patchwork::inset_element(inset_map, 0.6, 0.51, 0.99, 0.99)
```

```{r}
#| label: leaflet
# radical alternative
library(leaflet)
library(fontawesome)

# covert dead otter to sf and transform to lat-long WGS84
dead_otter_sf <- sf::st_as_sf(dead_otter, coords = c("east_coord", "north_coord"), crs = 25833) |> 
  sf::st_transform(4326)  # Transform to lat long

# make icons
icon_list <- awesomeIconList(
  Roadkill = makeAwesomeIcon(text = fa("car"), markerColor = "darkred"),
  "Found dead" = makeAwesomeIcon(text = fa("otter"), markerColor = "blue"),
  "Drowned in fishing net" = makeAwesomeIcon(text = fa("fish"), markerColor = "pink")
)

# leaflet map with icons
leaflet(dead_otter_sf) |>  # initialise map
#  setView(lat = (59.5 + 62.2) / 2, lng = (4.5 + 8) / 2, zoom = 7) |> 
  fitBounds(lng1 = 4.5, lng2 = 8, lat1 = 59.5, lat2 = 62.2) |> 
  addTiles() |> # add background map
  addAwesomeMarkers(icon = ~ icon_list[activity], popup = ~ as.Date(start_date)) |> 
  addScaleBar(position = "topleft", options = scaleBarOptions(imperial = FALSE)) |> 
  addLegend(position = "bottomright",
            colors = c("darkred", "pink", "lightblue"),
            values = ~activity,
            labels = c("Roadkill", "Drowned in fishing net", "Found dead"),
            title = "Cause of death",
            opacity = 1
  ) |> 
  addMiniMap(
    position = 'topright', 
    width = 200, height = 200,
    toggleDisplay = FALSE)

```
```{r}
#| label: ggoceanmaps-version
library(ggOceanMaps)
basemap(limits = c(4.5, 8, 59.5, 62.2), rotate = TRUE) + #Need rotate or slopes
  geom_spatial_point(data = dead_otter, mapping = aes(x = east_coord, y = north_coord, colour = activity), crs = 25833)
```