Whales movements – r.iresmi.net

Author

Michaël

Published

2024-11-05

Modified

2024-11-04

A photo of a Blue Whale — Blue Whale – CC-BY-NC-ND by Tom Benson

Day 5 of 30DayMapChallenge: « A Journey » (previously).

Thirteen Blue whales (Balaenoptera musculus) were satellite tagged in 2015 in Australia (Mӧller et al. 2020). We’ll follow their summer in the Great Southern Australian Coastal Upwelling System (GSACUS).

Data is available from the Australian Antarctic Data Centre (Andrews-Goff et al. 2020), directly as a R RDS file.

library(dplyr)
library(readr)
library(sf)
library(leaflet)

unzip("AAS_4101_pygmy_blue_whale_SSSM.zip", 
      files = "bw_3h_ssm.RDS")
bm <- read_rds("bw_3h_ssm.RDS")
# str(bm)

journeys <- bm$summary |> 
  st_as_sf(coords = c("lon", "lat"), crs = "EPSG:4326") |> 
  group_by(id) |> 
  arrange(date) |> 
  summarise(do_union = FALSE) %>%
  st_cast("LINESTRING") |> 
  group_by(indiv = as.factor(parse_number(as.character(id)))) |> 
  summarise()

After joining GPS points as lines and lines from the same whale as multilines, we can use {leaflet} for an interactive map.

pal <- colorFactor("viridis", sort(unique(journeys$indiv)))

journeys |> 
  leaflet() |> 
  addTiles() |> 
  addPolylines(color = ~ pal(indiv),
               popup = ~ indiv) |> 
  addLegend(pal = pal,
            values = sort(unique(journeys$indiv)))

Figure 1: Movements blue whales satellite tagged in an Australian upwelling system

References

Andrews-Goff, Virginia, Mike Double, Luciana Möller, Catherine Attard, Kerstin Bilgmann, Ian Jonsen, and Dave Paton. 2020. “Switching State Space Model for Pygmy Blue Whale Satellite Tag Derived Locations.” Australian Antarctic Data Centre. https://doi.org/10.26179/5E671120E52B4.

Mӧller, Luciana M., Catherine R. M. Attard, Kerstin Bilgmann, Virginia Andrews-Goff, Ian Jonsen, David Paton, and Michael C. Double. 2020. “Movements and Behaviour of Blue Whales Satellite Tagged in an Australian Upwelling System.” Scientific Reports 10 (1): 21165. https://doi.org/10.1038/s41598-020-78143-2.

---
title: "Whales movements"
description: "Day 5 of 30DayMapChallenge. Journey"
author: "Michaël"
date: "2024-11-05T00:00:00"
date-modified: last-modified
categories:
  - R
  - spatial
  - datavisualization
  - 30DayMapChallenge
  - ecology
draft: false
freeze: true
editor_options:
  chunk_output_type: console
chunk_output_type: console
execute:
  eval: true
---

```{r}
#| label: preview
#| echo: false
#| fig-cap: "Blue Whale -- CC-BY-NC-ND by Tom Benson"
#| fig-alt: "A photo of a Blue Whale"
#| fig-link: https://www.flickr.com/photos/40928097@N07/32850229427/
#| class-output: "preview-image"
#| out-width: "100%"

knitr::include_graphics("images/32850229427_7a5c9d7af5_c.jpg")
```

Day 5 of [30DayMapChallenge](https://30daymapchallenge.com/): « A Journey » ([previously](/#category=30DayMapChallenge)).

Thirteen [Blue whales](https://en.wikipedia.org/wiki/Blue_whale) (*Balaenoptera musculus*) were satellite tagged in 2015 in Australia [@MollerMovementsbehaviourblue2020].
We'll follow their summer in the Great Southern Australian Coastal Upwelling System ([GSACUS](https://en.wikipedia.org/wiki/Great_South_Australian_Coastal_Upwelling_System)).

Data is available from the Australian Antarctic Data Centre [@Andrews-GoffSwitchingstatespace2020], directly as a R RDS file.

```{r}
#| label: data

library(dplyr)
library(readr)
library(sf)
library(leaflet)

unzip("AAS_4101_pygmy_blue_whale_SSSM.zip", 
      files = "bw_3h_ssm.RDS")
bm <- read_rds("bw_3h_ssm.RDS")
# str(bm)

journeys <- bm$summary |> 
  st_as_sf(coords = c("lon", "lat"), crs = "EPSG:4326") |> 
  group_by(id) |> 
  arrange(date) |> 
  summarise(do_union = FALSE) %>%
  st_cast("LINESTRING") |> 
  group_by(indiv = as.factor(parse_number(as.character(id)))) |> 
  summarise()
```

After joining GPS points as lines and lines from the same whale as multilines, we can use {leaflet} for an interactive map.

```{r}
#| label: fig-map
#| fig-cap: "Movements blue whales satellite tagged in an Australian upwelling system"
#| fig-alt: "Map of blue whales satellite tagged in an Australian upwelling system"
#| out-width: "100%"

pal <- colorFactor("viridis", sort(unique(journeys$indiv)))

journeys |> 
  leaflet() |> 
  addTiles() |> 
  addPolylines(color = ~ pal(indiv),
               popup = ~ indiv) |> 
  addLegend(pal = pal,
            values = sort(unique(journeys$indiv)))
```

```{r}
#| label: clean
#| echo: false

rm("bw_3h_ssm.RDS")
```