Site icon R-bloggers

Birds in atmosphere

Michael
[This article was first published on r.iresmi.net, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

Northern Gannet – Morus bassanus – CC-BY by caroline legg

Day 18 of 30DayMapChallenge: « Atmosphere » (previously).

Thanks to a post from @ClareEGordon@mastodon.social I found a dataset (Warwick-Evans et al. 2017) that could (vaguely) relates to the theme of atmosphere.

It describes the trajectories of GPS tracked Northern Gannets (Morus bassanus L.) breeding on Alderney in the English Channel.

< section id="setup" class="level2">

Setup

library(tidyverse)
library(sf)
library(glue)
library(janitor)
library(rnaturalearth)
library(ggspatial)
< section id="data" class="level2">

Data

# GPS data
# https://datarepository.movebank.org/entities/datapackage/8e78d67d-24d9-49cd-9f0a-9b2bccaa70fa
mb_file <- "northern_gannets-les_etacs-alderney.csv"

if (!file.exists(mb_file)) {
  download.file("https://datarepository.movebank.org/bitstreams/dd6099d7-74fb-4be4-86e4-0e4b84177d65/download", mb_file)
}

mb <- read_csv(mb_file) |> 
  clean_names()

# countries from Natural Earth
countries <- ne_countries(scale = 10, returnclass = "sf") |> 
  st_make_valid()
< section id="build-polylines-from-points" class="level2">

Build polylines from points

The do_union = FALSE is important to keep the points’ ordering in the line.

mb_traj <- mb |> 
  st_as_sf(coords = c("location_long", "location_lat"), crs = "EPSG:4326") |> 
  group_by(tag_local_identifier) |> 
  summarise(do_union = FALSE) |> 
  st_cast("LINESTRING") |> 
  st_transform("EPSG:3035")
< section id="map" class="level2">

Map

bbox <- st_bbox(mb_traj)
min_year <- year(min(mb$timestamp))
max_year <- year(max(mb$timestamp))

mb_traj |> 
  ggplot() +
  geom_sf(data = countries, color = NA) +
  geom_sf(aes(color = tag_local_identifier), alpha = 0.4) +
  geom_sf(data = countries, fill = NA) +
  annotation_scale(height = unit(1, "mm"), 
                   text_col = "darkgrey", line_col = "grey", 
                   bar_cols = c("white", "grey")) +
  coord_sf(xlim = bbox[c(1, 3)], ylim = bbox[c(2, 4)]) +
  labs(title = "Northern Gannets tracking study",
       subtitle = glue("Alderney, {min_year} - {max_year}"),
       caption = glue("{st_crs(mb_traj)$Name}
                    Data: DOI:10.5441/001/1.30r98tb3
                    Basemap: Natural Earth
                    https://r.iresmi.net/ {Sys.Date()}")) +
  theme(legend.position = "none",
        plot.caption = element_text(size = 6), )

Figure 1: Northern Gannets from Alderney

Next stage would be to make an animation like @ClareEGordon@mastodon.social post with {gganimate}…

< section id="references" class="level2"> < !-- -->
< section class="quarto-appendix-contents">

References

Warwick-Evans, Victoria, Louise M. Soanes, Roland D. Gauvain, Phil W. Atkinson, John P. Y. Arnould, and Jon A. Green. 2017. “Data from: Changes in Behaviour Drive Inter‐annual Variability in the at‐sea Distribution of Northern Gannets.” Movebank Data Repository. https://doi.org/10.5441/001/1.30R98TB3.
To leave a comment for the author, please follow the link and comment on their blog: r.iresmi.net.
R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.
Exit mobile version