tools4watlas

The goal of tools4watlas is to provide tools for getting, processing and plotting WATLAS tracking data. More information on the WATLAS tracking system can be found in this article published in Animal Biotelemetry: WATLAS: high-throughput and real-time tracking of many small birds in the Dutch Wadden Sea.

Visit https://www.nioz.nl/watlas to follow tracked birds in real time and to read project news.

The package tools4watlas builds on the package atlastools. A pipeline with coding examples for cleaning high-throughput tracking data with atlastools is presented in this article in the Journal of Animal Ecology: A Guide to Pre-processing High-throughput Animal Tracking Data.

Documentation

tools4watlas is documented in detail on the package website. The package vignettes describe the basic workflow when working with WATLAS data and follow a logic order of steps. Further articles give additional tutorials and insights into the package development (read if you want to contribute to tools4watlas), some (indicated by an asterisk) require access to the local NIOZ file server.

Basic workflow (Vignettes):

• Step 1: Load and check data

• Step 2: Filter data - based on spatial boundaries, temporal specifications, error estimates and speed.

• Step 3: Smooth and thin data

• Step 4: Add tidal data

• Plot data - important in between all steps to check the data.

Additional tutorials:

• Fast plotting with ggplot2

• Add and plot bathymetry data*

Package development:

• Package maintenance - describes how to work on tools4watlas.

• Basemap data* - describes how the base map data were extracted. Can guide user to make customised base maps.

• tools4watlas logo

*requires access to the local NIOZ file server

Installation

You can install the latest version of tools4watlas from GitHub with:

library(remotes)
install_github("allertbijleveld/tools4watlas")

Example data

library(tools4watlas)

## Loading required package: data.table

library(ggplot2)

# Load example data
data <- data_example

# Create base map
bm <- atl_create_bm(data, buffer = 800)

# Plot points and tracks
bm +
  geom_path(
    data = data, aes(x, y, colour = species),
    alpha = 0.5, show.legend = FALSE
  ) +
  geom_point(
    data = data, aes(x, y, color = species),
    size = 1, show.legend = TRUE
  ) +
  scale_color_manual(
    values = atl_spec_cols(),
    labels = atl_spec_labs("multiline"),
    name = ""
  ) +
  guides(colour = guide_legend(
    nrow = 1, override.aes = list(size = 7, pch = 16, alpha = 1)
  )) +
  theme(
    legend.position = "top",
    legend.justification = "center",
    legend.key = element_blank(),
    legend.background = element_rect(fill = "transparent")
  )

Example tracks with one individual by species for two tide cycles

Work in progress

More examples of workflows aimed at processing, plotting and adding environmental data to WATLAS tracking data are being prepared. If you have a request, please contact Allert Bijleveld.

We are working on the following articles at the moment:

• Animate movement data
• Residency patch analysis

Contribute

If you want to contribute to tools4watlas fork the repository on GitHub and then submit a pull request. Besides clear bug fixes, it is best to discuss potential changes or additions with Allert Bijleveld. Check the article Package maintenance for more details.

Acknowledgments

Many people and organisations are involved in hosting the WATLAS equipment, without whom WATLAS would not be possible. We therefore thank Hoogheemraadschap Hollands Noorderkwartier, Koninklijke Nederlandse Redding Maatschappij, Staatsbosbeheer, Marine Eco Analytics, Koninklijke Luchtmacht, Het Posthuys (Vlieland), Natuurmonumenten, Wetterskip Fryslan, Afsluitdijk Wadden Center, Vermilion, Rijkswaterstaat, Carl Zuhorn, Lenze Hofstee and Lydia de Loos. We thank Natuurmonumenten for access to Griend and using their facilities. Also, we thank Hein de Vries, Klaas-Jan Daalder, Hendrik-Jan Lokhorst, Bram Fey, Wim-Jan Boon from the RV Navicula and RV Stern, as well as the many other NIOZ staff and volunteers that facilitated this work. We would particularly like to thank Anita Koolhaas, Hinke and Cornelis Dekinga for their help with building the receiver stations. We thank Jeras de Jonge, Martin Laan, Sander Asjes, and Aris van der Vis for their technical help, and Benjamin Gnep for persistently replacing broken LNA’s. Thanks to Marten Tacoma for visualizing the tracking data in real time on www.nioz.nl/watlas and Ingrid de Raad for help posting WATLAS-related news. We also thank the Minerva Foundation and the Minerva Center for Movement Ecology for supporting the development and maintenance of all ATLAS systems, and for Yotam Orchan and Yoav Bartan for their most valuable technical assistance.