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 Bijleveld et al. 2022. 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 the latest project news.

The package tools4watlas builds on the package atlastools (Gupte et al. 2021. A Guide to Pre-processing High-throughput Animal Tracking Data.). In tools4watlas, we have improved the data processing functions of atlastools with a more efficient approach using data.table by tag ID. This change enhances memory efficiency and significantly speeds up processing for large datasets. Additionally, tools4watlas includes functions to integrate tidal and raster data (e.g. bathymetry), and functions and tutorials on how to visualize movement data.

Documentation

The tools4watlas package is thoroughly documented on the official package website. The package vignettes outline the basic workflow for working with WATLAS data, while extended workflows guide through more specialized analyses. Additionally, we provide visualization tutorials that demonstrate various methods for plotting and animating the movement data. The package development section offers insights into package maintenance and how to contribute to the tools4watlas package. To completely run some articles (marked with an asterisk) access to the local NIOZ file server is required.

Basic workflow (Vignettes):

• Load and check data

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

• Smooth and thin data

Extended workflow:

• Add tidal and bathymetry data*

• Add residency patches - work in progress.

• Add SIBES data - work in progress.

Visualization tutorials:

• Create a basemap - (Bathymetry basemap option*)

• Plot data - an important step between all stages to check the data.

• Plot data in loop - quick way to make plots by tag ID.

• Fast plotting with ggplot2

• Plot data interactively

• Animate data

Package development:

• Package maintenance - describes how to work on tools4watlas.

• Basemap data* - describes how the basemap data were extracted and can guide the user in creating customized base maps.

• tools4watlas logo - describes how the tools4watlas logo is made.

*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)
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),
    linewidth = 0.5, alpha = 0.5, show.legend = FALSE
  ) +
  geom_point(
    data = data, aes(x, y, color = species),
    size = 1, alpha = 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:

• Residency patch analysis
• Connect WATLAS with SIBES data

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.

Acknowledgements

Many people and organisations are involved in developing and maintaining WATLAS. We particularly thank Sivan Toledo and Ran Nathan for the initial development of ATLAS, and Frank van Maarseveen and Bas Denissen for the initial development of the Wadden Sea ATLAS (WATLAS). Additionally, we thank Remko de Haan, Aris van der Vis, Yetzo de Hoo, and NMF colleagues for further developments, assemblage and support. Anne Dekinga is crucial for the field deployment and logistical solutions. We thank our colleagues from COS for help catching birds, especially Job ten Horn, Anne Dekinga, and Luc de Monte. Also, we thank all partners and stakeholders for hosting equipment and for access to their sites. Lastly, we thank the crews of the RV Wim Wolff and Wim-Jan Boon of the RV Adriaen Coenen for their help in the field, Marten Tacoma for visualizing the tracking data in real time on https://www.nioz.nl/watlas, and the many other NIOZ staff and volunteers that facilitated this work.