rkbauer / r_package_rchivaltag

A package to generate, access and analyze standard data products from archival tagging data.

An R-Package for Analyzing and Interactive Visualization of Archival Tagging Data

Author • Description • Key Features • Tutorial • Credits • Related • License

Author

Dr. Robert Bauer | Fishery Biologist & Data Scientist

Description

RchivalTag provides a toolbar of functions to analyze and visualize different data products from Archival Tags (Supported Models include amongst others: MiniPAT, sPAT, mk10, mk9 from Wildlife Computers as well as LOTEK PSAT Models. Models from other Manufactorers might be supported as well.

Key Features

• readhistos(), read_PDT(), read_TS(), get_geopos(): read in functions for different archival tag data products

• ts2histos(), bin_TempTS(), get_thermalstat(): Data conversion tools

• plot_Depth(), plot_DepthTS(), plot_DepthTempTS(), dy_DepthTS(): Interactive (Depth) time series data plots (related package: dygraphs)

• hist_tat() and hist_tad(): Time-at-Depth (TaD) and Time-at-Temperature (TaT) fequency plots

• image_TempDepthProfiles(): Depth Temperature profiles (low resolution time series data) plots, inclduding PDT (PAT-style Depth Temperature profiles)

• ggplot_geopos(), ggplotly_geopos() and leaflet_geopos(): (Interactive) plotting functions for geolocation estimates (related packages: oceanmap, ggplot2, plotly, leaflet)

• abacus_plot() and plot_data_coverage(): Data coverage abacus plots for different data products

These functions were written to facilitate data handling and visualizations, so that within 2-3 lines of code the user can obtain figures that are ready for publication.

Tutorial

You can find here an extensive online tutorial that covers the different functionalities of the package.

Credits

This package was developed during my PhD thesis at the IFREMER and a Postdoc at IRD, which are both part of the MARBEC lab. ggplot-based functions as well as interactive options have been added since.

Related libraries

• oceanmap - A R-Package to map oceanographic data.
• plotly - An open source library for interactive figures.
• dygraphs - An R interface to the interactive dygraphs JavaScript charting library.
• leaflet - A JavaScript-based map widget that can be rendered on HTML pages generated from R Markdown, Shiny, or other applications.

You may also like...

• IRATER - A R Interface for the Instantaneous RATEs (IRATE) Model to assess band recovery (conventional tagging) data (i.e. age-dependent or independent fishing and natural mortality rates).
• oceanmap - A R-Package to map oceanographic data.
• marine biologging - An online campaign for electronic tagging studies

References

• Bauer, R., F. Forget and JM. Fromentin (2015) Optimizing PAT data transmission: assessing the accuracy of temperature summary data to estimate environmental conditions. Fisheries Oceanography, 24(6): 533-539, doi: 10.1111/fog.12127

• Bauer, R., JM. Fromentin, H. Demarcq and S. Bonhommeau (2017) Habitat use, vertical and horizontal behaviour of Atlantic bluefin tuna (Thunnus thynnus) in the Northwestern Mediterranean Sea in relation to oceanographic conditions. Deep-Sea Research Part II: Topical Studies in Oceanography, 141: 248-261, doi: 10.1016/j.dsr2.2017.04.006

• Bauer, R., F. Forget, JM. Fromentin and M. Capello (2020) Surfacing and vertical behaviour of Atlantic bluefin tuna (Thunnus thynnus) in the Mediterranean Sea: implications for aerial surveys. ICES Journal of Marine Science, 77(5): 1979-1991, doi: 10.1093/icesjms/fsaa083

Visit my work on

GitHub  ·  Google Scholar  ·  ResearchGate  · 

License

GPL (>= 3)