An R-Package for Analyzing and Interactive Visualization of Archival Tagging Data
Package Tutorial
Author • Motivation • Details • Compatability • References • License
Author
Dr. Robert Bauer | Fishery Biologist & Data Scientist
Motivation
The idea behind the RchivalTag-package and this tutorial is to facilitate the analysis and visualization of archival and pop-up archival tagging data within R. The package (and tutorial) focuses mainly on the following data products:
- Time-at-Depth (TaD) and Time-at-Temperature (TaT) Histogram data
- Time series data (e.g. depth and temperature)
- PAT-style Depth Temperature profiles (PDT) data
- Tracks (Geolocation Estimates and Likelihood Areas from light levels, depth and temperature)
The package inlcudes specific functions to read in, clean, transform and visualize each of these data products with 2-3 lines of code. The package and tutorial do not require deep coding skills and are therefore suitable for beginners as well as more advanced users.
For more details see below as well as the package-documentation.
## install or load package
# install.packages("RchivalTag")
library("RchivalTag")
## Package overview:
?RchivalTag
help(package="RchivalTag") ## list of functionsDetails
TaD-/TaT-histogram data
- The package allows to read and generate standard summary data products (TaD-/TaT-profiles, see above) from recovered or transmitted time series data sets as well as to merge and visualize such summary data products from different tag setups/tagging programs. For more information on these data products, please see: (Wildlife Computers 2019; Bauer et al. 2017)
Depth and temperature time series data
- (interactive) data visualization, optionally highlighting temperature records and daytime differences (dawn, day, dusk, night).
Daily Depth-temperature time series data
- data visualization and examination of the thermal stratification of the water column (i.e. thermocline depth, gradient and stratification index), based on previously interpolated depth-temperature time series data or PAT Style depth temperature profiles (PDT). The paper by (Bauer, Forget, and Fromentin 2015) is highly recommended in this context.
Visualizing Geolocation Estimates and Likelihood Areas
- The newest version of RchivalTag includes a set of functions to illustrate geolocation estimates and likelihood areas from archival tags in (interactive) figures (e.g. see ggplot_geopos(), ggplotly_geopos() and leaflet_geopos()).
Compatability
So far, the package is mainly adapted for (pop-up) archival tagging data from Wildlife Computers and LOTEK PSAT tags, but can also be applied to data from other tag manufacturers (e.g. see ts2histos() in order to calculate TaD & TaT-frequencies from time series data). Function examples are based on the transmitted data sets of a miniPAT-tag from the BLUEMED-project, funded by the French National Research Agency (ANR).
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References
Bauer, Robert Klaus; Fabien; Forget, and Jean-Marc Fromentin. 2015. “Optimizing PAT data transmission - assessing the accuracy of temperature summary data to estimate environmental conditions.” Fisheries Oceanography 24 (6): 533–39. https://doi.org/10.1111/fog.12127.
Bauer, Robert Klaus, Fabien Forget, Jean Marc Fromentin, and Manuela 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): 1979–91. https://doi.org/10.1093/icesjms/fsaa083.
Bauer, Robert Klaus, Jean Marc Fromentin, Hervé Demarcq, and Sylvain 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 (April 2017): 248–61. https://doi.org/10.1016/j.dsr2.2017.04.006.
Wildlife Computers. 2019. “Spreadsheet File Descriptions v.201903.”
License
GPL (>= 3)