zc_series

This repository contains the data and code used to produce analysis for a manuscript:

Cioffi WR, Quick NJ, Swaim ZT, Foley HJ, Waples DM, Webster DL, Baird RW, Southall BL, Nowacek DP, Read AJ. 2023. Trade-offs in telemetry tag programming for deep-diving cetaceans: data longevity, resolution, and continuity. Animal Biotelemetry 11, 23; doi: 10.1186/s40317-023-00334-1

If you have questions about anything in this repository or are interested in using the included datasets please contact wrc14 [at] duke [dot] edu. You can also post to issues with questions or bugs.

details

directories: - 00_data contains input data as well as several intermediate data products - 01_helper_functions contains helper functions used in the analysis and loaded by the included scripts. - 02_figures contains code to produce all figures in the manuscript. - 03_tables contains csv versions of the tables included in the manuscript and 1 supplementary table.

input data files: - 00_data/tags/baseline_tags.rds dive data from a baseline tag configuration (SPLASH10) with some concurrent time-series and dive summary records. - 00_data/tags/series_tags_w_meta.rdata dive data from a set of experimental deployments of SPLASH10 tags which only recorded time-series dive records. - 00_data/tags/Tag17.csv depth data from a SPLASH10 tag deployed in the same group as the dtag Tag18. - 00_data/tags/Tag18_depth.mat depth data from a DTAG deployment in the same group as the sattag Tag17. - 00_data/gonio includes several files detailing the reception of messages from SPLASH10 tags on various platforms using the Argos Goniometer.

intermediate data products can be found in 00_data/working see R01_convert_compare_divesummary_series.r

More information on SPLASH10 Wildlife Computers satellite-linked tag can be found at the Wildlife Computers downloads page. The SPLASH10 manual and file descriptions are good places to start.

main analysis code files (figure specific code can be found in 02_figures): - R01_convert_compare_divesummary_series.r generates the bulk of the data used for analysis and to generate figures in the manuscript. A large portion of this script is interactive to allow manual inspection and qa/qc of the conversion from time-series to dive summary records (identifying discrete dives from time-series data). Intermediate outputs found in 00_data/working show the exact data generated and used in the present manuscript, but the code is fully operational and can be re-run by the user to generate similar output. - R02_comparison_summary_stats.r calculates some basic summaries from the data.

software versions

This code was written and initially run on R 3.6.2, but has been tested on R 4.0.5 as well.

github libraries: - sattagutils version 0.2.1

cran libraries: colorspace_1.4-1 ggplot2_3.2.1 reshape2_1.4.3 R.matlab_3.6.2

citation

Please cite this repository as:

Cioffi WR, Quick NJ, Swaim ZT, Foley HJ, Waples DM, Webster DL, Baird RW, Southall BL, Nowacek DP, Read AJ. 2022 zc_series: Dataset and code for Trade-offs in telemetry tag programming for deep-diving cetaceans: data longevity, resolution, and continuity. https://github.com/williamcioffi/zc_series. doi: 10.5281/zenodo.6589596

Please cite the manuscript as:

Cioffi WR, Quick NJ, Swaim ZT, Foley HJ, Waples DM, Webster DL, Baird RW, Southall BL, Nowacek DP, Read AJ. 2023. Trade-offs in telemetry tag programming for deep-diving cetaceans: data longevity, resolution, and continuity. Animal Biotelemetry 11, 23; doi: 10.1186/s40317-023-00334-1

contact information

If you have questions about anything in this repository or are interested in using the included datasets please contact wrc14 [at] duke [dot] edu.