This repository contains the data and code for our paper:
Simonis, A.E., Forney, K.A.; Hom-Weaver, C.; Margolina, T.; Joseph, J.; DeVogelaere, A., Ryan, J.; Rankin, S. (in review). Harbor porpoises (Phocoena phocoena) stop echolocating or leave the area following seal bomb explosions in Monterey Bay, California.
Following publication, please cite this compendium as:
Simonis, A.E., Forney, K.A.; Hom-Weaver, C.; Margolina, T.; Joseph, J.; DeVogelaere, A., Ryan, J.; Rankin, S. (2023). Compendium of R code and data for "Harbor porpoises (Phocoena phocoena) stop echolocating or leave the area following seal bomb explosions in Monterey Bay, California". Accessed 17 Feb 2023.
The repository contains:
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📁 R: Quarto source document for manuscript. Includes code to reproduce the figures and tables generated by the analysis. It also has a rendered version, Monterey-Seal-Bombs-and-Porpoises.pdf, suitable for reading (the code is replaced by figures and tables in this file).
- Explosion_Metrics.qmd: Quarto document with example code to calculate common noise metrics relevant to marine mammal noise exposure, including audiogram weighted spectra for different marine mammal hearing groups. Expected summary output is provided.
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📁 data: Data used in the analysis, including 20 example explosion sound clips
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📁 plots: Plots and other illustrations
This research compendium has been developed using the statistical programming language R. To work with the compendium, you will need installed on your computer the R software itself and optionally RStudio Desktop.
To use this code, start by opening the Explosions.Rproj file. Note - we use a project-oriented workflow and the Here package to set the default directory to the folder where the project is located. This makes it easier for any user to open and run the code.