Simulated underwater glider sampling for Antarctic krill
This repository contains the data and code used to generate the model results discussed in 'Acoustic sampling of Antarctic krill with simulated underwater buoyancy gliders: does the sawtooth dive pattern work?' (Kinzey et al., 2022). The results in the article were produced by simulating 500 replicate samples - the examples in the repository use only 6 replicates to reduce run time and output file sizes.
Simulations of one, three, and five underwater buoyancy gliders sampling Antarctic krill in two strata around the the Antarctic Peninsula are shown in the pdfs in this 'Main' directory. These were rendered from the r-scripts and data in the 'input_files' directory using the corresponding '.rmd' files in the 'rmarkdown' directory.
To reproduce these results, download the files in the 'input_files' and 'rmarkdown' directories onto a single working directory on your local computer. Maintain the files in 'input_files' in a subdirectory labeled 'input_files' and save the 'rmarkdown' files in the local working directory without a subdirectory. Start the simulation by running the 'Glider_simulation...rmd' scripts. I use the R package 'rmarkdown' with 'pandoc' installed to apply the command "rmarkdown::render('filename.rmd','pdf_document')" for this. The two .rmd files 'Glider_simulation...rmd' create a 'tables' directory on the local computer to store the simulation outputs. The 6-replicate simulation in this example produce about 1.57 GB of output files (not included in this repository). The files in 'tables' can then be called from the 'Figures...rmd' scripts to produce the figures. In this example there is a 'Glider_simulation' rmarkdown script for each of the two survey strata, 'Glider_simulation_SA.rmd' and 'Glider_simulation_WA.rmd'. These may be run simultaneously on a multicore computer to reduce run time. The simulation can also be run sequentially by stratum but it will take longer.
The rmarkdown file 'Glider_simulation_WA.rmd' takes the most time, about 3 hours. Both the 'Glider_simulation_WA.rmd' and 'Glider_simulation_SA.rmd' must finish before running the 'Figures1-10' rmd files because Fig. 9 plots results from both strata. More replicates will produce better statistical results but require more time and produce more stored output.
The data sampled in the simulations are acoustic densities of krill from AMLR research ship surveys in two sampling strata around the Antarctic Peninsula: the Southern Area ('SA', also called Bransfield Strait) and the Western Area ('WA', also called Cape Shirreff). Acoustic densities at depth (Nautical Area Scattering Coefficients, 'NASC') attributed to krill from 10 years of ship surveys (2001-2009, 2011) from these two strata are binned in 100 m long by 5 m deep cells down to 250 m (50 cells deep) in the input data file 'NASC_leg1.RData'.
Kinzey D, Cossio AM, Reiss CS and Watters GM (2022) Acoustic sampling of Antarctic krill with simulated underwater buoyancy gliders: Does the sawtooth dive pattern work? Front. Mar. Sci. 9:1064181. doi: 10.3389/fmars.2022.1064181
This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.