Sustainable Growth: Exploring Integrative Multi-Trophic Aquaculture on the West Coast

Contents

This repository (knitted HTML linked here: marine_aquaculture) contains an analysis of potential locations within the Economic Exclusion Zones (EEZ) along the West Coast of the US that are potentially suitable locations for integrative multi-trophic aquaculture (IMTA).

Techniques

This repository highlights a variety of skills and techniques including:

1. Data Management

   • Wrangling and tidying data using (Wickham et al. 2019), (Müller 2020), and (Firke 2023)

   • Visualizations with (Wickham 2016) and (Tennekes 2018)

   • Clear documentation and folder structures for reproducibility, collaboration, and modularity

   • Integration of conditional statements and custom checks to increase reproducibility, error handling, and modularity

   • Development of generalizable functions to allow for reproducibility and flexibility in analyses

2. Geospatial Analysis

   • Handling spatial data with (Hijmans 2024) and (Pebesma 2018)

   • Generating informative interactive maps with (Tennekes 2018)

   • Map algebra with spatial objects within (Hijmans 2024) and (Pebesma 2018)

3. Sustainable Fisheries Science

   • Adapting concepts from (Gentry et al. 2017) and (Troell et al. 2010) to analyze potential locations within the West Coast EEZs that are suitable for integrative multi-trophic aquaculture (IMTA) with oysters and a variety of potential finfish species

   • Integration of flexible species-specific tolerances throughout the spatial analyses

Data

• The first dataset is Sea Surface Temperature (SST) from the NOAA Coral Reef Watch Daily 5km Satellite Sea Surface Temperature (SST) (v3.1) to characterize the average annual sea surface temperature inside the region of interest for the years 2008 to 2012 (NOAA Coral Reef Watch (2024)).

• The second dataset is bathymetry data from the General Bathymetric Chart of the Oceans (GEBCO) which we used to generate a depth profile for the areas with the Economic Exclusion Zones (EEZ) (GEBCO Compilation Group (2024)).

• The third dataset is a shapefile from the Flanders Marine Institute that was used to define the area of U.S. waters within the EEZ (Flanders Marine Institute (VLIZ) (2024)).

• The fourth dataset was created in two steps:

  1. First, potential finfish species were identified through an evaluation of the harvested species managed by the West Coast NOAA Fisheries to compile a list of potentially compatible species (NOAA Fisheries: West Coast (2024)).
  2. Then, life history parameters (thermal range of tolerance and vertical distribution) were obtained from FishBase (FishBase Consortium (2024)).

Repository Structure

      .
      ├── README.md
      ├── bibs
      │   ├── packages.bib
      │   └── references.bib
      ├── code
      │   ├── custom.css
      │   ├── marine_aquaculture.html
      │   └── marine_aquaculture.qmd
      ├── data
      │   ├── average_annual_sst_2008.tif
      │   ├── average_annual_sst_2009.tif
      │   ├── average_annual_sst_2010.tif
      │   ├── average_annual_sst_2011.tif
      │   ├── average_annual_sst_2012.tif
      │   ├── depth.tif
      │   ├── potential_finfish_species.csv
      │   ├── wc_regions_clean.dbf
      │   ├── wc_regions_clean.prj
      │   ├── wc_regions_clean.shp
      │   └── wc_regions_clean.shx
      ├── figures
      │   ├── heatmap
      │   │   └── species_vs_region_heatmap.png
      │   ├── maps
      │   │   ├── NULL_map.png
      │   │   ├── anoplopoma_fimbria_map.html
      │   │   ├── anoplopoma_fimbria_map.png
      │   │   ├── ...
      │   └── tables
      │       ├── potential_species_kable.html
      │       ├── spatial_properties_kable.html
      │       ├── spatial_properties_kable_sst_bath.html
      │       ├── spatial_properties_kable_sst_bath_transform.html
      │       └── top_regions_kable.html
      ├── marine-aquaculture.Rproj
      └── structure.txt

References

Firke, Sam. 2023. Janitor: Simple Tools for Examining and Cleaning Dirty Data. https://CRAN.R-project.org/package=janitor.

FishBase Consortium. 2024. “FishBase: A Global Information System on Fishes.” https://www.fishbase.org.au/v4.

Flanders Marine Institute (VLIZ). 2024. “Maritime Boundaries Geodatabase: Exclusive Economic Zones (EEZ).” Flanders Marine Institute (VLIZ); https://www.marineregions.org/eez.php.

GEBCO Compilation Group. 2024. “General Bathymetric Chart of the Oceans (GEBCO).” General Bathymetric Chart of the Oceans (GEBCO); https://www.gebco.net/data_and_products/gridded_bathymetry_data/#area.

Gentry, Rebecca R., Halley E. Froehlich, Daniel Grimm, Peter Kareiva, Megan Parke, Michael Rust, Steven D. Gaines, and Benjamin S. Halpern. 2017. “Mapping the Global Potential for Marine Aquaculture.” Nature Ecology & Evolution 1 (9): 1317–24. https://doi.org/10.1038/s41559-017-0257-9.

Hijmans, Robert J. 2024. Terra: Spatial Data Analysis. https://CRAN.R-project.org/package=terra.

Müller, Kirill. 2020. Here: A Simpler Way to Find Your Files. https://CRAN.R-project.org/package=here.

NOAA Coral Reef Watch. 2024. “Coral Reef Watch Daily 5km Satellite Sea Surface Temperature (SST) (V3.1).” National Oceanic; Atmospheric Administration (NOAA); https://coralreefwatch.noaa.gov/product/5km/index_5km_sst.php.

NOAA Fisheries: West Coast. 2024. “Sustainable Seafood.” https://www.fisheries.noaa.gov/species-directory.

Pebesma, Edzer. 2018. “Simple Features for R: Standardized Support for Spatial Vector Data.” The R Journal 10 (1): 439–46. https://doi.org/10.32614/RJ-2018-009.

Tennekes, Martijn. 2018. “tmap: Thematic Maps in R.” Journal of Statistical Software 84 (6): 1–39. https://doi.org/10.18637/jss.v084.i06.

Troell, Max, Andrew Joyce, Thierry Chopin, Amir Neori, Alejandro H. Buschmann, and Jian-Gang Fang. 2010. “Ecological Engineering in Aquaculture — Potential for Integrated Multi-Trophic Aquaculture (IMTA) in Marine Offshore Systems.” Aquaculture 297 (1-4): 1–9. https://doi.org/10.1016/j.aquaculture.2009.09.010.

Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.

Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the tidyverse.” Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.