btupper / ohw23_proj_marinesdms

Tutorial for marine SDMs

ohw23_proj_marinesdms: Marine species distribution model (SDM) tutorial

This tutorial was developed during OceanHackWeek by members of the Marine Species Distribution Model group. It shows a simple workflow to develop a marine SDM focusing on the Arabian Sea and the Bay of Bengal.

Requirements

Some experience programming in R is needed to make the most of this tutorial. To run this tutorial make sure you clone this repository into your local machine by creating a new project that uses version control (git).

The tutorial content was developed in a R version 4.2.2 for Linux. Full session information is included below:

R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)

Matrix products: default
BLAS/LAPACK: /opt/conda/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.2.2 tools_4.2.2   

Additional resources

If you need additional support with R programming, you can check the following resources:

• R for Data Science - 2nd edition by Wickham, Çetinkaya-Rundel and Grolemund.
• Data analysis and visualisation in R for ecologists

For information on how to use git and GitHub with R, Happy Git and GitHub for the useR by Jenny Bryan is a great resource.

Tutorial developers

• Eli Holmes: Research Fisheries Biologist, Northwest Fisheries Science Center, NOAA Fisheries.

• Mackenzie Fiss: Fifth-year PhD student at Northeastern University studying carbon cycling and microbial interactions in salt marshes

• Paulo Freire

• Caitlin O'Brien

• Mary Solokas: John A. Knauss Marine Policy Fellow, National Oceanic and Atmospheric Administration

• Laura Tsang

• Tylar Murray: USF IMaRS Software Engineer - code whisperer, data viz enthusiast, scientific generalist, compulsive overengineerer, & UX PhD

• Catherine Courtier

• Jade Hong

• Collins Ongore

• Denisse Fierro Arcos: PhD candidate at the Institute for Marine and Antarctic Studies (IMAS) and Data Officer at the Integrated Marine Observing System (IMOS)

Add updates, barriers, etc. as issues.

Day 1

Jam Board/team formation

Day 2 / Day 3 check in

• eli: got the zarr file into R!
• caitlin:
• laura: familiarizing with data and getting species occurrence data into R
• paulo: learning about packages in R
• mackenzie: getting data from the zarr file into dataframes to make working with it easier
• mary: occurrence data and differentiating land and sea sitings
• jade: occurrence data and SDM nitty gritty

Day 2