Day 1
Presentation files
Presentation slides for the GitHub for Collaborative Workflows presentation.
Presentation slides for the Codespaces presentation.
Presentation slides for the Reproducible Environments presentation.
Presentation slides for the presentation on modifying and running stock synthesis models.
Presentation slides for the Part 2 presentation on modifying and running stock synthesis models.
Resources
Example code for modifying a Stock Synthesis input model file and running the modified model through R using the r4ss package can be found in the r-code/ directory on the course GitHub repo.
Briefly the r-code/01-modify-stock-synthesis.r file takes you through the steps of:
- reading in the Stock Synthesis input file (e.g.,
control.ss) using the r4ss package - modifying this file, in this case changing the steepness value \(h\) and thus modifying the shape of the stock-recruitment relationship (SRR)
- running the newly modified model
There is also code at the end of the file that wraps all three of those steps in a for loop in case multiple alternate model configurations want to be explored.