Workshop on using the samEst R package - non-stationary spawner-recruit models for Pacific salmon
Catarina Wor (catarina.wor@dfo-mpo.gc.ca) Dan Greenberg (dan.greenberg@dfo-mpo.gc.ca)
samEst depends on the R >= 4.0.5, make sure your R version is compatible. R > 4.0 on Windows also requires Rtools 4.X. Find out which Rtools version you need from here
samEst depends on the R packages TMB and the latest version of stan. So we need to ensure that these packages are installed and working. To install and test the dependencies before installing samEst run code/install_samEst.R
If you run into problems, please submit an issue in this repository.
Navigate to the exercises folder to find some Quarto workbooks to go through. There should be 4 exercises, the last of which will have you fitting models to real data.
You can run the workshop on your own data, if you have it available, you will just need to format it correctly (see examples in exercises4.qmd). We are providing ~88 stocks in BC to experiment with see 'data' that you can select for exercise 4.
If you have any questions about the content of this workshop feel free to add it to this public Google doc: https://docs.google.com/document/d/16u9KEdEqm47sS43yqLZKvmUXecy-3cstJGjgLIxhUUM/edit?usp=sharing