The purpose of this analysis is identify to what extent the relationship between salmon productivity (recruits-per-spawner) and the PDO and NPGO indices has changed over time, and to what extent these changes are shared among regions.
| Name | Description |
|---|---|
| /Figs | Figures produced by specific analysis scripts. |
| /Data | Input salmon and environmental data files. |
| /doc | Pertinent documents and manuscript drafts. |
| /Output | Model output files, mostly as .rds or .csv. Note: Some of the STAN .rds output files are large. |
| /R | Compilation of .R and .stan files containing individual models, helper functions, and plotting functions. |
| Name | Description |
|---|---|
| Fit-DLM-Ricker.R | Fits individual dynamic linear Ricker model to stock-recruitment data from each stock, with time-varying PDO and NPGO effects. |
| Fit-DLM-Ricker-plus.R | Same as Fit-DLM-Ricker.R but with time-varying PDO and NPGO effects treated as an AR(1) process. |
| Fit-MARSS-Ricker.R | Fits stock-specific DLM Ricker with MARSS package in R. |
| Fit-DLM-Region.R | Fits combined DLM Ricker, where PDO and NPGO effects are common within regions (EBS, GOA, CA, WC). |
| Fit-DLM-Region-ARMA.R | Same as Fit-DLM-Region.R, but with time-varying PDO and NPGO effects treated as ARMA(1) process. |
| Get-NPGO-PDO.R | Downloads up-to-date PDO and NPGO indices. |