Mathematical Biology Program at the Northwest Fisheries Science Center
Viability Report Packages
These are R code and data packages used for the PNW Salmonid 5-year Viability Report (prepared by NWFSC) which supports with 5-year Status Reviews (prepared by WRO).
VRData is a data package for the spawner and fraction wild data used in the PWN Salmonid Viability Reports.
NWCTrends runs the standardized trends metrics (figures, tables) used in the 2015 and 2020 5-year Viability Reports for listed PNW salmonids.
VRReport is in progress. This package will use VRData and NWCTrends to create a more reproducible Viability Report document using R Markdown.
Spawner-Recruit estimation
These are R packages used for fitting spawner-recruit functions to data from salmonid populations. The output is posterior distributions of the estimated spawner-recruit functions. These posteriors are used in a variety of analyses (such as risk impact analyses or forecasts) in order to incorporate the uncertainty in the underlying population dynamics into the analysis.
Recovery Exploitation Rate Modeling
These are R packages used for simulations and analyses supporting the analysis of harvest and bycatch effect on listed salmonids.
VRAP is the original code used for RER analyses. Includes covariates. VRAP can be run from a graphical interface from the NWFSC Shiny Server [VRAP Shiny](https://dataexplorer.northwestscience.fisheries.noaa.gov/nwc/VRAP/).
VRAPS (VRAP second generation) is a C++ version of VRAP that is much faster and allows batch jobs. Covariates are not used in VRAPS. Instead autocorrelation in survival is modeled using autoregressive models for survival.
DMVRAPS uses DM output (posteriors on SR function parameters) as input to VRAPS. Output is RERs with uncertainty estimates.
Contacts
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U.S. Department of Commerce ∣ National Oceanographic and Atmospheric Administration ∣ NOAA Fisheries