rebuilder: Conducting rebuilding projections for species managed by the Pacific Fishery Managment Council
U.S. West Coast species (or stocks) where the spawning biomass is estimated to be below the Minimum Stock Size Threshold or are currently managed under a rebuilding plan need to provide quantitative population projections to determine the probability of rebuilding by specific years under alternative harvest strategies. These rebuilding projections are conducted using the "rebuilder" (aka "The Puntalizer") program, created by Dr. Andre Punt, for species management by the Pacific Fishery Management Council (PFMC).
The rebuilder is designed to work with the rebuild.sso file created by Stock Synthesis when "#_Do_West_Coast_gfish_rebuilder_output" is set to 1 in the forecst.ss file. The rebuilder program produces a number of CSV files with the RES.CSV file containing the needed projection results. Additionally, an Echo.dat file is produced by the program to assist with troubleshooting if the executable fails to run with the rebuild.dat file provided.
This package includes several resources for conducting and analyzing projections conducted by the rebuilder. A user manual that aligns with the latest version of the executable is available in the manual folder and the corresponding executable is available in the inst folder. User instructions are available via a google doc, but access is limited to NOAA personel so a downloaded copy (updated Apr. 10, 2024) that is available to all is provided in the manual folder. Rebuilder originally came with a SUMMARY.xls file with macros for reading in results, which is provided in the inst folder for posterity, but more recent R helper functions are in the R folder for processing rebuilder output and to create visualization.
The current version of the rebuilder executable is 3.12j modified in December 2021. Older versions of the rebuilder executable are available upon request (chantel.wetzel@noaa.gov).
The Scientific and Statistical Committee of the PFMC provides guidance on how rebuilding projections should be conducted and what needs to be included in the rebulding plan. The 2023-2024 rebuilding Terms of Reference can be found online here.
There are a range of exisiting rebuilding plans documents that can be examined to understand the needed analysis and presentation of results for West Coast species:
- Updated rebuilding analysis for existing rebuilding plan: a) yelloweye rockfish 2017 b) petrale sole 2011
- New rebuilding analysis: a) quillback rockfish 2021 b) Pacific sardine 2020 b) petrale sole 2009
Wetzel and Punt (2016) conducted simulation work to evaluate the effectiveness of alternative rebuilding strategies across various West Coast life history types. The Methods sections contains a description of the general internal calculations conducted within the rebuilder software.
Please report any issues with this package by posting a new github issue at https://github.com/pfmc-assessments/rebuilder/issues.