Draft additional documentation for spmR
Jim Ianelli, Cole Monnahan
2026-08-11
more_documentation.RmdProjections for operational assessments
The R package spmR provides a tool to project assessment results in a consistent way over all “Tier 3” groundfish stocks. This is to conform to the Fishery Management Plan (FMP) for the Gulf of Alaska (GOA) and the Bering Sea and Aleutian Islands (BSAI). Specifically, as outlined in Amendment 56 of the FMP, age-structured assessment results are linked to the projection based on specified input files. These inputs allow estimation of fishing mortality rates based on spawning biomass per recruits (e.g., F40% and F35%). These rates (and variants) are applied to the estimated abundance at age from the most recent assessment model. The trend in spawning biomass is then contrasted with proxy reference points that align with the FMP. In summary, the model estimates proxy Fmsy values, applied to estimated population numbers at age, and compared against reference points to adjust the rates according to the control rule of the FMP.
Catch from the model follows three main scenarios given a selected model (approved by the SSC):
The maximum permissible ABC
The status determination relative to overfishing
The status determination to determine if the stock is overfished or approaching an overfished condition.
Additional “scenarios” are optionally included and were part of the historical requirement for an annual Environmental Assessment for ABC/OFL specifications by the Alaska Regional Office. They provide contrast and included scenarios based on the “author recommended” ABC, one with no fishing, one based on the recent 5-year average F, another with an alternative F-spr basis (varied between some stocks).
Biological assumptions used in the projections should follow the assessment model and decisions about expected future selectivity, maturity, weight-at-age etc should be considered best estimates and may reflect means over different recent periods. It should be noted that their specification should be clearly documented within the assessment.
Tier 3 stocks are based on expected trends and the extent to which these proxy estimates are determined with uncertainty is not explicitly part of the FMP ABC/OFL specification process. Nonetheless, the software runs simulations over the mean and variability of recruitment that is specified in the model input files. For FMP ABC/OFL specifications, the means are presented but longer-term trajectories accounting only for recruitment variability are presented figures as deemed useful.
Abbreviations
| A BC | Acceptable Biological Catch |
|
Initial Regulatory Flexibility Analysis |
|---|---|---|---|
| AI | Aleutian Islands | LLP | License Limitation Program |
| AP | Advisory Panel | M SFCMA |
Magnuson-Stevens Fishery Conservation and Management Act |
| AD FG | Alaska Dept. of Fish and Game |
|
Marine Mammal Protection Act |
| BS | Bering Sea | MRA | Maximum Retainable Amount |
| BS AI | Bering Sea and Aleutian Islands | MSY | Maximum Sustainable Yield |
| C DQ | Community Development Quota | t | Metric tons |
| EA/R IR |
Environmental Assessment/Regulatory Impact Review |
|
National Marine Fisheries Service |
| E BS | Eastern Bering Sea |
|
National Oceanic & Atmospheric Adm. |
| E EZ | Exclusive Economic Zone | NPFMC |
North Pacific Fishery Management Council |
| E FH | Essential Fish Habitat | OY | Optimum Yield |
| E FP | Exempted Fishing Permit |
|
Preview of Economic and Ecosystem Considerations |
| E SA | Endangered Species Act | PSC | Prohibited Species Catch |
| F EP | Fishery Ecosystem Plan |
|
Stock Assessment and Fishery Evaluation |
| F MP | Fishery Management Plan | SSC | Scientific and Statistical Committee |
| G HL | Guideline Harvest Level | SSL | Steller Sea Lion |
| G OA | Gulf of Alaska | TAC | Total Allowable Catch |
| HA PC | Habitat Areas of Particular Concern | USFWS | United States Fish & Wildlife Service |
|
I FQ |
Individual Fishing Quota | ||
|
IP HC |
International Pacific Halibut Commission |
Recommended usage
See readme on spmR package on github for installation options and vignettes (Articles here).
History of SPM
<links to the historical docs>
https://afsc-assessments.github.io/spmR/articles/background.html
How spmr grew out of “proj” and what the differences are
Definitions
Let
TY= this year - the year in which SPM is run
AY= the last year an assessment was done, AY<=TY
PY1= TY+1 = projection year 1 in the exec table
PY2= TY+2 = projection year 2 in the exec table
PYn=TY+n = projection year n in alternative scenarios
C_TY=estimate/assumed catch for the entirety of TY using e.g., an assumption about catch=ABC or some calculation to extrapolate for the remainder of TY (Oct - Dec).
N_AY= numbers at age on Jan-1 of AY
N_PY1= numbers at age on Jan-1 of PY1
N_PY2= numbers at age on Jan-1 of PY2
Summary of SPR calculations for Tier 3 stocks
SPM reads in the (average) biological input values: M, maturity, spawning and fisheries WAA, and fisheries selectivity. Uses a spawner per recruit (SPR) approach to calculate SPR at F=0, i.e., how much female spawning biomass (tons, kg, etc.) a single recruit produces in its lifetime.
Uses vector of recruitments to calculate mean recruits (Rbar), which is multiplied by spawning biomass per recruit at F=0 to get unfished SSB (SSB0 or SSB100%). From that define SSB35=.35*SB100 and SB40=0.40*SB100. These are equilibrium values given assumptions about Rbar, biology, and selectivity.
Uses a numerical solver to find F35%=FMSY=FOFL and F40%=FmaxABC in equilibrium by tuning F until SSB is SSB35 and SSB40, respectively. These go in the executive table.
Proj next takes N_AY and inputted catches to get N_PY1. It then applies F_ABC, as modified by the harvest control rule, to get ABC in PY1. An assumption is made about catch taken in PY1, and so N_PY2 is calculated and F_ABC applied again to get ABC in PY2. A similar approach is used for OFL. The assumption depends on the scenarios (see below), but scenario X should be used which dictates that the ABC is taken in PY1.
Summary of the alternative scenario simulations
There are 7 projection “scenarios” built into spmR, along with some others that have been customized to address specific questions.
How to specify catches in TY
Years between AY and TY will have finalized total catches available. The total catches in TY are not complete and must be assumed. Several approaches are used:
The full ABC is taken in TY. This will be reasonable for fully exploited stocks. It may be wise as a general rule to be conservative. But for lightly exploited stocks it may not.
Extrapolate catches in TY from the end of the year using catches through October and historical catch patterns in the fishery. E.g., if 80% of total catches are typically taken by October then they can be scaled up by that number.
Known issues
When using time-varying quantities in a model then the average values used by proj to construct N_PY1 will not match what is used in the assessment and thus not much. For instance if spawning WAA is different, the N_PY will match between the AM and SPM in TY, but spawning biomass in TY will not match. If fisheries selectivity is different, then N_PY1 will differ as different fish are killed off between the beginning and end of TY. When there are no time-varying inputs then SPM will be able to recreate the AM through TY identically and there is no issue.
Cases where SPM needs to be run more than once.
Weird issues arising when there’s a big gap between AY and TY.