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---
title: Draft additional documentation for spmR
author: "Jim Ianelli, Cole Monnahan"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Draft additional documentation for spmR}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
format:
viewport: width=device-width, initial-scale=1.0, user-scalable=yes
---

# Projections 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., *F~40%~* and *F~35%~*)*.* 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 | Acceptable Biological | * | Initial Regulatory |
| BC** | Catch | *IRFA** | Flexibility Analysis |
+======+========================+=========+=========================+
| ** | Aleutian Islands | **LLP** | License Limitation |
| AI** | | | Program |
+------+------------------------+---------+-------------------------+
| ** | Advisory Panel | **M | Magnuson-Stevens |
| AP** | | SFCMA** | Fishery |
| | | | |
| | | | Conservation and |
| | | | Management Act |
+------+------------------------+---------+-------------------------+
| **AD | Alaska Dept. of Fish | * | Marine Mammal |
| FG** | and Game | *MMPA** | Protection Act |
+------+------------------------+---------+-------------------------+
| ** | Bering Sea | **MRA** | Maximum Retainable |
| BS** | | | Amount |
+------+------------------------+---------+-------------------------+
| **BS | Bering Sea and | **MSY** | Maximum Sustainable |
| AI** | Aleutian Islands | | Yield |
+------+------------------------+---------+-------------------------+
| **C | Community Development | **t** | Metric tons |
| DQ** | Quota | | |
+------+------------------------+---------+-------------------------+
| ** | Environmental | * | National Marine |
| EA/R | Assessment/Regulatory | *NMFS** | Fisheries Service |
| IR** | | | |
| | Impact Review | | |
+------+------------------------+---------+-------------------------+
| **E | Eastern Bering Sea | * | National Oceanic & |
| BS** | | *NOAA** | Atmospheric Adm. |
+------+------------------------+---------+-------------------------+
| **E | Exclusive Economic | ** | North Pacific Fishery |
| EZ** | Zone | NPFMC** | |
| | | | Management Council |
+------+------------------------+---------+-------------------------+
| **E | Essential Fish Habitat | **OY** | Optimum Yield |
| FH** | | | |
+------+------------------------+---------+-------------------------+
| **E | Exempted Fishing | * | Preview of Economic and |
| FP** | Permit | *PEEC** | Ecosystem |
| | | | Considerations |
+------+------------------------+---------+-------------------------+
| **E | Endangered Species Act | **PSC** | Prohibited Species |
| SA** | | | Catch |
+------+------------------------+---------+-------------------------+
| **F | Fishery Ecosystem Plan | * | Stock Assessment and |
| EP** | | *SAFE** | Fishery Evaluation |
+------+------------------------+---------+-------------------------+
| **F | Fishery Management | **SSC** | Scientific and |
| MP** | Plan | | Statistical Committee |
+------+------------------------+---------+-------------------------+
| **G | Guideline Harvest | **SSL** | Steller Sea Lion |
| HL** | Level | | |
+------+------------------------+---------+-------------------------+
| **G | Gulf of Alaska | **TAC** | Total Allowable Catch |
| OA** | | | |
+------+------------------------+---------+-------------------------+
| **HA | Habitat Areas of | ** | United States Fish & |
| PC** | Particular Concern | USFWS** | Wildlife Service |
+------+------------------------+---------+-------------------------+
| # | Individual Fishing | | |
| **I | Quota | | |
| FQ** | | | |
+------+------------------------+---------+-------------------------+
| # | International Pacific | | |
| **IP | Halibut | | |
| HC** | | | |
| | Commission | | |
+------+------------------------+---------+-------------------------+

# Recommended usage

See readme on
[[spmR]{.underline}](https://github.com/afsc-assessments/spmR/tree/main)
package on github for installation options and vignettes (Articles
[[here]{.underline}](https://afsc-assessments.github.io/spmR/)).

# History of SPM

\<links to the historical docs\>

[[https://afsc-assessments.github.io/spmR/articles/01-Background.html]{.underline}](https://afsc-assessments.github.io/spmR/articles/01-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

1. 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.

2. 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.

3. 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.

4. 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 determine overfishing and overfished status.

To do

# 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:

1. 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.

2. 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.

# Multispecies and other advanced features

Jim this one is all you

- SRR conditioning

- Multispecies technical interactions

- Linear programming for total yield cap

-

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