## Surplus production model

### Dynamics equations

The surplus production model uses the Fletcher (1978) formulation. The biomass $B_t$ in year $t$ is $B_t = B_{t-1} + P_{t-1} - C_{t-1},$ where $C_t$ is the observed catch and $P_t$ is the surplus production given by: $P_t = \gamma \times MSY \times \left(\dfrac{B_t}{K}-\left[\dfrac{B_t}{K}\right]^n\right),$ where $K$ is the carrying capacity, $MSY$ is the maximum sustainable yield, and $n$ is the parameter that controls shape of the production curve, and $\gamma$ is $\gamma = \dfrac{1}{n-1}n^{n/(n-1)}.$

The fishing mortality $F_t$ is conditioned on the observed catch $C_t$. If fishing occurs as a pulse fishery, then $\hat{F}_t = \dfrac{C_t}{\hat{B}_t},$ where $F_t$ is effectively an exploitation rate. Alternatively, smaller time steps are used in the model to approximate continuous production and fishing. Given the biomass in the start of the year and assuming a constant fishing mortality over the time steps within a year, the fishing mortality that produces the observed annual catch is solved iteratively. By default, four sub-annual time steps are used to solve for $F_t$.

### Estimated and derived parameters

The model is configured with $F_{MSY}$ and $MSY$ as leading parameters to be estimated.

The biomass $B_{MSY}$ at $MSY$ is $B_{MSY} = \dfrac{MSY}{F_{MSY}},$ the carrying capacity $K$ is $K = n^{1/(n-1)} \times B_{MSY} ,$ and the intrinsic rate of population increase $r$ is $r = n \times F_{MSY}.$

#### Schaefer model

The production parameter $n$ is typically fixed, and the Schaefer model with a symmetric productive curve ($B_{MSY}/K = 0.5$) is produced when $n = 2$ (default).

#### Fox model (SP_Fox)

The Fox model is the limiting case of the Fletcher parameterization as $n \rightarrow 1$, where

$K = e \times B_{MSY}$ $r = F_{MSY}$ $P_t = -e \times MSY \times \dfrac{B_t}{K} \times \log\left(\dfrac{B_t}{K}\right)$ where $e$ is Euler’s number.

### State-space version (SP_SS)

In the state-state version, annual biomass deviates are estimated as random effects. Similar to Meyer and Millar (1999), the biomass $B_t$ in year $t$ is $B_t = (B_{t-1} + P_{t-1} - C_{t-1})\exp(\delta_t - 0.5 \tau^2),$ where $\delta_t \sim N(0, \tau^2)$ are biomass deviations in lognormal space and $\tau$ is the standard deviation of the biomass deviations.

### Likelihood

By conditioning the model on observed catch, the model is fitted to the indices of abundance $I_{s,t}$. The likelihood of the observed indices, using assuming a lognormal distribution, is $L^I = \sum_s \lambda_s \sum_t \left(-\log(\sigma_{s,t}) - 0.5\left[\dfrac{\log(I_{s,t}) - \log(\hat{q}_s \hat{B}_t)}{\sigma_{s,t}}\right]^2\right)$ where $lamba_s$ is the weighting coefficient of index $s$, $q_s$ is the cathabilitiy coefficient, and the circumflex denotes an estimate.

Log-biomass deviations $\hat{\delta}_t$ are typically estimated as penalized parameters towards the likelihood, with the penalty: $L^{\delta} = \sum_t \left(-\log(\tau) - 0.5\left[\dfrac{\delta_t}{\tau}\right]^2\right).$

#### Prior for r

To generate the prior for the intrinsic rate of increase, natural mortality $M$ and steepness $h$ are sampled from a distribution. Natural mortality is modelled to be age-invariant and is sampled from a lognormal distribution.

With either a Beverton-Holt or Ricker stock-recruit relationship, steepness is sampled from a transformed beta or transformed lognormal distribution, respectively.

For each pair of sampled M and h values, the corresponding value of $r$ is obtained by solving a modified Euler-Lotka equation: $\alpha \sum_a l_a f_a \exp(-r \times a) = 1.$

Equation 15 is modified to include the $\alpha$ term from the stock-recruit relationship (Stanley et al. 2009). In this way, the recruits-per-spawner at low stock sizes, i.e., as spawning biomass approaches zero, is considered for calculating $r$.

The numbers-per-recruit at age $a$ is $l_a = \begin{cases} 1 & a = 1\\ l_{a-1} \exp(-M_{a-1}) & a = 2, \ldots, A-1\\ \dfrac{l_{a-1} \exp(-M_{a-1})}{1 - \exp(-M_a)} & a = A \\ \end{cases}.$

Fecundity at age $f_a$ is $m_a = w_a\left[1 + \exp\left(-\log(19) \dfrac{a - \tilde{a}_{50}}{\tilde{a}_{95} - \tilde{a}_{50}}\right)\right]^{-1},$ where $\tilde{a}_{50}$ and $\tilde{a}_{95}$ are the ages of 50% and 95% maturity, respectively.

Weight-at-age $w_a$ is $w_a = W_{\infty}(1 - \exp[K\{a-a_0\}])^b.$

The recruits per spawner at the origin of the stock-recruit relationship $\alpha$ is $\alpha = \dfrac{4h}{(1-h)\phi_0},$ or $\alpha = \dfrac{(5h)^{1.25}}{\phi_0},$ for a Beverton-Holt and Ricker stock-recruit relationship, respectively. Unfished recruits-per-spawner $\phi_0$ is $\phi_0 = \sum_a l_a f_a.$

A normal distribution is assumed for the prior (a penalty to the likelihood) with the mean ($\mu_r$) and standard deviation ($\sigma_r$) calculated from the values of $r$ calculated using the above procedure:

$L^r = - 0.5\left(\dfrac{\hat{r} - \mu_r}{\sigma_r}\right)^2,$