Author: Joe Thorley
Date: 2022-08-29

# Get Started with ypr

#### Joe Thorley

#### 2022-08-29

## Introduction

> Fish are born, they grow, they reproduce and they die – whether from natural causes or from fishing. That’s it. Modelers just use complicated (or not so complicated) math to iron out the details. Cooper (2006)

Equilibrium based yield per recruit (YPR) methods (Walters and Martell 2004) estimate the capture rate that optimizes the yield under the assumption that there is no stochasticity and all density-dependence is captured by the stock-recruitment relationship. The remaining population processes of growth, reproduction and death are captured through a series of relatively straight-forward deterministic equations.

Table 1. The 32 parameters with their default values and descriptions.
Parameter | Value | Description
--- | --- | ---
tmax | 20.00 | The maximum age (yr).
k | 0.15 | The VB growth coefficient (yr-1).
Linf | 100.00 | The VB mean maximum length (cm).
t0 | 0.00 | The (theoretical) age at zero length (yr).
k2 | 0.15 | The VB growth coefficient after length L2 (yr-1).
Linf2 | 100.00 | The VB mean maximum length after length L2 (cm).
L2 | 1000.00 | The length (or age if negative) at which growth switches from the first to second phase (cm or yr).
Wb | 3.00 | The weight (as a function of length) scaling exponent.
Ls | 50.00 | The length (or age if negative) at which 50 % mature (cm or yr).
Sp | 100.00 | The maturity (as a function of length) power.
es | 1.00 | The annual probability of a mature fish spawning.
Sm | 0.00 | The spawning mortality probability.
fb | 1.00 | The fecundity (as a function of weight) scaling exponent.
tR | 1.00 | The age from which survival is density-independent (yr).
BH | 1.00 | Recruitment follows a Beverton-Holt (1) or Ricker (0) relationship.
Rk | 3.00 | The lifetime spawners per spawner at low density (or the egg to tR survival if between 0 and 1).
n | 0.20 | The annual interval natural mortality rate from age tR.
nL | 0.20 | The annual interval natural mortality rate from length Ln.
Ln | 1000.00 | The length (or age if negative) at which the natural mortality rate switches from n to nL (cm or yr).
Lv | 50.00 | The length (or age if negative) at which 50 % vulnerable to harvest (cm or yr).
Vp | 100.00 | The vulnerability to harvest (as a function of length) power.
Llo | 0.00 | The lower harvest slot length (cm).
Lup | 1000.00 | The upper harvest slot length (cm).
Nc | 0.00 | The slot limits non-compliance probability.
pi | 0.20 | The annual capture probability.
rho | 0.00 | The release probability.
Hm | 0.00 | The hooking mortality probability.
Rmax | 1.00 | The number of recruits at the carrying capacity (ind).
Wa | 0.01 | The (extrapolated) weight of a 1 cm individual (g).
fa | 1.00 | The (theoretical) fecundity of a 1 g female (eggs).
q | 0.10 | The catchability (annual probability of capture) for a unit of effort.
RPR | 1.00 | The relative proportion of recruits that are of the ecotype.

## Growth

### Length

In `ypr` length (in cm) at age (\(t\)) is assumed to follow a Von Bertalanffy growth curve

\[L = L_{\infty} \cdot (1 - \exp(-k \cdot (t-t_0)))\]

    population <- ypr_population()
    ypr_plot_schedule(population, "Age", "Length")

which can be biphasic

    ypr_plot_schedule(ypr_population_update(population, L2 = 75, Linf2 = 200), "Age", "Length")
    #> Warning: `ypr_population_update()` was deprecated in ypr  0.5.3.
    #> Please use `ypr_update()` instead.

### Weight

The weight (\(W\)) at a given length is assumed to follow the classic allometric relationship

\[W = w_\alpha \cdot L^{w_\beta}\]

    population <- ypr_population_update(population, Wa = 0.01, Wb = 3)
    #> Warning: `ypr_population_update()` was deprecated in ypr  0.5.3.
    #> Please use `ypr_update()` instead.
    ypr_plot_schedule(population, "Length", "Weight")

Its worth noting that \(w_\alpha\), which is the extrapolated weight (g) of a 1 cm individual, is a scaling constant that only affects the estimate of the yield (when calculated in terms of the biomass), ie, it does not affect the estimate of the optimal capture rate.

## Reproduction

### Fecundity

The fecundity (\(F\)) is assumed to scale allometrically with the weight according to the equation

\[F = f_\alpha \cdot W^{f_\beta}\]

    population <- ypr_population_update(population, fa = 1, fb = 1)
    #> Warning: `ypr_population_update()` was deprecated in ypr  0.5.3.
    #> Please use `ypr_update()` instead.
    ypr_plot_schedule(population, "Weight", "Fecundity")

\(f_\alpha\), which is the extrapolated eggs produced by a 1 g female, is a scaling constant with no effect on the yield or optimal capture rate.

### Spawning

The probability of spawning at length \(L\) is determined by the equation

\[S = \frac{L^{S_p}}{L_s^{S_p} + L^{S_p}} \cdot es\]

    population <- ypr_population_update(population, Ls = 50, Sp = 10, es = 0.8)
    #> Warning: `ypr_population_update()` was deprecated in ypr  0.5.3.
    #> Please use `ypr_update()` instead.
    ypr_plot_schedule(population, "Length", "Spawning")

## Death

### Natural Mortality

By default the natural annual interval mortality rate (\(n\)) is assumed to be constant

    ypr_plot_schedule(population, "Length", "NaturalMortality")

although like growth it can vary biphasically

    ypr_plot_schedule(ypr_population_update(population, nL = 0.15, Ln = 60), "Length", "NaturalMortality")
    #> Warning: `ypr_population_update()` was deprecated in ypr  0.5.3.
    #> Please use `ypr_update()` instead.

The natural mortality rate can also be affected by spawning mortality

    population <- ypr_population_update(population, Sm = 0.5)
    #> Warning: `ypr_population_update()` was deprecated in ypr  0.5.3.
    #> Please use `ypr_update()` instead.
    ypr_plot_schedule(population, "Length", "NaturalMortality")

### Fishing Mortality

The vulnerability to capture (\(V\)) is assumed to vary by length as follows

\[V = \frac{L^{V_p}}{L_v^{V_p} + L^{V_p}}\]

    population <- ypr_population_update(population, Lv = 50, Vp = 50)
    #> Warning: `ypr_population_update()` was deprecated in ypr  0.5.3.
    #> Please use `ypr_update()` instead.
    ypr_plot_schedule(population, "Length", "Vulnerability")

If \(V_p\) is 100 then vulnerability is effectively knife-edged.

The probabilty of being retained if captured (\(R\)) depends on the release rate (\(\rho\)), the slot limits (\(L_{lo}\) and \(L_{up}\)) and the non-compliance with the limits (\(N_c\))

    population <- ypr_population_update(population, rho = 0.5, Llo = 40, Lup = 70, Nc = 0.1)
    #> Warning: `ypr_population_update()` was deprecated in ypr  0.5.3.
    #> Please use `ypr_update()` instead.
    ypr_plot_schedule(population, "Length", "Retention")

The fishing mortality (\(U\)) depends on \(V\), \(R\) and the probability of capture when fully vulnerable (\(pi\)) as well as the hooking mortality (\(H_m\))

\[U = V \cdot \pi \cdot R + V \cdot \pi \cdot (1 - R) \cdot H_m\]

The calculation assumes that a released fish cannot be recaught in the same year.

    population <- ypr_population_update(population, pi = 0.3, Hm = 0.2)
    #> Warning: `ypr_population_update()` was deprecated in ypr  0.5.3.
    #> Please use `ypr_update()` instead.
    ypr_plot_schedule(population, "Length", "FishingMortality")

## Recruitment

With growth, reproduction and death defined, the final task is to estimate the recruitment (birth) rate.

This requires the lifetime number of spawners per spawner at low density (\(R_k\)) and the recruitment age (\(R_t\); by default 1) to be defined.

If recruitment follows a Beverton-Holt (\(BH = 1\)) curve then

\[R = \frac{\alpha \cdot E}{(\beta \cdot E + 1)}\]

    population <- ypr_population_update(population, Rk = 3)
    #> Warning: `ypr_population_update()` was deprecated in ypr  0.5.3.
    #> Please use `ypr_update()` instead.
    ypr_plot_sr(population, plot_values = FALSE)

where \(E\) is the annual eggs (stock) and \(R\) is the annual recruits at age \(R_t\).

With a Ricker curve (\(BH = 0\)) the relationship is as follows

\[R = \alpha \cdot E \cdot \exp (-\beta \cdot E)\]

    population <- ypr_population_update(population, BH = 0L)
    #> Warning: `ypr_population_update()` was deprecated in ypr  0.5.3.
    #> Please use `ypr_update()` instead.
    ypr_plot_sr(population, plot_values = FALSE)

The number of recruits at the carrying capacity (\(R_\text{max}\)) is a scaling constant that only affects the estimate of the yield.

Before calculating the recruitment it is important to introduce the concept of the (unfished) survivorship (\(lx_a\)) which is the probability of a recruit surviving to age \(a\) in the absence of fish mortality.

    ypr_plot_schedule(population, "Age", "Survivorship")

The unfished survivorship (\(lx_a\)) is defined recursively by

\[lx_{R_t} = 1, lx_a = lx_{a-1} \cdot (1-N_{a-1}) \;\text{for}\; a > R_t\] where \(N_a\) is the annual interval natural mortality at age \(a\).

And the fished survivorship (\(lx_a^F\)) is

\[lx_{R_t}^F = 1, lx_a^F = lx_{a-1}^F \cdot (1 - (1 - N_{a-1}) \cdot (1 - U_{a-1})) \;\text{for}\; a > R_t\]

The lifetime number of eggs deposited per (unfished) recruit (\(\phi\)) is then just

\[\phi = \sum_{a = R_t}^{t_\text{max}} lx_a \cdot F_a/2 \cdot S_a\] where \(t_\text{max}\) is the maximum age considered (by default 20) and \(F_a\) the fecundity at age \(a\) is divided by two as the sex ratio is assumed to 1:1 and \(S_a\) is the probability of spawning.

The fished equivalent is denoted \(\phi_F\).

It important to realize that at the unfished equilibrium the annual number of recruits (\(R_0\)) is related to the annual egg deposition according to the following equation

\[E_0 = \phi \cdot R_0\]

By definition

\[\alpha = \frac{R_k \cdot R_0}{E_0} = \frac{R_k}{\phi}\]

The \(\beta\) term of the Beverton-Holt curve can then be found by rearranging the following formula

\[R_0 = \frac{\alpha \cdot \phi \cdot R_0}{\beta \cdot \phi \cdot R_0 + 1}\]

\[\beta \cdot \phi \cdot R_0 + 1 = \alpha \cdot \phi\]

\[\beta = \frac{\alpha \cdot \phi - 1}{\phi \cdot R_0}\]

The equivalent equation for the Ricker curve is arrived at as follows

\[R_0 = \alpha \cdot \phi \cdot R_0 \cdot \exp (-\beta \cdot \phi \cdot R_0)\]

\[\frac{1}{\exp (-\beta \cdot \phi \cdot R_0)} = \alpha \cdot \phi\]

\[\beta \cdot \phi \cdot R_0 = \log(\alpha \cdot \phi)\]

\[\beta = \frac{\log(\alpha \cdot \phi)}{\phi \cdot R_0}\]

The number of recruits at the fished equilibrium (\(R_{0F}\)) can then be found for the Beverton-Holt curve as follows

\[R_{0F} = \frac{\alpha \cdot \phi_F \cdot R_{0F}}{\beta \cdot \phi_F \cdot R_{0F} + 1}\]

\[\beta \cdot \phi_F \cdot R_{0F} + 1 = \alpha \cdot \phi_F\] \[R_{0F} = \frac{\alpha \cdot \phi_F - 1}{\beta \cdot \phi_F}\]

and for the Ricker

\[R_{0F} = \alpha \cdot \phi_F \cdot R_{0F} \cdot \exp (-\beta \cdot \phi_F \cdot R_{0F})\]

\[\frac{1}{\exp(-\beta \cdot \phi_F \cdot R_{0F})} = \alpha \cdot \phi_F\]

\[\beta \cdot \phi_F \cdot R_{0F} = \log(\alpha \cdot \phi_F)\]

\[R_{0F} = \frac{\log(\alpha \cdot \phi_F)}{\beta \cdot \phi_F}\]

Finally the estimates are rescaled so that the carrying capacity is identical to \(R_\text{max}\) through the following transformations

\[ \beta = \beta \cdot \kappa / R_\text{max} \] \[ R_0 = R_0 / \kappa \cdot R_\text{max} \] \[ R_{0F} = R_{0F} / \kappa \cdot R_\text{max} \]

where \(\kappa\), which is the carrying capacity in the original scale, is \(\alpha/\beta\) for the Beverton-Holt and \(\alpha/(\beta \cdot e)\) for the Ricker curve.

## Yield

When the yield is simply the number of fish caught (irrespective of the weight or whether or not its harvested) then it is given by

\[Y = \sum_{a = R_t}^{t_\text{max}} R_{0F} \cdot lx_a^F \cdot \pi \cdot V_a\]

if only harvested fish are considered it becomes

\[Y = \sum_{a = R_t}^{t_\text{max}} R_{0F} \cdot lx_a^F \cdot \pi \cdot V_a \cdot R\]

and if the total weight (in kg) is important then its

\[Y = \sum_{a = R_t}^{t_\text{max}} R_{0F} \cdot lx_a^F \cdot \pi \cdot V_a \cdot R \cdot W_a/1000\]

and if only trophy fish are to be considered then its

\[Y = \sum_{a = R_t}^{t_\text{max}} \text{if}(La < L_y)\ 0\ \text{else}\ R_{0F} \cdot lx_a^F \cdot \pi \cdot V_a \cdot R \cdot W_a/1000\] where \(L_y\) is the minimum length of a trophy fish.

    ypr_plot_yield(population, harvest = TRUE, biomass = TRUE, Ly = 60)

    ypr_tabulate_yield(population, harvest = TRUE, biomass = TRUE, Ly = 60)
    #> # A tibble: 2 × 8
    #>   Type       pi     u  Yield   Age Length Weight Effort
    #>   <chr>   <dbl> <dbl>  <dbl> <dbl>  <dbl>  <dbl>  <dbl>
    #> 1 actual  0.3   0.18  0.0505  7.39   66.8  3006.   3.39
    #> 2 optimal 0.441 0.265 0.0553  7.35   66.7  2978.   5.53

## Efficiency

The catchability `q` indicates the probability of capture for a unit of effort (\(E\)). It is assumed to be related to \(\pi\) according to the relationship \[\pi = 1 - \exp(\log(1-q)\cdot E)\] which can be rearranged to give \[E = \frac{\log(1-\pi)}{\log(1-q)}.\]

    ypr_plot_yield(population, y = "Effort", harvest = TRUE, biomass = TRUE, Ly = 60)

    ypr_plot_yield(population, y = "YPUE", harvest = TRUE, biomass = TRUE, Ly = 60)
    #> Warning: Removed 1 row(s) containing missing values (geom_path).

## References

Cooper, Andrew B. 2006. A Guide to Fisheries Stock Assessment: From Data to Recommendations. University of New Hampshire, Sea Grant College Program.
Walters, Carl J., and Steven J. D. Martell. 2004. Fisheries Ecology and Management. Princeton, N.J: Princeton University Press.