Description Usage Arguments Details Value References See Also Examples

Calculates the catchability for each fishing gear.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ```
calc_Q(
curve = rep("logistic", nfish),
species = ((0:(length(curve) - 1))%%nfish) + 1,
max_catchability = rep(1, length(curve)),
gear_name = paste("gear_", 1:length(curve), sep = ""),
custom = NULL,
nsc,
nfish,
l_bound,
u_bound,
mid,
eps = 1e-05,
species_names,
...
)
get_Q(curve, species, gear_name, nsc, nfish, l_bound, u_bound, mid, eps, ...)
logistic_catch(species, nsc, nfish, mid, eps, L50 = 50, eta = 0.25, ...)
log_gaussian_catch(species, nsc, nfish, mid, eps, Lmu = 50, Lsigma = 1, ...)
knife_edge_catch(species, nsc, nfish, l_bound, u_bound, Lmin = 50, ...)
``` |

`curve` |
A character vector of almost any length describing the type of curve to be used to determine the catchability of each species by the fishing gear. By default, |

`species` |
A numeric or character vector of the same length as |

`max_catchability` |
A numeric vector of length |

`gear_name` |
A character vector of the same length as |

`custom` |
An array of dimensions |

`nsc` |
A numeric value representing the number of length classes in the model. |

`nfish` |
A numeric value representing the number of fish species in the model. |

`l_bound` |
A numeric vector of length |

`u_bound` |
A numeric vector of length |

`mid` |
A numeric vector of length |

`eps` |
A numeric value specifying a numerical offset. The default is |

`species_names` |
A character vector of length |

`...` |
Vectors of the same length as |

`L50` |
A numeric value representing the length at 50% of the maximum catchability of the catchability curve. This is used with the |

`eta` |
A numeric value representing the steepness of the slope of the catchability curve. This is used with the |

`Lmu` |
A numeric value representing the length at the maximum catchability of the catchability curve. This is used with the |

`Lsigma` |
A numeric value representing the standard deviation of the catchability curve. See 'Details' for more information. This is used with the |

`Lmin` |
A numeric value representing the minimum length that is caught by the catchability curve. This is used with the |

This function allows three different models for catchability, all of which are rescaled so that their maximum catchability is equal to one:

(1) `"logistic"`

is proportional to

`1/(1+exp(-eta*(mid-L50)))`

;

(2) `"log-gaussian"`

is proportional to

`dlnorm(mid, log(Lmu), Lsigma)`

;

and (3) `"knife-edge"`

is equal to 1 for the length classes indexed by `max(which(l_bound<Lmin)):nsc`

and 0 for all other length classes. This means that all of the individuals in the length class containing `Lmin`

will have a catchability of 1.

In `calc_Q`

the catchability is rescaled so that the maximum catchability is one.

`calc_Q`

returns an array of dimensions `nsc`

, `nfish`

and `gear`

representing the catchability of each species by each of the fishing gears, scaled from 0 to `max_catchability`

.

`get_Q`

returns a catchability curve for a given species and gear scaled from 0 to 1. If an invalid catchability curve is selected, `NULL`

is returned and a warning message is shown.

`logistic_catch`

returns a matrix with dimensions `nsc`

and `nfish`

with all elements set to zero excluding one column that represents the logistic catchability curve for the selected species scaled from 0 to 1.

`log_gaussian_catch`

returns a matrix with dimensions `nsc`

and `nfish`

with all elements set to zero excluding one column that represents the log-gaussian catchability curve for the selected species scaled from 0 to 1.

`knife_edge_catch`

returns a matrix with dimensions `nsc`

and `nfish`

with all elements set to zero excluding one column that represents the knife-edge catchability curve for the selected species scaled from 0 to 1.

Hall, S. J., Collie, J. S., Duplisea, D. E., Jennings, S., Bravington, M., & Link, J. (2006). A length-based multispecies model for evaluating community responses to fishing. *Canadian Journal of Fisheries and Aquatic Sciences*, 63(6):1344-1359.

Thorpe, R.B., Jennings, S., Dolder, P.J. (2017). Risks and benefits of catching pretty good yield in multispecies mixed fisheries. *ICES Journal of Marine Science*, 74(8):2097-2106.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ```
# Set up the inputs to the function
nfish <- nrow(NS_par)
nsc <- 32
maxsize <- max(NS_par$Linf)*1.01 # the biggest size is 1% bigger than the largest Linf
l_bound <- seq(0, maxsize, maxsize/nsc); l_bound <- l_bound[-length(l_bound)]
u_bound <- seq(maxsize/nsc, maxsize, maxsize/nsc)
mid <- l_bound+(u_bound-l_bound)/2
# Set up the inputs to the function - species-specific parameters
Linf <- NS_par$Linf # the von-Bertalanffy asymptotic length of each species (cm).
W_a <- NS_par$W_a # length-weight conversion parameter.
W_b <- NS_par$W_b # length-weight conversion parameter.
k <- NS_par$k # the von-Bertalnaffy growth parameter.
Lmat <- NS_par$Lmat # the length at which 50\% of individuals are mature (cm).
# Calculate gear catchability
Qs <- calc_Q(curve=rep("logistic", nfish), species=NS_par$species_names,
max_catchability=rep(1, nfish), gear_name=NS_par$species_names,
nsc=nsc, nfish=nfish, mid=mid, l_bound=l_bound, u_bound=u_bound,
species_names=NS_par$species_names, eta=rep(0.25, nfish), L50=Lmat)
# Calculate logistic catchability for the first species
logistic_catch(species=1, nsc, nfish, mid, eps=1e-5,L50=Lmat[1], eta=0.25)
# Calculate log-gaussian catchability for the first species
log_gaussian_catch(species=1, nsc, nfish, mid, eps=1e-5, Lmu=50, Lsigma=1)
# Calculate knife-edge catchability for the first species
knife_edge_catch(species=1, nsc, nfish, l_bound, u_bound, Lmin=50)
``` |

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