Set fishing parameters

Usage

setFishing(
  params,
  selectivity = NULL,
  catchability = NULL,
  reset = FALSE,
  initial_effort = NULL,
  ...
)

getCatchability(params)

catchability(params)

catchability(params) <- value

getSelectivity(params)

selectivity(params)

selectivity(params) <- value

getInitialEffort(params)

Arguments

params: A MizerParams object
selectivity: Optional. An array (gear x species x size) that holds the selectivity of each gear for species and size, $S_{g,i,w}$.
catchability: Optional. An array (gear x species) that holds the catchability of each species by each gear, $Q_{g,i}$.
reset: If set to TRUE, then both catchability and selectivity will be reset to the values calculated from the gear parameters, even if it was previously overwritten with a custom value. If set to FALSE (default) then a recalculation from the gear parameters will take place only if no custom value has been set.
initial_effort: Optional. A number or a named numeric vector specifying the fishing effort. If a number, the same effort is used for all gears. If a vector, must be named by gear.
...: Unused
value: .

Value

setFishing(): A MizerParams object with updated fishing parameters.

getCatchability() or equivalently catchability(): An array (gear x species) that holds the catchability of each species by each gear, $Q_{g,i}$. The names of the dimensions are "gear, "sp".

getSelectivity() or equivalently selectivity(): An array (gear x species x size) that holds the selectivity of each gear for species and size, $S_{g,i,w}$. The names of the dimensions are "gear, "sp", "w".

getInitialEffort() or equivalently initial_effort(): A named vector with the initial fishing effort for each gear.

Setting fishing

Gears

In mizer, fishing mortality is imposed on species by fishing gears. The total per-capita fishing mortality (1/year) is obtained by summing over the mortality from all gears, $$\mu_{f.i}(w) = \sum_g F_{g,i}(w),$$ where the fishing mortality $F_{g,i}(w)$ imposed by gear $g$ on species $i$ at size $w$ is calculated as: $$F_{g,i}(w) = S_{g,i}(w) Q_{g,i} E_{g},$$ where $S$ is the selectivity by species, gear and size, $Q$ is the catchability by species and gear and $E$ is the fishing effort by gear.

Selectivity

The selectivity at size of each gear for each species is saved as a three dimensional array (gear x species x size). Each entry has a range between 0 (that gear is not selecting that species at that size) to 1 (that gear is selecting all individuals of that species of that size). This three dimensional array can be specified explicitly via the selectivity argument, but usually mizer calculates it from the gear_params slot of the MizerParams object.

To allow the calculation of the selectivity array, the gear_params slot must be a data frame with one row for each gear-species combination. So if for example a gear can select three species, then that gear contributes three rows to the gear_params data frame, one for each species it can select. The data frame must have columns gear, holding the name of the gear, species, holding the name of the species, and sel_func, holding the name of the function that calculates the selectivity curve. Some selectivity functions are included in the package: knife_edge(), sigmoid_length(), double_sigmoid_length(), and sigmoid_weight(). Users are able to write their own size-based selectivity function. The first argument to the function must be w and the function must return a vector of the selectivity (between 0 and 1) at size.

Each selectivity function may have parameters. Values for these parameters must be included as columns in the gear parameters data.frame. The names of the columns must exactly match the names of the corresponding arguments of the selectivity function. For example, the default selectivity function is knife_edge() that a has sudden change of selectivity from 0 to 1 at a certain size. In its help page you can see that the knife_edge() function has arguments w and knife_edge_size. The first argument, w, is size (the function calculates selectivity at size). All selectivity functions must have w as the first argument. The values for the other arguments must be found in the gear parameters data.frame. So for the knife_edge() function there should be a knife_edge_size column. Because knife_edge() is the default selectivity function, the knife_edge_size argument has a default value = w_mat.

The most commonly-used selectivity function is sigmoid_length(). It has a smooth transition from 0 to 1 at a certain size. The sigmoid_length() function has the two parameters l50 and l25 that are the lengths in cm at which 50% or 25% of the fish are selected by the gear. If you choose this selectivity function then the l50 and l25 columns must be included in the gear parameters data.frame.

In case each species is only selected by one gear, the columns of the gear_params data frame can alternatively be provided as columns of the species_params data frame, if this is more convenient for the user to set up. Mizer will then copy these columns over to create the gear_params data frame when it creates the MizerParams object. However changing these columns in the species parameter data frame later will not update the gear_params data frame.

Catchability

Catchability is used as an additional factor to make the link between gear selectivity, fishing effort and fishing mortality. For example, it can be set so that an effort of 1 gives a desired fishing mortality. In this way effort can then be specified relative to a 'base effort', e.g. the effort in a particular year.

Catchability is stored as a two dimensional array (gear x species). This can either be provided explicitly via the catchability argument, or the information can be provided via a catchability column in the gear_params data frame.

In the case where each species is selected by only a single gear, the catchability column can also be provided in the species_params data frame. Mizer will then copy this over to the gear_params data frame when the MizerParams object is created.

Effort

The initial fishing effort is stored in the MizerParams object. If it is not supplied, it is set to zero. The initial effort can be overruled when the simulation is run with project(), where it is also possible to specify an effort that varies through time.

Examples

str(getCatchability(NS_params))
#>  num [1:4, 1:12] 1 0 0 0 1 0 0 0 1 0 ...
#>  - attr(*, "dimnames")=List of 2
#>   ..$ gear: chr [1:4] "Industrial" "Pelagic" "Beam" "Otter"
#>   ..$ sp  : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
str(getSelectivity(NS_params))
#>  num [1:4, 1:12, 1:100] 0 0 0 0 0 0 0 0 0 0 ...
#>  - attr(*, "dimnames")=List of 3
#>   ..$ gear: chr [1:4] "Industrial" "Pelagic" "Beam" "Otter"
#>   ..$ sp  : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   ..$ w   : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
str(getInitialEffort(NS_params))
#>  Named num [1:4] 0 1 0.5 0.5
#>  - attr(*, "names")= chr [1:4] "Industrial" "Pelagic" "Beam" "Otter"