Set fishing parameters
setFishing(params, initial_effort = NULL)
| params | A MizerParams object |
|---|---|
| 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. |
MizerParams object
Gears
In mizer, fishing mortality is imposed on species by fishing gears. The
total fishing mortality 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.
At the moment a species can only be selected by one fishing gear, although
each gear can select more than one species (this is a limitation with the
current package that will be developed in future releases). The gear
selecting each species can be specified in the gear column in the
species_params data frame. If no gear is specified, the default gear is
"knife_edge_gear".
Selectivity
The selectivity at size of each gear has a range between 0 (not selected at
that size) to 1 (fully selected at that size). It is given by a selectivity
function. The name of the selectivity function is given by the sel_func
column in the species parameters data frame. Some selectivity functions are
included in the package: knife_edge(), sigmoid_length(),
double_sigmoid_length(), and sigmoid_weight(). New functions can be defined
by the user. Each
gear has the same selectivity function for all the species it selects, but
the parameter values for each species may be different, e.g. the lengths of
species that a gear selects may be different.
Each selectivity function has a range of parameters. Values for these
parameters must be included as columns in the species 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() which 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 species 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.
Catchability
Catchability is used as an additional scalar 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.
Because currently mizer only allows one gear to select each species, the
catchability matrix \(Q_{g,i}\) reduces to a catchability vector
\(Q_{i}\), and this is given as a column catchability in the species
parameter data frame. If it is not specified, it defaults to 1.
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.
Other functions for setting parameters:
setBMort(),
setInitial(),
setIntakeMax(),
setInteraction(),
setMetab(),
setParams(),
setPlankton(),
setPredKernel(),
setReproduction(),
setSearchVolume()
if (FALSE) { params <- NS_params # Change knife edge size for species 1 params@species_params$knife_edge_size[1] <- 15 params <- setFishing(params) }