2.8.6. Fishing parameters (Osmose >= 4.3)

In the Osmose versions >= 4.3, changes in the parameterization of fisheries have been implemented, although the spirit remains close to the one in versions 4.

2.8.6.1. Fishing period

There is now the possibility to define a fishing period, i.e. a period when the fishery is active.

Table 2.37 Fishing period parameters

fisheries.period.number.fsh#

Number of fishing periods within one year (\(N_{per}\))

fisheries.period.start.fsh#

Start of the fishing period (fraction of year, default = 0, \(Y_{start}\))

fisheries.rate.byperiod.fsh#

Fishing mortality rate. **Must me in \(year^{-1}\)

Note that the number of values expected in the fisheries.rate.byperiod.fsh# parameter depends on \(Y_{start}\).

If \(Y_{start} = 0\), then \(N_{per} \times N_{year}\) values are expected (one value for each fishing and non-fishing season).

If \(Y_{start} \neq 0\), then \(N_{per} \times N_{year} + 1\) values are expected.

../../_images/fishing-period.svg

Fig. 2.8 Fishing period for two values of \(Y_{start}\)

2.8.6.2. Fishing seasonality

In order to distribute the fishery mortality over the season, the user can define a seasonality file.

Table 2.38 Fishing seasonality parameters

fisheries.seasonality.fsh#

Array of fishing seasonality. Must contain \(\frac{N_{step}}{N_{season}}\)

fisheries.seasonality.file.fsh#

File containing the fishing seasonalities (must contain \(N_{step}\) values)

Danger

The sum of fishing seasonalities must equal one over the fishing seasons! No automatic normalisation is performed by Osmose!

2.8.6.3. Size selectivities

Table 2.39 Fishing size-selectivity parameters

fisheries.selectivity.tiny.fsh#

Selectivities values below which selectivity if forced to 0 (\(\epsilon\))

fisheries.selectivity.type.file.fsh#

File containing the selectivity types

fisheries.selectivity.type.shift.fsh#

Array containing the selectivity periods

fisheries.selectivity.type.fsh#

Selectivity types (one value per shift period). Must be 0, 1 or 2

fisheries.selectivity.a50.file.fsh#

File containing the age selectivities.

fisheries.selectivity.a50.shift.fsh#

Array containing the \(A_{50}\) shift periods

fisheries.selectivity.a50.fsh#

Age selectity (one value per shift period). If set, assumes that fishery selectivity is age-based

fisheries.selectivity.l50.file.fsh#

File containing the \(L_{50}\).

fisheries.selectivity.l50.shift.fsh#

Array containing the \(L_{50}\) shift periods

fisheries.selectivity.l50.fsh#

\(L_{50}\) (one value per shift period).

fisheries.selectivity.l75.file.fsh#

File containing the \(L_{75}\)

fisheries.selectivity.l75.shift.fsh#

Array containing the \(L_{75}\) shift periods

fisheries.selectivity.l75.fsh#

\(L_{75}\) (one value per shift period).

Note that type, a50, l50 and l75 are parameterized in the same way. If the .file parameter is defined, then it is used. If it is not set, then values are defined by using the other two parameters. The shift array contains thresholds, where the values are to change.

The selectivity type must contain 0 (knife-edge), 1 (sigmoid) or 2 (Gaussian).

If one of the a50 parameter, it is assumed that age selectivity is used.

Warning

Only knife-edge selectivity can be used with age.

Note

If only knife-edge selectivity is used, then the l75 parameters are not used.

2.8.6.3.1. Knife-edge selectivity

Knife-edge selectivity is computed as follows:

\[S(L) = 1\ if\ L \ge L_{50}\]

2.8.6.3.2. Sigmoid selectivity

Sigmoid selectivity is computed as follows:

\[ \begin{align}\begin{aligned}S(L) = \frac{1} {1 + exp^{S_1 - S_2 L}}\\S_1 = \frac{L_{50} \times \ln 3}{L_{75} - L_{50}}\\S_2 = \frac{S_1}{L_50}\end{aligned}\end{align} \]

2.8.6.3.3. Gaussian selectivity

Gaussian selectivity is computed as follows:

\[ \begin{align}\begin{aligned}S(L) = \frac{F(L)}{F(L_{50})}\\F(L) = exp\left(-\frac{L - L_{50}}{2 \sigma^2}\right)\\\sigma = \frac{L_{75} - L_{50}}{q_{75}}\end{aligned}\end{align} \]

with \(q_{75}\) is the inverse cumulative standard normal distribution for the 75th percentile.

2.8.6.4. Catchability

Fishery cathabilities are parameterized in a similar way as predation accessibility matrix.

Table 2.40 Fisheries catchabilities

fisheries.catchability.file

Name of the catchability file

fisheries.catchability.file.cat#

Name of the catchability file

fisheries.catchability.initialYear.cat#

First year when the catchability matrix should be used

fisheries.catchability.finalYear.cat#

Last year when the catchability matrix should be used

fisheries.catchability.years.cat#

List of years when the catchability should be used.

fisheries.catchability.steps.cat#

List of steps within a year when the catchability should be used.

Fishery catchabilities should be provided as a CSV file, with fisheries as column (predators) and species (background and focal) as rows (preys).

2.8.6.5. Discards

There is also the possibility to define fisheries discards. It is defined in the same way as catchabilies.

Table 2.41 Fisheries discards

pref= fisheries.catchability

suf = cat

fisheries.discards.file

Name of the catchability file

fisheries.discards.file.dis#

Name of the catchability file

fisheries.discards.initialYear.dis#

First year when the catchability matrix should be used

fisheries.discards.finalYear.dis#

Last year when the catchability matrix should be used

fisheries.discards.years.dis#

List of years when the catchability should be used.

fisheries.discards.steps.dis#

List of steps within a year when the catchability should be used.

Fishery catchabilities should be provided as a CSV file, with fisheries as column (predators) and species (background and focal) as rows (preys).