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These functions allow you to get or set the species parameters stored in a MizerParams object.

Usage

species_params(params)

species_params(params) <- value

Arguments

params

A MizerParams object

value

A data frame with the species parameters

Details

The species_params data frame holds species-specific parameters. The data frame has one row for each species and one column for each species parameter. There are a lot of species parameters and we will list them all below, but most of them have sensible default values. The only required columns are species for the species name and w_inf for its asymptotic size. However if you have information about the values of other parameters then you should include them in the species_params data frame.

There are some species parameters that are used to set up the size-dependent parameters that are used in the mizer model:

  • gamma and q are used to set the search volume, see setSearchVolume().

  • h and n are used to set the maximum intake rate, see setMaxIntakeRate().

  • k, ks and p are used to set activity and basic metabolic rate, see setMetabolicRate().

  • z0 is used to set the external mortality rate, see setExtMort().

  • w_mat, w_mat25, w_inf and m are used to set the allocation to reproduction, see setReproduction().

  • pred_kernel_type specifies the shape of the predation kernel. The default is a "lognormal", for other options see the "Setting predation kernel" section in the help for setPredKernel().

  • beta and sigma are parameters of the lognormal predation kernel, see lognormal_pred_kernel(). There will be other parameters if you are using other predation kernel functions.

When you change one of the above species parameters in an already existing MizerParams object using species_params<-(), the new value will be used to update the corresponding size-dependent rates automatically, unless you have set those size-dependent rates manually, in which case the corresponding species parameters will be ignored.

There are some species parameters that are used directly in the model rather than being used for setting up size-dependent parameters:

  • alpha is the assimilation efficiency, the proportion of the consumed biomass that can be used for growth, metabolism and reproduction, see the help for getEReproAndGrowth().

  • w_min is the egg size.

  • interaction_resource sets the interaction strength with the resource, see "Predation encounter" section in the help for getEncounter().

  • erepro is the reproductive efficiency, the proportion of the energy invested into reproduction that is converted to egg biomass, see getRDI().

  • Rmax is the parameter in the Beverton-Holt density dependence added to the reproduction, see setBevertonHolt(). There will be other such parameters if you use other density dependence functions, see the "Density dependence" section in the help for setReproduction().

Two parameters are used only by functions that need to convert between weight and length:

  • a and b are the parameters in the allometric weight-length relationship \(w = a l ^ b\).

Not all of species parameters have to be specified by the user. If they are missing, newMultispeciesParams() will give them default values, sometimes by using other species parameters. The parameters that are only used to calculate default values for other parameters are:

  • k_vb and t0 are the von Bertalanffy growth parameters and are used together with the length-weight relationship exponent b and the egg size w_min to get a default value for the coefficient of the maximum intake rate h, see get_h_default().

  • f0 is the feeding level and is used to get a default value for the coefficient of the search volume gamma, see get_gamma_default().

  • fc is the critical feeding level below which the species can not maintain itself. This is used to get a default value for the coefficient of the metabolic rate ks, see get_ks_default().

Note that these parameters are ignored if the parameters for which they allow defaults to be calculated have instead been set explicitly. Also, these parameters will only be used when setting up a new model with newMultispeciesParams(). Changing them later will have no effect because the default for the other parameters will not be recalculated.

There are other species parameters that are used in tuning the model to observations:

  • biomass_observed and biomass_cutoff allow you to specify for each species the total observed biomass above some cutoff size. This is used by calibrateBiomass() and matchBiomasses().

  • yield_observed allows you to specify for each species the total annual fisheries yield. This is used by calibrateYield() and matchYields().

Finally there are two species parameters that control the way the species are represented in plots:

  • linecolour specifies the colour and can be any valid R colour value.

  • linetype specifies the line type ("solid", "dashed", "dotted", "dotdash", "longdash", "twodash" or "blank")

Other species-specific information that is related to how the species is fished is specified in a gear parameter data frame, see gear_params(). However in the case where each species is caught by only a single gear, this information can also optionally be provided as columns in the species_params data frame and newMultispeciesParams() will transfer them to the gear_params data frame. However changing these parameters later in the species parameter data frame will have no effect.

You are allowed to include additional columns in the species_params data frame. They will simply be ignored by mizer but will be stored in the MizerParams object, in case your own code makes use of them.