These functions allow you to get or set the species parameters stored in a MizerParams object.
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_max for its maximum 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:
qare used to set the search volume, see
nare used to set the maximum intake rate, see
pare used to set activity and basic metabolic rate, see
z0is used to set the external mortality rate, see
mare used to set the allocation to reproduction, see
pred_kernel_typespecifies the shape of the predation kernel. The default is a "lognormal", for other options see the "Setting predation kernel" section in the help for
sigmaare 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:
alphais the assimilation efficiency, the proportion of the consumed biomass that can be used for growth, metabolism and reproduction, see the help for
w_minis the egg size.
interaction_resourcesets the interaction strength with the resource, see "Predation encounter" section in the help for
ereprois the reproductive efficiency, the proportion of the energy invested into reproduction that is converted to egg biomass, see
Rmaxis 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
Two parameters are used only by functions that need to convert between weight and length:
bare the parameters in the allometric weight-length relationship \(w = a l ^ b\).
If you have supplied these, then you can replace weight parameters
w_min by their corresponding length
Not all species parameters have to be specified by the user. If they are
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:
f0is the feeding level and is used to get a default value for the coefficient of the search volume
fcis the critical feeding level below which the species can not maintain itself. This is used to get a default value for the coefficient
ksof the metabolic rate, see
age_matis the age at maturity and is used to get a default value for the coefficient
hof the maximum intake rate, see
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.
In the past mizer also used the von Bertalanffy parameters
t0 to determine a default for
h. This is unreliable and is therefore
There are other species parameters that are used in tuning the model to observations:
Finally there are two species parameters that control the way the species are represented in plots:
linecolourspecifies the colour and can be any valid R colour value.
linetypespecifies 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
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
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.