These functions allow you to get or set the species parameters stored in a MizerParams object.
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_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:
gamma
andq
are used to set the search volume, seesetSearchVolume()
.h
andn
are used to set the maximum intake rate, seesetMaxIntakeRate()
.k
,ks
andp
are used to set activity and basic metabolic rate, seesetMetabolicRate()
.z0
is used to set the external mortality rate, seesetExtMort()
.w_mat
,w_mat25
,w_max
andm
are used to set the allocation to reproduction, seesetReproduction()
.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 forsetPredKernel()
.beta
andsigma
are parameters of the lognormal predation kernel, seelognormal_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 forgetEReproAndGrowth()
.w_min
is the egg size.interaction_resource
sets the interaction strength with the resource, see "Predation encounter" section in the help forgetEncounter()
.erepro
is the reproductive efficiency, the proportion of the energy invested into reproduction that is converted to egg biomass, seegetRDI()
.Rmax
is the parameter in the Beverton-Holt density dependence added to the reproduction, seesetBevertonHolt()
. There will be other such parameters if you use other density dependence functions, see the "Density dependence" section in the help forsetReproduction()
.
Two parameters are used only by functions that need to convert between weight and length:
a
andb
are the parameters in the allometric weight-length relationship \(w = a l ^ b\).
If you have supplied these, then you can replace weight parameters
like w_max
, w_mat
, w_mat25
and w_min
by their corresponding length
parameters l_max
, l_mat
, l_mat25
and l_min
.
Not all 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:
f0
is the feeding level and is used to get a default value for the coefficient of the search volumegamma
, seeget_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 coefficientks
of the metabolic rate, seeget_ks_default()
.age_mat
is the age at maturity and is used to get a default value for the coefficienth
of the maximum intake rate, seeget_h_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.
In the past mizer also used the von Bertalanffy parameters k_vb
, w_inf
and t0
to determine a default for h
. This is unreliable and is therefore
now deprecated.
There are other species parameters that are used in tuning the model to observations:
biomass_observed
andbiomass_cutoff
allow you to specify for each species the total observed biomass above some cutoff size. This is used bycalibrateBiomass()
andmatchBiomasses()
.yield_observed
allows you to specify for each species the total annual fisheries yield. This is used bycalibrateYield()
andmatchYields()
.
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.
See also
Other functions for setting parameters:
gear_params()
,
setExtMort()
,
setFishing()
,
setInitialValues()
,
setInteraction()
,
setMaxIntakeRate()
,
setMetabolicRate()
,
setParams()
,
setPredKernel()
,
setReproduction()
,
setSearchVolume()