R/MizerParams-class.R
MizerParams-class.RdMizerParams objects can be created using a range of constructor functions.
Dynamic simulations are performed using the project function on
objects of this class.
wThe size grid for the fish part of the spectrum. An increasing vector of weights (in grams) running from the smallest egg size to the largest asymptotic size.
dwThe spacing in the size grid. So dw[i] = w[i+1] - w[i]. A vector the same length as the w_full slot. The last entry is not determined by the w slot but represents the size of the last size bin.
w_fullThe size grid for the full size range including the plankton spectrum. An increasing vector of weights (in grams) running from the smallest plankton size to the largest asymptotic size of fish. The last entries of the vector have to be equal to the content of the w slot.
dw_fullThe spacing in the full size grid. So dw_full[i] = w_full[i+1] - w_full[i]. The last entries have to be equal to the content of the dw slot.
w_min_idxA vector holding the index of the weight of the egg size of each species
maturityAn array (species x size) that holds the proportion of
individuals of each species at size that are mature. This enters in the
calculation of the spawning stock biomass with getSSB. Set
with setReproduction.
psiAn array (species x size) that holds the allocation to reproduction
for each species at size, \(\psi_i(w)\). Changed with
setReproduction.
intake_maxAn array (species x size) that holds the maximum intake for
each species at size. Changed with setIntakeMax.
search_volAn array (species x size) that holds the search volume for
each species at size. Changed with setSearchVolume.
metabAn array (species x size) that holds the metabolism
for each species at size. Changed with setMetab.
mu_bAn array (species x size) that holds the background death
\(\mu_{b.i}(w)\). Changed with setBMort.
pred_kernelAn array (species x predator size x prey size) that holds
the predation coefficient of each predator at size on each prey size. If
this is NA then the following two slots will be used. Changed with
setPredKernel.
ft_pred_kernel_eAn array (species x log of predator/prey size ratio)
that holds the Fourier transform of the feeding kernel in a form
appropriate for evaluating the encounter rate integral. If this is NA
then the pred_kernel will be used to calculate the available
energy integral. Changed with setPredKernel.
ft_pred_kernel_pAn array (species x log of predator/prey size ratio)
that holds the Fourier transform of the feeding kernel in a form
appropriate for evaluating the predation mortality integral. If this is NA
then the pred_kernel will be used to calculate the integral.
Changed with setPredKernel.
rr_ppA vector the same length as the w_full slot. The size specific
growth rate of the plankton spectrum. Changed with setPlankton.
cc_ppA vector the same length as the w_full slot. The size specific
carrying capacity of the plankton spectrum. Changed with
setPlankton.
plankton_dynamicsName of the function for projecting the plankton abundance
density by one timestep. The default is
plankton_semichemostat.
Changed with setPlankton.
other_dynamicsA named list of functions for projecting the values of other dynamical components of the ecosystem that may be modelled by a mizer extensions you have installed. The names of the list entries are the names of those components.
other_encounterA named list of functions for calculating the contribution to the encounter rate from each other dynamical component.
other_pred_mortA named list of functions for calculating the contribution to the predation mortality rate from each other dynamical component.
other_paramsA list containing the parameters needed by any mizer extensions you may have installed to model other dynamical components of the ecosystem.
rates_funcA string with the name of the function that should be used to calculate the rates needed by `project()`. By default this will be set to "getRates" so that the built-in `getRates()` function is used.
scThe community abundance of the scaling community
species_paramsA data.frame to hold the species specific parameters.
See newMultispeciesParams for details.
interactionThe species specific interaction matrix, \(\theta_{ij}\).
Changed with setInteraction.
srrString holding the name of the function to calculate the realised (density dependent) recruitment. The function should have two arguments which are rdi and species_params.
selectivityAn array (gear x species x w) that holds the selectivity of
each gear for species and size, \(S_{g,i,w}\). Changed with
setFishing.
catchabilityAn array (gear x species) that holds the catchability of
each species by each gear, \(Q_{g,i}\). Changed with
setFishing.
initial_effortA vector containing the initial fishing effort for each
gear. Changed with setFishing.
initial_nAn array (species x size) that holds the initial abundance of each species at each weight.
initial_n_ppA vector the same length as the w_full slot that describes the initial plankton abundance at each weight.
initial_n_otherA list with the initial abundances of all other ecosystem components. Has length zero if there are no other components.
plankton_paramsParameters for plankton. See setPlankton.
AAbundance multipliers.
linecolourA named vector of colour values, named by species. Used to give consistent colours in plots.
linetypeA named vector of linetypes, named by species. Used to give consistent line types in plots.
The MizerParams class is fairly complex with a large number of
slots, many of which are multidimensional arrays. The dimensions of these
arrays is strictly enforced so that MizerParams objects are
consistent in terms of number of species and number of size classes.
Although it is possible to build a MizerParams object by hand it is
not recommended and several constructors are available.
The MizerParams class does not hold any dynamic information, e.g.
abundances or harvest effort through time. These are held in
MizerSim objects.