A class to hold the parameters for a size based model.

Although it is possible to build a MizerParams object by hand it is not recommended and several constructors are available. Dynamic simulations are performed using project() function on objects of this class. As a user you should never need to access the slots inside a MizerParams object directly.

Details

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.

The MizerParams class does not hold any dynamic information, e.g. abundances or harvest effort through time. These are held in MizerSim objects.

Slots

metadata: A list with metadata information. See setMetadata().
mizer_version: The package version of mizer (as returned by packageVersion("mizer")) that created or upgraded the model.
extensions: A named vector of strings where each name is the name of and extension package needed to run the model and each value is a string giving the information that the remotes package needs to install the correct version of the extension package, see https://remotes.r-lib.org/.
time_created: A POSIXct date-time object with the creation time.
time_modified: A POSIXct date-time object with the last modified time.
w: The 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 maximum size.
dw: The widths (in grams) of the size bins
w_full: The size grid for the full size range including the resource spectrum. An increasing vector of weights (in grams) running from the smallest resource size to the largest maximum size of fish. The last entries of the vector have to be equal to the content of the w slot.
dw_full: The width of the size bins for the full spectrum. The last entries have to be equal to the content of the dw slot.
w_min_idx: A vector holding the index of the weight of the egg size of each species
maturity: An 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().
psi: An array (species x size) that holds the allocation to reproduction for each species at size, \(\psi_i(w)\). Changed with setReproduction().
intake_max: An array (species x size) that holds the maximum intake for each species at size. Changed with setMaxIntakeRate().
search_vol: An array (species x size) that holds the search volume for each species at size. Changed with setSearchVolume().
metab: An array (species x size) that holds the metabolism for each species at size. Changed with setMetabolicRate().
mu_b: An array (species x size) that holds the external mortality rate \(\mu_{ext.i}(w)\). Changed with setExtMort().
ext_encounter: An array (species x size) that holds the external encounter rate \(E_{ext.i}(w)\). Changed with setExtEncounter().
pred_kernel: An 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_e: An 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_p: An 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_pp: A vector the same length as the w_full slot. The size specific growth rate of the resource spectrum.
cc_pp: A vector the same length as the w_full slot. The size specific carrying capacity of the resource spectrum.
resource_dynamics: Name of the function for projecting the resource abundance density by one timestep.
other_dynamics: A 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_encounter: A named list of functions for calculating the contribution to the encounter rate from each other dynamical component.
other_mort: A named list of functions for calculating the contribution to the mortality rate from each other dynamical components.
other_params: A list containing the parameters needed by any mizer extensions you may have installed to model other dynamical components of the ecosystem.
rates_funcs: A named list with the names of the functions that should be used to calculate the rates needed by project(). By default this will be set to the names of the built-in rate functions.
sc: The community abundance of the scaling community
species_params: A data.frame to hold the species specific parameters. See species_params() for details.
given_species_params: A data.frame to hold the species parameters that were given explicitly rather than obtained by default calculations.
gear_params: Data frame with parameters for gear selectivity. See setFishing() for details.
interaction: The species specific interaction matrix, \(\theta_{ij}\). Changed with setInteraction().
selectivity: An array (gear x species x w) that holds the selectivity of each gear for species and size, \(S_{g,i,w}\). Changed with setFishing().
catchability: An array (gear x species) that holds the catchability of each species by each gear, \(Q_{g,i}\). Changed with setFishing().
initial_effort: A vector containing the initial fishing effort for each gear. Changed with setFishing().
initial_n: An array (species x size) that holds the initial abundance of each species at each weight.
initial_n_pp: A vector the same length as the w_full slot that describes the initial resource abundance at each weight.
initial_n_other: A list with the initial abundances of all other ecosystem components. Has length zero if there are no other components.
resource_params: List with parameters for resource.
A: Abundance multipliers.
linecolour: A named vector of colour values, named by species. Used to give consistent colours in plots.
linetype: A named vector of linetypes, named by species. Used to give consistent line types in plots.
ft_mask: An array (species x w_full) with zeros for weights larger than the maximum weight of each species. Used to efficiently minimize wrap-around errors in Fourier transform calculations.

A class to hold the parameters for a size based model.

Details

Slots

See also