mizer (version 1.0.1)

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

Description

These parameters include the model species, their life history parameters and the size ranges of the model.

Slots

w

A numeric vector of size bins used for the community (i.e. fish) part of the model. These are usually spaced on a log10 scale

dw

The absolute difference between the size bins specified in the w slot. A vector the same length as the w slot. The final value is the same as the second to last value

w_full

A numeric vector of size bins used for the whole model (i.e. the community and background spectra) . These are usually spaced on a log10 scale

dw_full

The absolute difference between the size bins specified in the w_full slot. A vector the same length as the w_full slot. The final value is the same as the second to last value

psi

An array (species x size) that holds the allocation to reproduction for each species at size, \(\psi_i(w)\)

intake_max

An array (species x size) that holds the maximum intake for each species at size, \(h_i w^n\)

search_vol

An array (species x size) that holds the search volume for each species at size, \(\gamma_i w^q\)

activity

An array (species x size) that holds the activity for each species at size, \(k_i w\)

std_metab

An array (species x size) that holds the standard metabolism for each species at size, \(k_{s.i} w^p\)

mu_b

An array (species x size) that holds the background death \(\mu_{b.i}(w)\)

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 available energy integral

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

rr_pp

A vector the same length as the w_full slot. The size specific growth rate of the background spectrum, \(r_0 w^{p-1}\)

cc_pp

A vector the same length as the w_full slot. The size specific carrying capacity of the background spectrum, \(\kappa w^{-\lambda}\)

sc

The community abundance of the scaling community

species_params

A data.frame to hold the species specific parameters (see the mizer vignette, Table 2, for details)

interaction

The species specific interaction matrix, \(\theta_{ij}\)

srr

Function to calculate the realised (density dependent) recruitment. Has two arguments which are rdi and species_params

selectivity

An array (gear x species x w) that holds the selectivity of each gear for species and size, \(S_{g,i,w}\)

catchability

An array (gear x species) that holds the catchability of each species by each gear, \(Q_{g,i}\)

initial_n

An array (species x size) that holds abundance of each species at each weight at our candidate steady state solution.

initial_n_pp

A vector the same length as the w_full slot that describes the abundance of the background background resource at each weight.

n

Exponent of maximum intake rate.

p

Exponent of metabolic cost.

lambda

Exponent of resource spectrum.

q

Exponent for volumetric search rate.

f0

Initial feeding level.

kappa

Magnitude of resource spectrum.

A

Abundance multipliers.

linecolour

A named vector of colour values, named by species. Used to give consistent colours to species in plots.

linetype

A named vector of linetypes, named by species. Used to give consistent colours to species in plots.

Details

'>MizerParams objects can be created using a range of MizerParams constructor methods.

Dynamic simulations are performed using the project method on objects of this class.

See Also

project MizerSim