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

Description Details Slots Note See Also

Description

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

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.

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, ψ_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, γ_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 μ_{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, κ w^{-λ}

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, θ_{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.

Note

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.

See Also

project MizerSim


mizer documentation built on May 1, 2018, 9:04 a.m.