MizerParams-class: MizerParams

Description Details Slots Note See Also

Description

A class to hold the parameters for a size based model. These parameters include the model species, their life history parameters and the size ranges of the model.

Details

MizerParam 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

intake_max:

An array (species x size) that holds the maximum intake for each species at size

search_vol:

An array (species x size) that holds the search volume for each species at size

activity:

An array (species x size) that holds the activity for each species at size

std_metab:

An array (species x size) that holds the standard metabolism for each species at size

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

rr_pp:

A vector the same length as the w_full slot. The size specific growth rate of the background spectrum

cc_pp:

A vector the same length as the w_full slot. The size specific carrying capacity of the background spectrum

species_params:

A data.frame to hold the species specific parameters (see Details)

interaction:

The species specific interaction matrix.

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 species by gear and species size

catchability:

An array (gear x species) that holds the catchability of each species by each gear

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 MizerParam 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 29, 2017, 5:15 p.m.