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

In pwoodworth-jefcoats/Size-Based-Modeling: Mizer With The Effects Of Temperature Included

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.

Details

therMizerParams objects can be created using a range of therMizerParams constructor methods.

Dynamic simulations are performed using the project_therMizer 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 the mizer vignette, Table 2, for 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

ontogenetic_migration

An array (realm x species x w) that holds the proportion of time each species spends in a given realm by size

exposure

An array (realm x species) that holds the exposure of each species by each realm

Note

The therMizerParams 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 therMizerParams objects are consistent in terms of number of species and number of size classes.

Although it is possible to build a therMizerParams object by hand it is not recommended and several constructors are available.

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

See Also

project_therMizer therMizerSim

pwoodworth-jefcoats/Size-Based-Modeling documentation built on Sept. 15, 2023, 8:13 a.m.