validGearParams: Check validity of gear parameters and set defaults

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Check validity of gear parameters and set defaults

Description

The function returns a valid gear parameter data frame that can be used by setFishing() or it gives an error message.

Usage

validGearParams(gear_params, species_params)

Arguments

gear_params	Gear parameter data frame
species_params	Species parameter data frame

Details

The gear_params data frame is allowed to have zero rows, but if it has rows, then the following requirements apply:

• There must be columns species and gear and any species - gear pair is allowed to appear at most once. Any species that appears must also appear in the species_params data frame.

• There must be a sel_func column. If a selectivity function is not supplied, it will be set to "knife_edge".

• There must be a catchability column. If a catchability is not supplied, it will be set to 1.

• All the parameters required by the selectivity functions must be provided.

If gear_params is empty, then this function tries to find the necessary information in the species_params data frame. This restricts each species to be fished by only one gear. Defaults are used for information that can not be found in the species_params dataframe, as follows:

• If there is no gear column or it is NA then a new gear named after the species is introduced.

• If there is no sel_func column or it is NA then knife_edge is used.

• If there is no catchability column or it is NA then this is set to 1.

• If the selectivity function is knife_edge and no knife_edge_size is provided, it is set to w_mat.

The row names of the returned data frame are of the form "species, gear".

When gear_params is NULL and there is no gear information in species_params, then a gear called knife_edge_gear is set up with a knife_edge selectivity for each species and a knive_edge_size equal to w_mat. Catchability is set to 0.3 for all species.

Value

A valid gear parameter data frame

See Also

gear_params()

mizer documentation built on Oct. 17, 2024, 9:07 a.m.