emptyParams: Create empty MizerParams object of the right size

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Create empty MizerParams object of the right size

Description

An internal function. Sets up a valid MizerParams object with all the slots initialised and given dimension names, but with some slots left empty. This function is to be used by other functions to set up full parameter objects.

Usage

emptyParams(
  species_params,
  gear_params = data.frame(),
  no_w = 100,
  min_w = 0.001,
  max_w = NA,
  min_w_pp = 1e-12
)

Arguments

species_params	A data frame of species-specific parameter values.
gear_params	A data frame with gear-specific parameter values.
no_w	The number of size bins in the consumer spectrum.
min_w	Sets the size of the eggs of all species for which this is not given in the w_min column of the species_params dataframe.
max_w	The largest size of the consumer spectrum. By default this is set to the largest w_max specified in the species_params data frame.
min_w_pp	The smallest size of the resource spectrum.

Value

An empty but valid MizerParams object

Size grid

A size grid is created so that the log-sizes are equally spaced. The spacing is chosen so that there will be no_w fish size bins, with the smallest starting at min_w and the largest starting at max_w. For the resource spectrum there is a larger set of bins containing additional bins below min_w, with the same log size. The number of extra bins is such that min_w_pp comes to lie within the smallest bin.

Changes to species params

The species_params slot of the returned MizerParams object may differ from the data frame supplied as argument to this function because default values are set for missing parameters.

See Also

See newMultispeciesParams() for a function that fills the slots left empty by this function.

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