Calculate the proportion of large fish

Calculates the proportion of large fish through time in the MizerSim class within user defined size limits. The default option is to use the whole size range. You can specify minimum and maximum size ranges for the species and also the threshold size for large fish. Sizes can be expressed as weight or size. Lengths take precedence over weights (i.e. if both min_l and min_w are supplied, only min_l will be used). You can also specify the species to be used in the calculation. This function can be used to calculate the Large Fish Index. The proportion is based on either abundance or biomass.

getProportionOfLargeFish(
  sim,
  species = 1:nrow(sim@params@species_params),
  threshold_w = 100,
  threshold_l = NULL,
  biomass_proportion = TRUE,
  ...
)

Arguments

sim	A MizerSim object
species	Numeric or character vector of species to include in the calculation.
threshold_w	the size used as the cutoff between large and small fish. Default value is 100.
threshold_l	the size used as the cutoff between large and small fish.
biomass_proportion	a boolean value. If TRUE the proportion calculated is based on biomass, if FALSE it is based on numbers of individuals. Default is TRUE.
...	Arguments passed on to get_size_range_array min_w Smallest weight in size range. Defaults to smallest weight in the model. max_w Largest weight in size range. Defaults to largest weight in the model. min_l Smallest length in size range. If supplied, this takes precedence over min_w. max_l Largest length in size range. If supplied, this takes precedence over max_w.

Value

A vector containing the proportion of large fish through time

See also

Other functions for calculating indicators: getCommunitySlope(), getMeanMaxWeight(), getMeanWeight()

Examples

if (FALSE) {
data(NS_species_params_gears)
data(inter)
params <- newMultispeciesParams(NS_species_params_gears, inter)
sim <- project(params, effort=1, t_max=10)
getProportionOfLargeFish(sim)
getProportionOfLargeFish(sim, species=c("Herring","Sprat","N.pout"))
getProportionOfLargeFish(sim, min_w = 10, max_w = 5000)
getProportionOfLargeFish(sim, min_w = 10, max_w = 5000, threshold_w = 500)
getProportionOfLargeFish(sim, min_w = 10, max_w = 5000,
    threshold_w = 500, biomass_proportion=FALSE)
}