getProportionOfLargeFish: Calculate the proportion of large fish

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Calculate the proportion of large fish

Description

Calculates the proportion of large fish in a MizerSim or MizerParams object 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 length. Lengths take precedence over weights (i.e. if both min_l and min_w are supplied, only min_l will be used, and if threshold_l is supplied it takes precedence over threshold_w). 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.

Usage

getProportionOfLargeFish(
  object,
  species = NULL,
  threshold_w = 100,
  threshold_l = NULL,
  biomass_proportion = TRUE,
  ...
)

Arguments

object	A MizerSim or MizerParams object
species	The species to be selected. Optional. By default all target species are selected. A vector of species names, or a numeric vector with the species indices, or a logical vector indicating for each species whether it is to be selected (TRUE) or not.
threshold_w	The weight used as the cutoff between large and small fish. Default value is 100.
threshold_l	The length used as the cutoff between large and small fish. If supplied, this takes precedence over threshold_w.
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, or a single value if called with a MizerParams object.

See Also

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

Examples

lfi <- getProportionOfLargeFish(NS_sim, min_w = 10, max_w = 5000,
                                threshold_w = 500)
years <- c("1972", "2010")
lfi[years]
getProportionOfLargeFish(NS_sim)[years]
getProportionOfLargeFish(NS_sim, species=c("Herring","Sprat","N.pout"))[years]
getProportionOfLargeFish(NS_sim, min_w = 10, max_w = 5000)[years]
getProportionOfLargeFish(NS_sim, min_w = 10, max_w = 5000,
    threshold_w = 500, biomass_proportion = FALSE)[years]
getProportionOfLargeFish(NS_params)

mizer documentation built on Aug. 31, 2026, 5:08 p.m.