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.

Usage

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

Arguments

sim

A MizerSim 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 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

lfi <- getProportionOfLargeFish(NS_sim, min_w = 10, max_w = 5000, 
                                threshold_w = 500)
years <- c("1972", "2010")
lfi[years]
#>      1972      2010 
#> 0.1425938 0.2573979 
getProportionOfLargeFish(NS_sim)[years]
#>      1972      2010 
#> 0.3115163 0.4441647 
getProportionOfLargeFish(NS_sim, species=c("Herring","Sprat","N.pout"))[years]
#>       1972       2010 
#> 0.06371869 0.21844009 
getProportionOfLargeFish(NS_sim, min_w = 10, max_w = 5000)[years]
#>      1972      2010 
#> 0.3474937 0.5662073 
getProportionOfLargeFish(NS_sim, min_w = 10, max_w = 5000,
    threshold_w = 500, biomass_proportion = FALSE)[years]
#>       1972       2010 
#> 0.00441820 0.01212436