mizer (version 1.0.1)

getProportionOfLargeFish: Calculate the proportion of large fish

Description

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 method can be used to calculate the Large Fish Index. The proportion is based on either abundance or biomass.

Usage

getProportionOfLargeFish(object, ...)
# S4 method for MizerSim
getProportionOfLargeFish(object,
  species = 1:nrow(object@params@species_params), threshold_w = 100,
  threshold_l = NULL, biomass_proportion = TRUE, ...)

Arguments

object

An object of class MizerSim.

...

Other arguments to select the size range of the species to be used in the calculation (min_w, max_w, min_l, max_l).

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.

Value

An array containing the proportion of large fish through time

Examples

# NOT RUN {
data(NS_species_params_gears)
data(inter)
params <- MizerParams(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)
# }