# getProportionOfLargeFish: Calculate the proportion of large fish In drfinlayscott/mizer: Multi-Species sIZE Spectrum Modelling in R

## 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.

Calculate the proportion of large fish from a `MizerSim` object.

## Usage

 ```1 2 3 4 5 6``` ```getProportionOfLargeFish(object, ...) ## S4 method for signature '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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13``` ```## 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) ## End(Not run) ```

drfinlayscott/mizer documentation built on May 18, 2018, 9:20 a.m.