Plot the relative difference in between the total biomasses of each each species within a size range at steady state

This functions creates a barplot with the relative change in biomass of each species within a size range between either (1) two different mizerParams objects (two models) or (2) two different size ranges.

Usage

plotTotalBiomassRelative(
  object1,
  object2,
  diff_method,
  species = NULL,
  min_fishing_l1 = NULL,
  max_fishing_l1 = NULL,
  min_fishing_l2 = NULL,
  max_fishing_l2 = NULL,
  return_data = FALSE,
  ...
)

plotlyTotalBiomassRelative(object1, object2, diff_method, ...)

Arguments

object1

First MizerParams or MizerSim object.

object2

Second MizerParams or MizerSim object.

diff_method

The method to calculate the relative change between models. If percent_change, the percent change is calculated relative to the value from object 1 with formula 100*(new-old)/old. If rel_diff the relative difference is returned given by (new - old)/(old + new).

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.

min_fishing_l1

Optional. The minimum length (cm) of fished individuals for model 2. Defaults to 7cm. A parameter passed to getProductivity().

max_fishing_l1

Optional. The maximum length (cm) of fished individuals for model 1. Defaults to max length. A parameter passed to getProductivity().

min_fishing_l2

Optional. The minimum length (cm) of fished individuals for model 2. Defaults to 7cm. A parameter passed to getProductivity().

max_fishing_l2

Optional. The maximum length (cm) of fished individuals for model 1. Defaults to max length. A parameter passed to getProductivity().

return_data

A boolean value that determines whether the formatted data used for the plot is returned instead of the plot itself. Default value is FALSE.

...

Arguments passed on to plotTotalBiomass

object

An object of class MizerParams or MizerSim. If a MizerSim object is provided, the biomass at the last time step is used.

min_fishing_l

The minimum length (cm) for biomass estimates. Defaults to smallest size.

max_fishing_l

The maximum length (cm) of for biomass estimates. Defaults to max length.

Value

A ggplot2 object, unless return_data = TRUE, in which case a data frame with the the total steady state biomass for each functional group by model is returned as well as another column called rel_diffthat gives the relative difference between the two values.

Details

This function is usually used in conjunction with plotProductivityRelative() to check for decoupling between biomass and productivity.

The individual productivity rates are calculated by the plotTotalBiomass() function which is passed all additional arguments you supply. See plotTotalBiomass() for more details.

To compare between different size ranges, use the min_fishing_l1 and max_fishing_l1 arguments for the first size range and the min_fishing_l2and max_fishing_l2 arguments for the second.

See also

plotBiomass(), plot2TotalBiomass(), plotTotalBiomassRelative(), plotProductivity(), plot2Productivity(), plotProductivityRelative()

Other plotting functions: plot2Productivity(), plot2TotalBiomass(), plotDegScale(), plotDegradationScale(), plotProductivity(), plotProductivityRelative(), plotRefugeDensity(), plotRefugeProfile(), plotRelativeContribution(), plotSpectraChange(), plotTotalAbundance(), plotTotalBiomass(), plotVulnerable()