Plot the relative difference between the potential fisheries productivity rates of two models or two different size ranges in the same plot

This function creates a barplot with the percent change in potential fisheries productivity between either: (1) two different mizerParams objects (2) two different size ranges. If comparing two mizerParams objects, they must have the same species groups.

Usage

plotProductivityRelative(
  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,
  ...
)

plotlyProductivityRelative(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 groups to be selected. Optional. By default all target groups are selected. A vector of groups names, or a numeric vector with the groups indices, or a logical vector indicating for each group 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 plotProductivity

object

An object of class MizerParams or MizerSim

start_time

The first time to be plotted. Default is the beginning of the time series.

end_time

The last time to be plotted. Default is the end of the time series.

facet

A boolean value indicating whether to facet the result plot by species group. Defaults to TRUE.

total

A boolean value that determines whether the total productivity from all species is plotted as well. Default is TRUE.

min_fishing_l

parameters be passed to getProductivity(). The minimum length (cm) of fished individuals for productivity estimates. Defaults to 7 cm.

max_fishing_l

parameters be passed to getProductivity(). The maximum length (cm) of fished individuals for productivity estimates. Defaults to max length.

Value

A ggplot2 object, unless return_data = TRUE, in which case a data frame with the the productivity for each Species Group by model is returned as well as another column called rel_diff that gives the relative difference between the two values.

Details

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

The individual productivity rates are calculated by the plotProductivity() function which is passed all additional arguments you supply. See plotProductivity() 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(), plotBiomass(), plotProductivity(), plotRefuge(), plotRelativeContribution(), plotSpectraRelative(), plotTotalAbundance(), plotTotalBiomass(), plotTotalBiomassRelative(), plotVulnerable()