Plot the total productivity for each species Group

When called with a MizerParams object the total steady state productivity is plotted for each group. When called with a MizerSim object the productivity of each species through time is plotted.

Usage

plotProductivity(
  object,
  start_time = NULL,
  end_time = NULL,
  facet = TRUE,
  species = NULL,
  total = TRUE,
  min_fishing_l = NULL,
  max_fishing_l = NULL,
  include_repro = FALSE,
  include_inverts = FALSE,
  return_data = FALSE,
  ...
)

plotlyProductivity(object, species = NULL, ...)

Arguments

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.
species: The species to be selected. Optional. By default all 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.
total: A boolean value that determines whether the total productivity from all species is plotted as well. Default is TRUE.
min_fishing_l: The minimum length (cm) of fished individuals for productivity estimates. Defaults to 7 cm.
max_fishing_l: The maximum length (cm) of fished individuals for productivity estimates. Defaults to max length.
include_repro: A boolean value that indicates whether to include energy for reproduction in productivity estimates. Defaults to using getEGrowthTime() if FALSE or mizer's mizer::getEReproAndGrowth() if TRUE.
include_inverts: A boolean value that determines whether the "inverts" species group is included. Default is FALSE, since invertebrate productivity is typically not relevant to fishing yield. Only takes effect when species is not explicitly provided.
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.
...: unused

Value

A ggplot2 object, unless return_data = TRUE, in which case a data frame with the the productivity for each Species Group is returned.

Potential fisheries productivity

Productivity refers to the rate at which fish biomass is produced and available for harvest in a given area over a given period of time. Productivity cannot be measured in situ.

The productivity $P_i(w)$ of species group $i$ is given by

$$P_i(w) = \int_w^{w+dw} N_i(w)\, g_i(w) \, dw.$$

$N_i(w)$ is the abundance density $(no./m^{2})$ and $g_i(w)$ is the energy rate available for growth after metabolism, movement, and reproduction have been accounted for $(grams/year)$. The productivity is calculated for all fish in the size range between min_fishing_length and max_fishing_length. These lengths can be the same for all groups or can be specified as a vector with one value for each species in the model. The minimum length defaults to $7 cm$ regardless of species group and maximum length defaults to the maximum weight in the model.

Plot the total productivity for each species Group

Usage

Arguments

Value

Potential fisheries productivity

See also