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Plot the biomass of species and unstructured components through time

Source: R/plots.R
plotBiomass.Rd

After running a projection, the biomass of each species and each unstructured component can be plotted against time. The biomass is calculated within user defined size limits (min_w, max_w, min_l, max_l, see get_size_range_array()).

Usage

plotBiomass(
  sim,
  species = NULL,
  start_time,
  end_time,
  y_ticks = 6,
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  highlight = NULL,
  return_data = FALSE,
  ...
)

plotlyBiomass(
  sim,
  species = NULL,
  start_time,
  end_time,
  y_ticks = 6,
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  highlight = NULL,
  ...
)

Arguments

sim

An object of class MizerSim

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.

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.

y_ticks

The approximate number of ticks desired on the y axis.

ylim

A numeric vector of length two providing lower and upper limits for the y axis. Use NA to refer to the existing minimum or maximum. Any values below 1e-20 are always cut off.

total

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

background

A boolean value that determines whether background species are included. Ignored if the model does not contain background species. Default is TRUE.

highlight

Name or vector of names of the species to be highlighted.

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

Value

A ggplot2 object, unless return_data = TRUE, in which case a data frame with the four variables 'Year', 'Biomass', 'Species', 'Legend' is returned.

Examples

# \donttest{
NWMed_sim <- project(NWMed_params, t_max = 15, effort = 0.6)
#> Error in project(NWMed_params, t_max = 15, effort = 0.6): could not find function "project"
plotBiomass(NWMed_sim, species = c("Hake", "Red mullet"))
#> Error in plotBiomass(NWMed_sim, species = c("Hake", "Red mullet")): object 'params' not found
plotBiomass(NWMed_sim, start_time = 5, end_time = 15)
#> Error in plotBiomass(NWMed_sim, start_time = 5, end_time = 15): object 'params' not found

# Returning the data frame
fr <- plotBiomass(NWMed_sim, return_data = TRUE)
#> Error in plotBiomass(NWMed_sim, return_data = TRUE): object 'params' not found
str(fr)
#> Error in eval(expr, envir, enclos): object 'fr' not found
# }