Plotting outputs

Many mizer functions return values that depend on species and either size or time. plot() creates a ggplot2 figure with one line for each species showing the values against size or against time (depending on the type of output). ggplotly() creates an interactive version of the same figure.

Usage

# S3 method for class 'ArraySpeciesBySize'
plot(
  x,
  species = NULL,
  all.sizes = FALSE,
  highlight = NULL,
  return_data = FALSE,
  log_x = TRUE,
  log_y = FALSE,
  log = NULL,
  wlim = c(NA, NA),
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  y_ticks = 6,
  ...
)

# S3 method for class 'ArraySpeciesBySize'
ggplotly(x, ...)

# S3 method for class 'ArrayTimeBySpecies'
plot(
  x,
  species = NULL,
  start_time = NULL,
  end_time = NULL,
  y_ticks = 6,
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  highlight = NULL,
  log_x = FALSE,
  log_y = TRUE,
  log = NULL,
  return_data = FALSE,
  ...
)

# S3 method for class 'ArrayTimeBySpecies'
ggplotly(x, ...)

# S3 method for class 'ArrayTimeBySpeciesBySize'
plot(
  x,
  species = NULL,
  time = NULL,
  all.sizes = FALSE,
  highlight = NULL,
  return_data = FALSE,
  log_x = TRUE,
  log_y = FALSE,
  log = NULL,
  wlim = c(NA, NA),
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  y_ticks = 6,
  ...
)

# S3 method for class 'ArrayTimeBySpeciesBySize'
ggplotly(x, ...)

Arguments

x

An ArraySpeciesBySize or ArrayTimeBySpecies object.

species

Character vector of species to include. NULL (default) means all species.

all.sizes

If FALSE (default), values outside a species' size range (w_min to w_max) are removed. Only applies to ArraySpeciesBySize.

highlight

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

return_data

If TRUE, return the data frame instead of the plot.

log_x

If TRUE, use a log10 x-axis. Default is TRUE for size spectra and FALSE for time series.

log_y

If TRUE, use a log10 y-axis. Default is FALSE for ArraySpeciesBySize and TRUE for ArrayTimeBySpecies.

log

Character string specifying which axes should use log10 scales, in the same form as the base plot() argument. For example, "x", "y", "xy" or "". If supplied, this overrides log_x and log_y.

wlim

A numeric vector of length two providing lower and upper limits for the weight (x) axis. Use NA to refer to the existing minimum or maximum. Only applies to ArraySpeciesBySize.

ylim

A numeric vector of length two providing lower and upper limits for the value (y) axis. Use NA to refer to the existing minimum or maximum.

total

A boolean value that determines whether the total over all selected 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.

y_ticks

The approximate number of ticks desired on the y axis.

...

Further arguments (currently unused).

start_time

The first time to be plotted. Default (NULL) is the beginning of the time series. Only applies to ArrayTimeBySpecies.

end_time

The last time to be plotted. Default (NULL) is the end of the time series. Only applies to ArrayTimeBySpecies.

time

The time to display. Default (NULL) is the final time step. Only applies to ArrayTimeBySpeciesBySize.

Value

plot() returns a ggplot2 object, unless return_data = TRUE, in which case a data frame is returned.

ggplotly() returns a plotly object.

Details

This works because the mizer functions that give values that depend on species and size return an ArraySpeciesBySize object and those that give values that depend on species and time return an ArrayTimeBySpecies object. These objects have attributes that store the name of the value, its units, and a reference to the MizerParams object that the value was computed from. This allows the plots to be automatically labelled and coloured appropriately.

See also

Other plotting functions: addPlot(), animate.ArrayTimeBySpeciesBySize(), plot2(), plotBiomass(), plotCDF(), plotCDF2(), plotDiet(), plotFMort(), plotFeedingLevel(), plotGrowthCurves(), plotMizerParams, plotMizerSim, plotPredMort(), plotRelative(), plotSpectra(), plotSpectra2(), plotSpectraRelative(), plotYield(), plotYieldGear(), plotting_functions

Examples

# \donttest{
plot(getEncounter(NS_params))

plot(getFeedingLevel(NS_params), species = c("Cod", "Herring"))

# }
# \donttest{
ggplotly(getEncounter(NS_params))

# }
# \donttest{
plot(getBiomass(NS_sim))

plot(getBiomass(NS_sim), species = c("Cod", "Herring"), total = TRUE)

plot(getYield(NS_sim), species = c("Cod", "Herring"))

# }
# \donttest{
ggplotly(getBiomass(NS_sim))

# }
# \donttest{
plot(getFMort(NS_sim))

plot(getFMort(NS_sim), time = 2010)

# }
# \donttest{
ggplotly(getFMort(NS_sim))

# }