Compare two mizer array objects in one plot

plot2() compares two compatible mizer array objects in a single ggplot. Colours identify species or groups, and linetype identifies which object the values came from.

Usage

plot2(x, y, ...)

# S3 method for class 'ArraySpeciesBySize'
plot2(
  x,
  y,
  name1 = "First",
  name2 = "Second",
  species = NULL,
  all.sizes = 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 'ArrayTimeBySpecies'
plot2(
  x,
  y,
  name1 = "First",
  name2 = "Second",
  species = NULL,
  start_time = NULL,
  end_time = NULL,
  y_ticks = 6,
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  log_x = FALSE,
  log_y = TRUE,
  log = NULL,
  ...
)

# S3 method for class 'ArrayTimeBySpeciesBySize'
plot2(
  x,
  y,
  name1 = "First",
  name2 = "Second",
  species = NULL,
  time = NULL,
  all.sizes = FALSE,
  log_x = TRUE,
  log_y = FALSE,
  log = NULL,
  wlim = c(NA, NA),
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  y_ticks = 6,
  ...
)

Arguments

x, y

Two compatible mizer array objects of the same class.

...

Further arguments (currently unused).

name1, name2

Labels for the two objects, used in the linetype legend.

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.

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.

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

A ggplot2 object.

See also

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

Examples

# \donttest{
enc <- getEncounter(NS_params)
plot2(enc, enc, name1 = "Original", name2 = "Changed")

plot2(getBiomass(NS_sim), getBiomass(NS_sim), species = "Cod")

# }