Compare two mizer arrays in a single 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,
  name1 = "First",
  name2 = "Second",
  species = NULL,
  log_x,
  log_y,
  log = NULL,
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  y_ticks = 6,
  ...
)

Arguments

x

The first of two compatible mizer array objects to compare. Can be an ArraySpeciesBySize, ArrayTimeBySpecies, or ArrayTimeBySpeciesBySize object.

y

The second mizer array object, compatible with x.

name1, name2

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

species

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

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.

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 used by only some of the methods:

For ArraySpeciesBySize and ArrayTimeBySpeciesBySize methods:

all.sizes

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

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.

llim

A numeric vector of length two providing lower and upper limits for the length (x) axis when size_axis = "l". Use NA to refer to the existing minimum or maximum.

size_axis

Whether to plot size as weight ("w", default) or length ("l"), using the allometric weight-length relationship.

For ArrayTimeBySpecies methods:

tlim

A numeric vector of length two providing lower and upper limits for the time axis, e.g. c(1980, 2000). Use NA to apply no limit at that end. Default is c(NA, NA).

For ArrayTimeBySpeciesBySize methods:

time

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

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{
plot2(getEncounter(NS_params), getEncounter(NS_params))

# }