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Compare two mizer arrays in a single plot

Source: R/ArraySpeciesBySize-class.R, R/ArrayTimeBySpecies-class.R, R/ArrayTimeBySpeciesBySize-class.R, and 1 more
plot2.Rd

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,
  highlight = NULL,
  y_ticks = 6,
  ...
)

Arguments

x

The first of two compatible mizer array objects to compare. Can be an ArraySpeciesBySize, ArrayTimeBySpecies, ArrayTimeBySpeciesBySize, ArrayResourceBySize or ArrayTimeByResourceBySize 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. A resource array holds a single spectrum, so this argument is not used by the resource methods, which warn if it is set.

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 and for the resource classes.

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 is plotted as well. The total is the total of everything the array holds, every species and every size, whatever is drawn. Default is FALSE. Not used by the resource methods, which warn if it is set.

background

A boolean value that determines whether background species are included. Ignored if the model does not contain background species. Default is TRUE. Not used by the resource methods, which warn if it is set.

highlight

Name or vector of names of the species to be highlighted with a thicker line.

y_ticks

The approximate number of ticks desired on the y axis.

...

Further arguments used by only some of the methods:

For the ArraySpeciesBySize, ArrayTimeBySpeciesBySize, ArrayResourceBySize and ArrayTimeByResourceBySize methods:

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.

For the ArraySpeciesBySize and ArrayTimeBySpeciesBySize methods:

all.sizes

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

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 of each species, or of the resource, see resource_params().

per_log_size

For an array that holds a density, whether to plot it per logarithmic size (TRUE) rather than per size (FALSE). The default, NULL, plots the density as it stands. Unlike size_axis this needs no weight-length relationship, so it is available for the resource classes too. An error for an array that does not hold a density.

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 the ArrayTimeBySpeciesBySize and ArrayTimeByResourceBySize methods:

time

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

Value

A ggplot2 object.

See also

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

Examples

# \donttest{
plot2(getEncounter(NS_params), getEncounter(NS_params))

plot2(getResourceMort(NS_params), getResourceMort(NS_params))

# }