Plot mizer arrays

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). plotHover() creates an interactive version of the same figure.

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.

The resource classes ArrayResourceBySize and ArrayTimeByResourceBySize work the same way, except that they hold a single spectrum rather than one per species.

To compare two mizer arrays in a single plot, use plot2(). To show the relative difference between two arrays, use plotRelative(). To add an array to an existing plot, use addPlot(). All three, and animate(), have methods for every mizer array class.

All methods return a ggplot2 object, unless return_data = TRUE, in which case they return the underlying data frame instead. plotHover() returns a plotly object.

Arguments used by all methods:

species: Character vector of species to include. NULL (default) means all species.
highlight: Name or vector of names of the species to be highlighted.
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.
background: A boolean value that determines whether background species are included. Ignored if the model does not contain background species. Default is TRUE.
return_data: If TRUE, return the data frame instead of the plot.
log_x: If TRUE, use a log10 x-axis. The default depends on the method; see its own help page.
log_y: If TRUE, use a log10 y-axis. The default depends on the method; see its own help page.
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.
y_ticks: The approximate number of ticks desired on the y axis.

Additional arguments for plot.ArraySpeciesBySize() and plot.ArrayTimeBySpeciesBySize():

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. Densities are transformed to match the chosen axis.
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.

Additional argument for plot.ArrayTimeBySpecies():

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).

Additional argument for plot.ArrayTimeBySpeciesBySize() and plot.ArrayTimeByResourceBySize():

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

See the individual method help pages for each method's exact arguments and defaults: plot.ArraySpeciesBySize(), plot.ArrayTimeBySpecies(), plot.ArrayTimeBySpeciesBySize(), plot.ArrayResourceBySize(), plot.ArrayTimeByResourceBySize().

Examples

# \donttest{
plot(getEncounter(NS_params))
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.

plot(getFeedingLevel(NS_params), species = c("Cod", "Herring"))
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.

plot(getPredMort(NS_params), species = c("Cod", "Herring"),
     size_axis = "l")
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.

plot(getBiomass(NS_sim))

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

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

plot(getFMort(NS_sim), time = 2010)

plot(getResourceMort(NS_params))
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.

plot(initialNResource(NS_params))
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.

plot(NResource(NS_sim))

# }

Details

See also

Examples