plotSpectra: Plot the abundance spectra

Description Usage Arguments Details Value Examples

Description

What is plotted is the number density multiplied by a power of the weight, with the power specified by the power argument.

Plot the abundance spectra using a MizerSim object.

Plot the abundance spectra using a MizerParams object.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
plotSpectra(object, ...)

## S4 method for signature 'MizerSim'
plotSpectra(object, species = NULL,
  time_range = max(as.numeric(dimnames(object@n)$time)),
  min_w = min(object@params@w)/100, ylim = c(NA, NA), power = 1,
  biomass = TRUE, print_it = TRUE, total = FALSE, plankton = TRUE,
  background = TRUE, ...)

## S4 method for signature 'MizerParams'
plotSpectra(object, species = NULL,
  min_w = min(object@w)/100, ylim = c(NA, NA), power = 1,
  biomass = TRUE, print_it = TRUE, total = FALSE, plankton = TRUE,
  background = TRUE, ...)

Arguments

object

An object of class MizerSim or MizerParams.

...

Other arguments (currently unused)

species

Name or vector of names of the species to be plotted. By default all species are plotted.

time_range

The time range (either a vector of values, a vector of min and max time, or a single value) to average the abundances over. Default is the final time step. Ignored when called with a MizerParams object.

min_w

Minimum weight to be plotted (useful for truncating the background spectrum). Default value is a hundredth of the minimum size value of the community.

ylim

A numeric vector of length two providing limits of for the y axis. Use NA to refer to the existing minimum or maximum. Any values below 1e-20 are always cut off.

power

The abundance is plotted as the number density times the weight raised to power. The default power = 1 gives the biomass density, whereas power = 2 gives the biomass density with respect to logarithmic size bins.

biomass

Obsolete. Only used if power argument is missing. Then biomass = TRUE is equivalent to power=1 and biomass = FALSE is equivalent to power=0

print_it

Display the plot, or just return the ggplot2 object. Defaults to TRUE

total

A boolean value that determines whether the total over all species in the system is plotted as well. Default is FALSE

plankton

A boolean value that determines whether plankton is included. Default is TRUE.

background

A boolean value that determines whether background species are included. Ignored if the model does not contain background species. Default is TRUE.

Details

When called with a MizerSim object, the abundance is averaged over the specified time range (a single value for the time range can be used to plot a single time step). When called with a MizerParams object the initial abundance is plotted.

Value

A ggplot2 object

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
## Not run: 
data(NS_species_params_gears)
data(inter)
params <- MizerParams(NS_species_params_gears, inter)
sim <- project(params, effort=1, t_max=20, t_save = 2)
plotSpectra(sim)
plotSpectra(sim, min_w = 1e-6)
plotSpectra(sim, time_range = 10:20)
plotSpectra(sim, time_range = 10:20, power = 0)
plotSpectra(sim, species = c("Cod", "Herring"), power = 1)

## End(Not run)

drfinlayscott/mizer documentation built on May 18, 2018, 9:20 a.m.