Plots the number density multiplied by a power of the weight, with the power
specified by the power
argument.
plotSpectra( object, species = NULL, time_range, wlim = c(NA, NA), ylim = c(NA, NA), power = 1, biomass = TRUE, total = FALSE, resource = TRUE, background = TRUE, highlight = NULL, return_data = FALSE, ... ) plotlySpectra( object, species = NULL, time_range, wlim = c(NA, NA), ylim = c(NA, NA), power = 1, biomass = TRUE, total = FALSE, resource = TRUE, background = TRUE, highlight = NULL, ... )
object | An object of class MizerSim or MizerParams. |
---|---|
species | The species to be selected. Optional. By default all target species are selected. A vector of species names, or a numeric vector with the species indices, or a logical vector indicating for each species whether it is to be selected (TRUE) or not. |
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. |
wlim | A numeric vector of length two providing lower and upper limits for the w axis. Use NA to refer to the existing minimum or maximum. |
ylim | A numeric vector of length two providing lower and upper limits 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 |
biomass |
|
total | A boolean value that determines whether the total over all species in the system is plotted as well. Note that even if the plot only shows a selection of species, the total is including all species. Default is FALSE. |
resource | A boolean value that determines whether resource 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. |
highlight | Name or vector of names of the species to be highlighted. |
return_data | A boolean value that determines whether the formatted data used for the plot is returned instead of the plot itself. Default value is FALSE |
... | Other arguments (currently unused) |
A ggplot2 object, unless return_data = TRUE
, in which case a data
frame with the four variables 'w', 'value', 'Species', 'Legend' is
returned.
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.
Other plotting functions:
animateSpectra()
,
plot,MizerSim,missing-method
,
plotBiomass()
,
plotDiet()
,
plotFMort()
,
plotFeedingLevel()
,
plotGrowthCurves()
,
plotPredMort()
,
plotYieldGear()
,
plotYield()
,
plotting_functions
# \donttest{ params <- NS_params sim <- project(params, effort=1, t_max=20, t_save = 2, progress_bar = FALSE) plotSpectra(sim)plotSpectra(sim, time_range = 10:20)plotSpectra(sim, time_range = 10:20, power = 0)#> 'data.frame': 1024 obs. of 4 variables: #> $ w : num 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 ... #> $ value : num 1.83e+10 6.92e+09 1.30e+11 1.46e+10 1.69e+08 ... #> $ Species: chr "Sprat" "Sandeel" "N.pout" "Herring" ... #> $ Legend : chr "Sprat" "Sandeel" "N.pout" "Herring" ...# }