Compare abundance and biomass spectra from two objects

plotSpectra2() compares the abundance spectra from two MizerParams or MizerSim objects in a single plot. Colours identify species or groups and linetype identifies the object.

Usage

plotSpectra2(
  object1,
  object2,
  name1 = "First",
  name2 = "Second",
  species = NULL,
  wlim = c(NA, NA),
  llim = c(NA, NA),
  ylim = c(NA, NA),
  power = NULL,
  biomass = NULL,
  per_log_size = NULL,
  total = FALSE,
  resource = TRUE,
  background = TRUE,
  highlight = NULL,
  log_x = TRUE,
  log_y = TRUE,
  log = NULL,
  size_axis = c("w", "l"),
  ...
)

Arguments

object1: First MizerParams or MizerSim object.
object2: Second MizerParams or MizerSim object.
name1, name2: Labels for the two objects, used in the linetype legend.
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.
wlim: A numeric vector of length two providing lower and upper limits for the w axis. Use NA for the default: the lower default is min(params@w) / 100 when resource = TRUE (to show some resource below the fish grid) or min(params@w) when resource = FALSE; the upper default is max(params@w_full). Data is filtered to this range and the axis limits are set accordingly.
llim: A numeric vector of length two providing lower and upper limits for the length axis when size_axis = "l". Use NA to auto-scale to the data range. Data is filtered to this range and the axis limits are set accordingly.
ylim: A numeric vector of length two providing lower and upper limits for the y axis. Use NA to auto-scale to the data range. Values below 1e-20 are always filtered out from the data regardless of ylim[1]. Data above ylim[2] is filtered and the upper axis limit is set accordingly.
power: The abundance is plotted as the number density times the weight raised to power. An alternative to the biomass and per_log_size arguments, with which it must agree if they are given as well; see Details. The default is power = 1, the biomass density.
biomass: Whether to plot the biomass density (TRUE, the default) or the number density (FALSE).
per_log_size: Whether to plot the density with respect to logarithmic size (TRUE) or with respect to size (FALSE, the default).
total: A boolean value that determines whether the total is plotted as well. The total is the total of everything the object holds — every species and the resource — whatever is drawn, so it does not move when species, resource or background change. 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 by being plotted with thicker lines.
log_x: If TRUE (default), use a log10 x-axis.
log_y: If TRUE (default), use a log10 y-axis.
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.
size_axis: Whether to plot size as weight ("w", default) or length ("l"), using the allometric weight-length relationship. Spectrum densities and their units are transformed to match the chosen axis.
...: Additional arguments passed to plotSpectra() for preparing the spectra data, for example time_range or geometric_mean for MizerSim objects.

Value

A ggplot2 object. plotlySpectra2() returns a plotly object.

Details

plotlySpectra2() is the interactive plotly version.

Examples

# \donttest{
sim1 <- project(NS_params, t_max = 10, progress_bar = FALSE)
sim2 <- project(NS_params, effort = 0.5, t_max = 10, progress_bar = FALSE)
plotSpectra2(sim1, sim2, "Original", "Effort = 0.5")

# }