Compare cumulative abundance or biomass distributions from two objects

plotCDF2() compares cumulative distributions from two MizerParams or MizerSim objects in a single plot. Colours identify species or groups and linetype identifies the object.

Usage

plotCDF2(
  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 = FALSE,
  background = TRUE,
  highlight = NULL,
  normalise = TRUE,
  log_x = TRUE,
  log_y = FALSE,
  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 number density is multiplied by the weight raised to power before being integrated. An alternative to the biomass argument, with which it must agree if that is given as well. The default is power = 1, the cumulative biomass.
biomass: Whether to plot the cumulative biomass (TRUE, the default) or the cumulative abundance (FALSE).
per_log_size: Only FALSE (the default) is accepted; see Details.
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 FALSE.
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.
normalise: If TRUE (default), plot the cumulative proportion. If FALSE, plot the cumulative abundance, biomass, or other unnormalised integral.
log_x: If TRUE (default), use a log10 x-axis.
log_y: If TRUE, use a log10 y-axis. Default is FALSE.
log: Character string specifying which axes should use a log10 scale, in the same form as the base plot() argument. 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.
...: Additional arguments passed to plotCDF() for preparing the cumulative distribution data, for example time_range or geometric_mean for MizerSim objects.

Value

A ggplot2 object. plotlyCDF2() returns a plotly object.

Details

plotlyCDF2() 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)
plotCDF2(sim1, sim2, "Original", "Effort = 0.5")

# }