plotCDF2: Compare cumulative abundance or biomass distributions from two objects

Description

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 = 1,
  biomass = TRUE,
  total = FALSE,
  resource = FALSE,
  background = TRUE,
  highlight = NULL,
  normalise = TRUE,
  log_x = TRUE,
  log_y = FALSE,
  log = NULL,
  size_axis = c("w", "l"),
  ...
)

Value

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

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. The default power = 1 gives the biomass density, whereas power = 2 gives the biomass density with respect to logarithmic size bins.
biomass: Only used if power argument is missing. Then biomass = TRUE is equivalent to power=1 and biomass = FALSE is equivalent to power=0
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 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.

Details

plotlyCDF2() is the interactive plotly version.

Examples

Run this code

# \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")
# }