plotCDF: Plot cumulative abundance or biomass distributions

Description

plotCDF() plots the cumulative distribution over body size from small to large sizes. It uses the same spectra data preparation as plotSpectra(): the number density is multiplied by w^power and then integrated over size. With normalise = TRUE, each curve is divided by its final value so that it ends at 1.

Usage

plotCDF(
  object,
  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"),
  return_data = FALSE,
  ...
)

Value

A ggplot2 object, unless return_data = TRUE, in which case a data frame with the four variables 'w' (or 'l' if size_axis = "l"), 'value', 'Species', 'Legend' is returned. plotlyCDF() returns a plotly object.

Arguments

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.

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.

return_data

A boolean value that determines whether the formatted data used for the plot is returned instead of the plot itself. Default is FALSE.

...

Further arguments used by only some of the methods:

For MizerSim methods:

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.
geometric_mean: If TRUE then the average of the abundances over the time range is a geometric mean instead of the default arithmetic mean.

Details

Unlike for plotSpectra(), the only choice that matters here is biomass: whether to accumulate numbers or biomass. Whether a density is expressed with respect to size or with respect to logarithmic size makes no difference to its integral, because the change of variable cancels the factor of the weight, and so plotCDF() does not accept per_log_size = TRUE.

plotlyCDF() is the interactive plotly version. To compare cumulative distributions from two objects, use plotCDF2().

Examples

Run this code

# \donttest{
plotCDF(NS_params, species = c("Cod", "Herring"))
plotCDF(NS_sim, power = 0, normalise = FALSE)
# }