convert_plot_density_axis: Express plotting data on the requested size axis

Description

Converts the size coordinate of the plotting data to the requested axis and, when the values are a density, multiplies them by the Jacobian that restates them in the density measure that axis calls for (see density_target_measure()). Values that are not a density are left alone.

Usage

convert_plot_density_axis(
  plot_dat,
  params,
  size_axis,
  density_wrt = NA_character_,
  per_log_size = NULL,
  species_col = "Species",
  value_col = 2
)

Value

The plotting data with its size coordinate, and where called for its values, expressed for the requested axis. The size coordinate is the first column.

Arguments

plot_dat: A data frame of plotting data with a w column and a species column.
params: A MizerParams object providing the weight-length parameters.
size_axis: Either "w" (weight) or "l" (length).
density_wrt: The measure the values are a density with respect to, see density_measures. NA (the default) means the values are not a density.
per_log_size: Whether to express the values per logarithmic size. NULL (the default) keeps whichever the values already are.
species_col: Name of the column identifying the species. Default is "Species".
value_col: Name or index of the value column. Defaults to the second column.

Details

Anything involving a length is a per-species quantity, because the weight-length relationship is, so rows whose species is not one of the model's species — the "Total" row, for instance — are dropped when a length is needed. Going from a density per size to one per logarithmic size needs no length, and keeps those rows.