plot.fcs2EQR: Plot EQR Samples

Description Usage Arguments Details See Also

View source: R/plot.fcs2EQR.R

Description

Plots a series of EQR variables or the corresponding probabilities of each WFD class.

Usage

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## S3 method for class 'fcs2EQR'
plot(
  x,
  survey = 1,
  species = 1,
  boundaries,
  type = "density",
  title,
  adjust = 1,
  ...
)

Arguments

x

an object of class "fcs2EQR" containing Monte Carlo EQR samples, as calculated from fcs2SingleEQR, fcs2JointEQR or fcs2JointAndSingleEQR.

survey

index specifying which surveys (or water bodies etc if surveys joined) to plot.

species

index specifying which species to plot. This should correspond to the plots defined by survey.

boundaries

a vector of length 4 giving the EQR boundaries separating the classes Bad, Poor, Good, Moderate and High. These are used only to colour the plot. If missing, regularly spaced boundaries of c(0.2, 0.4, 0.6, 0.8) are used with a warning. If NULL and type = "density", the plot is not coloured.

type

either "density" or 1 for a density estimate of the EQR variable, or "class" or 2 to plot the probability of each class (as produced by fcs2Classify).

title

an optional character vector giving the title for each plot. Should have one entry per selection in survey and species.

adjust

the bandwidth adjustment for the density estimate of the EQR, if type = "density". See density for further details.

...

further arguments that are passed to either plot (if type = "density") or barplot otherwise.

Details

Plot EQR Samples

See Also

fcs2SingleEQR, fcs2JointEQR or fcs2JointAndSingleEQR for producing "fcs2EQR" objects.

fcs2InteractivePrediction can be used to interactively view how the EQR changes with covariates.


aquaMetrics/fcs2 documentation built on Aug. 21, 2021, 12:55 p.m.