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Graphical summaries of an assessment

Source: R/graphics_functions.R
plot_assessment.Rd

Generates a series of assessment plots for each time series. The plots are exported as either png or pdf files.

Usage

plot_assessment(
  assessment_obj,
  subset = NULL,
  output_dir = ".",
  file_type = c("data", "index", "auxiliary"),
  file_format = c("png", "pdf"),
  auxiliary = "default"
)

Arguments

assessment_obj

An assessment object resulting from a call to run_assessment

subset

An optional vector specifying which timeseries are to be plotted. An expression will be evaluated in the timeSeries component of assessment_obj; use series to identify individual timeseries.

output_dir

The output directory for the assessment plots (possibly supplied using file.path). The default is the working directory. The output directory must already exist.

file_type

A character vector specifying the types of assessment plot. The default c("data", "index", "auxiliary") produces three plots for each time series. See details

file_format

A character string specifying Whether the files should be png (the default) or pdf.

auxiliary

A character string specifying the auxiliary variables plotted if file_type = "auxiliary". See details

Value

A series of png or pdf files with graphical summaries of an assessment.

Details

Types of assessment plots

  • file_type = "data" shows the raw data with the fitted trend and pointwise two-sided 90% confidence bands

  • file_type = "index" shows annual indices that summarise the data for each year with the fitted trend and pointwise two-sided 90% confidence bands

  • file_type = "auxiliary" shows the raw data and key auxiliary variables see below)

Auxiliary variables

The default (auxiliary = "default") is to plot the following variables:

  • biota: determinand concentration, LNMEA (mean length), DRYWT% (dry weight content), LIPIDWT% (lipi weight content)

  • sediment: non-normalised determinand concentration, normalised determinand concentration, AL (aluminium concentration), CORG (organic carbon content)

  • water: no plots are generated at present

For biota, the determinand concentration will always be plotted, but it is possible to change the three auxiliary variables. For example, to plot WTMEA (mean weight) instead of LIPIDWT% you would set auxiliary = c("LNMEA", "WTMEA", "DRYWT%). For this to work, WTMEA must previously have been specified as an auxiliary variable for the determinand in question using the biota_auxliary column in the determinand reference table. At present, there must always be three auxiliary variables for biota.

For sediment, the non-normalised determinand concentration and the normalised determinand concentration will always be plotted, but it is possible to change the two auxiliary variables. For example, for metals in sediment, you might set auxiliary = c("AL", "LI") to plot aluminium and lithium concentrations instead of aluminium and organic carbon concentrations. Again, for this to work, LI must previously have been specified as an auxiliary variable for the determinand in question using the sediment_auxliary column in the determinand reference table. At present, there must always be two auxiliary variables for sediment.

At present, plots for only a limited range of auxiliary variables are supported. More flexibility in these plots, such as changing the number of auxiliary variables, is desirable and will emerge in due course.