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Write assessment summary to a csv file

Source: R/reporting_functions.R
write_summary_table.Rd

Creates a data frame summarising the assessment of each time series and writes it to a csv file. The summary includes:

  • meta-data such as the monitoring location and number of years of data for each time series

  • the fitted values in the last monitoring year with associated upper one-sided 95% confidence limits

  • the trend assessments (p-values and trend estimates)

  • the status assessments (if there any thresholds)

  • (optionally) a symbology summarising the trend (shape) and status (colour) of each time series. This is experimental.

Usage

write_summary_table(
  assessment_obj,
  output_file = NULL,
  output_dir = ".",
  export = TRUE,
  collapse_AC = NULL,
  extra_output = NULL,
  symbology = NULL,
  determinandGroups = NULL,
  append = FALSE
)

Arguments

assessment_obj

An assessment object resulting from a call to run_assessment.

output_file

The name of the output csv file. If using NULL, the file will be called biota_summary.csv, sediment_summary.csv or water_summary.csv as appropriate. By default the file will be written to the working directory. If a file name is provided, a path to the output file can also be provided (e.g. using file.path). The `output_dir“ option can also be used to specify the output file directory.

output_dir

The output directory for output_file. The default is the working directory. Any file path provided in output_file, will be appended to output_dir. The resulting output directory must already exist.

export

Logical. TRUE (the default) writes the summary table to a csv file. FALSE returns the summary table as an R object (and does not write to a csv file).

collapse_AC

A names list of valid assessment criteria that allows assessment criteria of the same 'type' to be reported together. See details.

extra_output

A character vector specifying extra summary metrics to be included in the output. Currently only recognises "power" to give the seven power metrics computed for lognormally distributed data. Defaults to NULL; i.e. no extra output.

symbology

Experimental. Specifies the output symbology. Currently assumes the thresholds are presented in increasing magnitude of environmental risk.

determinandGroups

optional, a list specifying labels and levels to label the determinands

append

Logical. FALSE (the default) overwrites any existing summary file. TRUE appends data to it, creating it if it does not yet exist.

Value

a summary object, when export is FALSE