calc_Metric_EQR: Calculate diatom water quality metrics, EQRs and WFD class...

In nsj3/darleq3: Diatom-based water quality indices

Calculate diatom water quality metrics, EQRs and WFD class for samples, and uncertainties of site classification

Description

Calculate diatom water quality metrics, EQRs and WFD class for samples, and uncertainties of site classification

Usage

calc_Metric_EQR(x, metrics = "TDI5LM", truncate_EQR = TRUE, verbose = TRUE)

Arguments

x	list containing diatom and header (environmental) data. This will usually be the data structure imported by read_DARLEQ.
metrics	character vector of metric codes. Currently one or more of the following: "TDI3", "TDI4", "TDI5LM" (for river LM TDI calculations), "TDI5NGS" for river NGS metric, "LTDI1", "LTDI2" for lake LM TDI metric or "DAMLM" for river diatom acidification metric.
truncate_EQR	logical to truncate EQRs at 1.0
verbose	logical to indicate should function stop immediately on error (TRUE) or return a simpleError (FALSE). Defaults to TRUE.

Details

This is a wrapper function to calc_Metric and calc_EQR that calculates multiple metrics, EQRs and WFD classes. The output can be saved to an Excel file using function save_DARLEQ.

Value

A list with a named element for each metric calculated. Each element in the list is itself a list containing the output from calc_EQR (ie. the sample and site metrics, EQRs and WFD classes), and the job summary produced by calc_Metric.

Author(s)

Steve Juggins [e-mail]

References

Kelly, M., S. Juggins, R. Guthrie, S. Pritchard, J. Jamieson, B. Rippey, H. Hirst, and M. Yallop, Assessment of ecological status in UK rivers using diatoms. Freshwater Biology, 2008. 403-422.

Juggins, S., M. Kelly, T. Allott, M. Kelly-Quinn, and D. Monteith, A Water Framework Directive-compatible metric for assessing acidification in UK and Irish rivers using diatoms. Science of The Total Environment, 2016. 671-678.

Bennion, H., M.G. Kelly, S. Juggins, M.L. Yallop, A. Burgess, J. Jamieson, and J. Krokowski, Assessment of ecological status in UK lakes using benthic diatoms. Freshwater Science, 2014. 639-654.

Examples

fn <- system.file("extdata/DARLEQ2TestData.xlsx", package="darleq3")
d <- read_DARLEQ(fn, "Rivers TDI Test Data")
x <- calc_Metric_EQR(d)
save_DARLEQ(x, outFile="results.xlsx")

nsj3/darleq3 documentation built on Oct. 11, 2023, 4:37 a.m.