calc_EQR: Calculate EQRs and WFD status classes from diatom metric and...

Description Usage Arguments Value Author(s) References Examples

View source: R/calc_eqr.R

Description

Calculate EQRs and WFD status classes from diatom metric and sample environmental data

Usage

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calc_EQR(x, header, truncate_EQR = TRUE, verbose = TRUE)

Arguments

x

an object of class DIATOM_METRIC, usually the output from function calc_Metric.

header

data frame containing sample and site environmental information for calculating the expected value of the 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.

Value

A object of class DIATOM_EQR, a list with the following named elements:

EQR

data frame containing, for each sample, sample codes, water chemistry data and other columns from the header in original Excel file, metric and summary information from function calc_Metric, expected EQRs (eEQR), calculated EQRs, predicted WFD class, percentage diatoms in diagnostic ecological groups, and a flag to indicate missing or out of range environmental data.

Uncertainty

data frame containing, for each site, mean EQRS, predicted WFD class, and confidence of class (CoC) for each WFD class and HG/MPB boundary (CoCCHG, COCMPB), and risk of misclassification for the predicted class (ROM) and for the G/M boundary (ROM_GM)

.

Author(s)

Steve Juggins [email protected]

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

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fn <- system.file("extdata/DARLEQ2TestData.xlsx", package="darleq3")
d <- read_DARLEQ(fn, "Rivers TDI Test Data")
x <- calc_Metric(d$diatom_data, metric="TDI4")
eqr <- calc_EQR(x, d$header)
head(eqr$EQR)
head(eqr$Uncertainty)

nsj3/darleq3 documentation built on June 21, 2018, 8:01 a.m.