CalcDARLEQ: Diatom Assessment of River and Lake Ecological Quality

In aquaMetrics/aquaMetrics: Freshwater Biotic indices

Description

DARLEQ is one of the methods used to evaluate phytobentos (algae) in rivers and lakes. Assessment is focused on the diatoms, a large and diverse group of algae using a metric called the Trophic Diatom Index (TDI), based on the principle that different diatoms have different environmental preferences.

Usage

CalcDARLEQ(data = NULL, metric = NULL, version = "latest")

Arguments

data	A dataframe containing diatoms taxa with eight columns in the specified order (naming of the columns is not important): Type (one character, either "L" -lake- or "R" -river-), SampleID, SiteID, Date (Date object), Taxon Code, Taxon name, Abundance, Alkalinity.
metric	Specifies which metric to compute. It can take any of the following values: "rivers", "lakes" or "all".
version	Specifies which version of the metric to compute. It can take any of the following values: "latest" (TDI4/LTDI2), "previous" (TDI3/LTDI1) or "all".

Details

This routine does also compute the uncertainty associated to the ecological status assessments of lakes and rivers. Calculation of the confidence of class (CoC) and risk of misclassification is based in a polynomial fitting of the SD of EQR as a function of mean EQR. The parameters of those polynomial curves are the same found in DARLEQ2 software (Kelly et al, 2014). This polynomial function makes it possible to compute an expected SD for any given EQR and by relating this SD to the position of the status class boundaries enables the confidence to be calculated.

Value

A list containing up to 10 dataframes, depending on the metric and version parameters.

• rivers: Dataframe containing river results for every metric computed (TDI3/TDI4).

• tdi4.CoC: Dataframe containing the confidence of classification for the metric TDI4.

• tdi3.CoC: Dataframe containing the confidence of classification for the metric TDI3.

• taxa.lacking.tdi4: Dataframe containing all those taxa which lack TDI4 scores in the database. It will be empty if all taxa find a match.

• taxa.lacking.tdi3: Dataframe containing all those taxa which lack TDI3 scores in the database. It will be empty if all taxa find a match.

• lakes: Dataframe containing lake results for every metric computed (LTDI1/LTDI2).

• ltdi2.CoC: Dataframe containing the confidence of classification for the metric LTDI2.

• ltdi1.CoC: Dataframe containing the confidence of classification for the metric LTDI1.

• taxa.lacking.ltdi2: Dataframe containing all those taxa which lack LTDI2 scores in the database. It will be empty if all taxa find a match.

• taxa.lacking.ltdi1: Dataframe containing all those taxa which lack LTDI1 scores in the database. It will be empty if all taxa find a match.

References

Bennion H., Kelly M.G., Juggins S., Yallop M., Burgess A., Jamieson J., Krokowski J. 2014. Assessment of ecological status in UK lakes using benthic diatoms. Freshwater Science. 33(2): 639-654.

Ellis J., Adriaenssens V. 2006. Uncertainty estimation for monitoring results by the WFD biological classification tools. WFD REport: GEHO1006BLOR-E-P. Environment Agency (UK)

Kelly M.G., Juggins S., Bennion, H., Burgess A., Yallop M., Hirst H., King L., Jamieson B.J., Guthrie R., Rippey B. 2008. Use of diatoms for evaluating ecological status in UK freshwaters. Science Report: SC030103/SR4. Environment Agency (UK)

Kelly M., Juggins S., Guthrie R., Pritchard S., Jamieson J., Rippey B., Hirst H., Yallop M. 2008. Assessment of ecological status in UK rivers using diatoms. Freshwater Biology. 56: 403-422

Kelly M., Bennion H., Burgess A., Ellis J., Juggins S., Guthrie R., Jamieson J., Adrianssens V., Yallop M. 2009. Uncertainty in ecological status assessments of lakes and rivers using diatoms. Hydrobiologia. 633: 5-15.

Kelly M., Juggins S., Bennion H., Burgess A., Yallop M., Hirst H., Jamieson J., Guthrie R., Rippey B. 2014. Software for Freshwater Status Classification using benthic diatoms (Version 2.0.1) Available from http://www.wfduk.org/sites/default/files/Media/Characterisation of the water environment/Biological Method Statements/DARLEQ2Setup.zip

WFD - UK Technical Advisory Group. 2014. Phytobentos - Diatoms for Assessing River and Lake Ecological Quality (Lake DARLEQ2). WFD - UKTAG.

WFD - UK Technical Advisory Group. 2014. Phytobentos - Diatoms for Assessing River and Lake Ecological Quality (River DARLEQ2). WFD - UKTAG.

Examples

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aquaMetrics/aquaMetrics documentation built on May 6, 2019, 7:26 a.m.