algae.IBIs: Generate IBI report

In SCCWRP/algaeMetrics: Algae metrics and IBIs

Description

Returns a report containing D18, S2, and H20 IBIs, along with relevant QC metrics

Usage

algae.IBIs(data, metadata = NULL)

Arguments

data	A data frame containing necessary algae data. See details
metadata	A data frame contain taxonomic lookup data. If null (default), uses metadata distributed with this package

Details

To be valid, your data should contain the following columns:

• StationCode: The name of the site where the sample was taken

• SampleDate: Date the sample was taken

• Replicate: Identifier for multiple samples at a given site

• SampleTypeCode: Acceptable values: Epiphyte, Macroalgae, Microalgae, Qualitative

• FinalID: Taxa names. These names must match exactly with a FinalID in the metadata, or the row will be discarded

• BAResult: Results for Integrated and Epiphyte fractions

• Result: Results for Macro/Microalgae algae

• ActualOrganismCount: Sample-wide count

A SampleID column, while not required, is strongly encouraged. If missing, it will be generated as a concatenation of columns StationCode, SampleDate, and Replicate.

Value

A data frame containing the following:

• SampleID

• S2: S2 soft algae IBI score

• S2.QCmin: Lowest QC score among metrics used in S2

• D18: D18 diatom IBI score

• D18.QCmin: Lowest QC score among metrics used in D18

• DH20: H20 hybrid (soft algae and diatom) IBI score

• DH20.QCmin: Lowest QC score among metrics used in DH20

• DiatomSamplePresent: Indicates whether diatom count was non-zero

• SoftAlgaeSampleTypesPresent: List of fractions present in sample

• QualPresent: Indicates whether qualitative fraction was present

• DiatomCountFlag: Flags for low diatom count (threshold of 450)

• SoftAlgaeEntityCountFlag: Flags for low entity count (threshold of 225)

• PurgedTaxa: Number of rows discarded due to FinalID not matching any entry in metadata

Examples

data(algaeSamples)
ibiReport <- algae.IBIs(algaeSamples)

SCCWRP/algaeMetrics documentation built on Oct. 27, 2021, 2:29 a.m.