IBI: Compute the Index of Biotic Integrity (IBI) and IBI condition...

In SCCWRP/SQOUnified: Tools for calculating SQO scores based on three Lines of Evidence (Benthic, Tox, Chem)

Compute the Index of Biotic Integrity (IBI) and IBI condition category.

Description

The IBI compares the values of four different metrics to the ranges expected under reference conditions. Each metric that is outside of the reference range increases the IBI score by one. Therefore, if all four metrics were inside the reference range, the score would be 0. Conversely, if all four metrics were outside the reference range, the value would be 4.

Usage

IBI(benthic_data)

Arguments

BenthicData

a data frame with AT LEAST the following information with these headings: StationID - an alpha-numeric identifier of the location; Replicate - a numeric identifying the replicate number of samples taken at the location; SampleDate - the date of sample collection; Latitude - latitude in decimal degrees; Longitude - longitude in decimal degrees. Make sure there is a negative sign for the Western coordinates; Species - name of the fauna, ideally in SCAMIT ed12 format, do not use sp. or spp., use sp only or just the Genus. If no animals were present in the sample use NoOrganismsPresent with 0 abundance; Abundance - the number of each Species observed in a sample; Salinity - the salinity observed at the location in PSU, ideally at time of sampling.

Details

The IBI compares the values of four different metrics to the ranges expected under reference conditions. Each metric that is outside of the reference range increases the IBI score by one. Therefore, if all four metrics were inside the reference range, the score would be 0. Conversely, if all four metrics were outside the reference range, the value would be 4.

The data needed to calculate the IBI are: (1) the total number of taxa, (2) the total number of mollusc taxa, (3) the abundance of Notomastus sp., and (4) the number of sensitive taxa.

The total numnber of taxa, number of mollusc taxa, and abundance of Notomastus sp. can be obtained directly from the data. The list of sensitive species should be based on the species list for Southern California Marine Bays and the percentage of sensitive taxa present is calulated as:

\% \textrm{sensitive taxa} = (\textrm{number of sensistive taxa} / \textrm{total number of taxa}) \times 100

The value for each metric is then compared to a reference range for that metric (Table 2). The IBI score is set to zero before comparison to the reference range. For each metric that is out of the reference range (above or below), the IBI score goes up by one.

<Include Table 2>

The IBI score is then compared to condition category thresholds (Table 3) in order to determine the IBI category and score.

<Include Table 3>

Examples

data(benthic_sampledata)
IBI(BenthicData)

SCCWRP/SQOUnified documentation built on Nov. 3, 2024, 12:54 a.m.