BRI: Compute the benthic response index (BRI) score and BRI...

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

Compute the benthic response index (BRI) score and BRI condition category.

Description

The BRI is the abundance weighted pollution tolerance score of the organisms present in a benthic sample. The higher the BRI score, the more degraded the benthic community represented by the sample.

Usage

BRI(benthic_data)

Arguments

BenthicData

a data frame with the following 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;

Details

The BRI is the 4th root relative abundance weighted pollution tolerance score of the organisms present in a benthic sample. The higher the BRI score, the more degraded the benthic community represented by the sample.

Two types of data are needed to calculate the BRI:

(1) the abundance of each species (2) species-specific pollution tolerance score (aka, P Value)

Tolerance Values are stored in the Southern California SQO Species List provided with this coded. Species names are periodically updated by benthic experts.

The BRI is only calculated from those taxa with a tolerance score. The first step in the BRI calculation is to compute the 4th root of the abundance of each taxon in the sample that have an associated tolerance score The next step is to multiply the 4th root abundance value by the tolerance score for each taxon. The next step is to sum all of the 4th root abundance values in a given sample. The actual BRI score is calculated as:

\frac{\sum \left(\sqrt[p]{\textrm{Abundance}} \right) \times P}{\sum \sqrt[p]{\textrm{Abundance}}}

The last step is to convert the BRI score to condition category using the category thresholds listed in Table 5.

<Table 5. To be included in R markdown file>

Examples

data(benthic_sampledata) # load sample data
BRI(benthic_sampledata) # see the output

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