CalcPSI: Proportion of Sediment-sensitive Invertebrates

In aquaMetrics/aquaMetrics: Freshwater Biotic indices

Description

A sediment-sensitive macro-invertebrate metric that provides a proxy to describe the extent to which the surface of river bed are composed, or covered by sediments. It can be calculated at Taxonomic Levels 3, 4 & 5.

Usage

CalcPSI(data, season = NULL, TL = 3L)

Arguments

data	A dataframe containing standardised taxa with at least eight columns and in the specified order. Extra columns can be added, but they must be related to Sampling Point. See 'Details'
season	Optional. An integer vector containing up to 7 elements, from 1L to 7L. It is only needed when the input data frame contains Season and Year instead of Sample ID and Date. See 'Details' for more info about input columns.
TL	An integer vector containing up to 3 elements which would represent the taxonomic level to calulate PSI at.

Details

The input dataframe data must contain a minimum of eight columns in the specified order: TL (Taxonomic Level), Site, Season or Sample ID, Year or Date (Date object), Maitland Code, Maitland Name, Abundance, Infered (Code returned by the function StandardiseRawTaxa which can be declared as 0 if StandardiseRawTaxa is not used).

If the data frame contains Season and Year instead of Sample ID / Date, the season parameter must be a vector of the form c(1L, 3L, 5L), indicating which seasons, and combination of seasons, must be computed.

The available codes for Season and a general description of Taxonomic Levels are defined in the main help page of the aquaMetrics package.

Value

A dataframe with the following columns: TL, Site, Season or Sample ID, Year or Date (Date object), Infered, extra columns - if any, PSIScore and R.Bed.Condition.

Note

More extra columns can be added to aggregate data by different criteria, i.e., other than season or Sample ID. For doing so you must fill all season fields with a dummy value: 1.Thus, the aggregation would disregard season/Sample ID as an aggregation column.

Please note that this application applies some changes to standardised families included in Ancylidae and Oligochaeta to accomodate the results to those displayed in RIVPACS database (even though it may not be technically correct).

References

Extence C., Chadd R., England J., Dunbar M., Wood P., Taylor, E. 2013. The assessment of fine sediment accumulation in rivers using macro-invertebrate community response. River Res Applic. 29: 17-55.

See Also

StandardiseRawTaxa

Examples

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