abc: Abundance and Biomass Comparison Method

Description Usage Arguments Details Value Note Author(s) References Examples

Description

This function performs the ABC and W statistic calculation.

Usage

1
  abc(df, Perm, confInt)

Arguments

df

a numeric data frame containing the abundance and biomass as columns and taxa as rows. NAs are not allowed.

Perm

the number of permutations to be realized for calculating the Confidence Interval.

confInt

the Confidence interval range (90%, 95% or 99%, any other values will cause an error).

Details

The function generates a list of cumulative percentage values of Abundance, Biomass and Biomass - Abundance for each taxon (Warwick 1986), which are used for W statistic (Warwick & Clarke 1994) calculation and posterior k-dominance curve plotting.

Value

An abc S4 object has the fallowing elements:

An abc slot with:

Accum.Abun

The cumulative percentage of abundance contribution.

Accum.Biomass

The cumulative percentage of biomass contribution.

BiAi

Biomass - Abundance calculation results.

and a W.Stat slot with:

W.Stat

The result of the W statistic calculation and its Confidence Interval.

Note

The list elementes are ordered according to Accum.Abun, but the calculation is based on the contribution decreasing order, independently of any of the variables or taxon.

Author(s)

Rodrigo Aluizio

References

Warwick, R.M. (1986). A new method for detecting pollution effects on marine macrobenthic communities. Marine Biology 92 (4), 557-562.

Warwick, R.M., & Clarke, K.R. (1994). Relearning the ABC: taxonomic changes and abundance/biomass relationships in disturbed benthic communities. Marine Biology 118 (4), 739-744.

Examples

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data(NB)
MyABC <- abc(NB)
plot(MyABC)

Example output



forams documentation built on May 29, 2017, 9:26 a.m.