forams (version 1.0)

abc: Abundance and Biomass Comparison Method

Description

This function performs the ABC and W statistic calculation.

Usage

abc(df)
abc.plot(X, xlim = c(0, ceiling(log(length(X$Accum.Abund)))),
  ylim = c(0, 100), yaxp = c(0, 100, 10), lty.bio = 'dotted',
  lty.abu = 'solid', lwd = 2, col.bio = 'black', col.abu = 'black',
  xlab = expression('Species Rank'~(Log[e]~Scale)),
  ylab = 'Cumulative Dominance %', leg = TRUE, W = TRUE,
  col.pol = "#f5f5f5", ...)

Value

An abc object has the fallowing elements:Accum.AbunThe cumulative percentage of abundance contribution.Accum.BiomassThe cumulative percentage of biomass contribution.BiAiBiomass - Abundance calculation results.W.StatThe result of the W statistic calculation.attr(, "row.names")Taxa labels.

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. The plot produces a two lines plot with a ln abscissa and uses the axis function, so a complete customization (i.e. side) of the axes is not possible at this moment.

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

data(NB)
MyABC <- abc(NB)
abc.plot(MyABC)
## To generate an taxa based data frame ordered alphabeticaly, use:
Table <- as.data.frame(MyABC[1:3])
rownames(Table) <- attr(MyABC, 'row.names')
Table <- Table[sort(rownames(Table)),] 
## This table doesn't contain the result of the W statistic