| abc {forams} | R Documentation |
Abundance and Biomass Comparison Method
Description
This function performs the ABC and W statistic calculation.
Usage
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
data(NB)
MyABC <- abc(NB)
plot(MyABC)