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)