forams (version 1.0)

fi: The FORAM Index

Description

This function implements the FORAM Index (FI) in community abundance datasets.

Usage

fi(df, groups)
fi.plot(X, ylim = c(1, 10), yaxp = c(1, 10, 9), xlab = 'Samples',
  ylab = 'FORAM Index', pch.urg = 25, pch.mrg = 21, pch.crg = 24,
  bg.urg = 'red', bg.mrg = 'yellow', bg.crg = 'green', pt.cex = 1,
  limits = TRUE, ...)

Value

A fi object has the fallowing elements:PlotOrdera numerical vector defining the sites plot order, only used for plotting.FIa numerical vector with the sites FORAM Index values.attr(, "row.names")the sites labels, also used durring plotting or table creation.

Details

This analysis is directed for health evaluation and monitoring of reef environments (Hallock et al. 2003) and it is based in foraminiferal total fauna methodology. The taxa classification that determines the groups are originally based on genera, but species data from literature or experiments will be accepted as well. The grouping factor must be composed solely by Ps (simbiont-bearing), Po (opportunistic), or Ph (other small heterotrophic) levels. NAs are not allowed. The plot uses the axis function, so a complete customization (i.e. side) of the axes is not possible at this moment, and some other parameters may show improperly if changed.

References

Hallock, P., Lidz, B.H., Cockey-Burkhard, E.M. & Donnelly, K.B. (2003). Foraminifera as bioindicators in coral reef assessment and monitoring: The foram index. Environmental monitoring and assessment 81, 221-238.

Examples

data(LF)
data(Factors)
MyFI <- fi(LF, Factors)
fi.plot(MyFI)
## To generate a site based data frame, use:
Table <- as.data.frame(MyFI[2])
rownames(Table) <- attr(MyFI, 'row.names')