forams (version 1.0)

she: SHE Analysis

Description

This function implements the SHE method in community abundance datasets.

Usage

she(df, method = "abundance")
she.plot(X, pch = 20, pcol = "black", pcex = 1,
  pbg = "black", lcol = "black",   lwd = 1, lty = "dotted",
  ylab = expression("ln" ~ italic(E)), bty = "l", ...)

Value

Srichness values.Hshannon diversity values.Eequitability values.N or Lnumber of specimens (N) or sites rank based on specimens frequency (L).attr(, "row.names")sites labels.

Details

This method is intended to determine boundaries between abundance biozones, based in raw abundance (SHEbi) or in frequency (SHEbip) (Buzas et al. 1998, Wilson et al. 2010). The plot produces a line plot with points on 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

Buzas, M.A. & Hayek, L.A.C. (1998). SHE analysis for biofacies identification. Journal of Foraminiferal Research 28 (3), 233-239. Wilson, B., Dawe, R., Gopee, A., Grant, S., Kissoon, A., Young, T., Noon, C., McLean, A. & Singh, K. (2010). Determining Boundaries between Abundance Biozones Using Minimal Equipment. International Journal of Ecology 2010, 1-14.

Examples

data(LF)
MySHE <- she(LF, "abun")
she.plot(MySHE)
## To generate an site based data frame ordered alphabeticaly, use:
Table <- as.data.frame(MySHE[1:4])
rownames(Table) <- attr(MySHE, 'row.names')
Table <- Table[sort(rownames(Table)),]