she {forams}

SHE Analysis

Description

This function implements the SHE method in community abundance datasets.

Usage

  she(df, method)

Arguments

df

a numerical data frame with samples as columns and taxa as rows.

method

the method to be used, ("abundance" or "frequency"), defaults to "abundance".

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 custom 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.

Value

S

richness values.

H

shannon diversity values.

E

equitability values.

N or L

number of specimens (N) or sites rank based on specimens frequency (L).

Note

This function implements great part of the process, but a small part must be caried out for the researcher when defining where to cut biozones before reruning the test. For more details on other graphic prameters see par.

Author(s)

Rodrigo Aluizio

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")
plot(MySHE)