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SHE Analysis

Source: R/AllGenerics.R, R/plot_diversity.R
she.Rd

SHE Analysis

Usage

she(object, ...)

# S4 method for class 'matrix'
she(
  object,
  unbiased = FALSE,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes,
  panel.first = NULL,
  panel.last = NULL,
  legend = list(x = "right"),
  ...
)

# S4 method for class 'data.frame'
she(
  object,
  unbiased = FALSE,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes,
  panel.first = NULL,
  panel.last = NULL,
  legend = list(x = "right"),
  ...
)

Arguments

object

A \(m \times p\) numeric matrix or data.frame of count data (absolute frequencies giving the number of individuals for each category, i.e. a contingency table). A data.frame will be coerced to a numeric matrix via data.matrix().

...

Further graphical parameters to be passed to graphics::lines() and graphics::points().

unbiased

A logical scalar: should the bias-corrected estimator be used (see index_shannon())?

main

A character string giving a main title for the plot.

sub

A character string giving a subtitle for the plot.

ann

A logical scalar: should the default annotation (title and x, y and z axis labels) appear on the plot?

axes

A logical scalar: should axes be drawn on the plot?

frame.plot

A logical scalar: should a box be drawn around the plot?

panel.first

An an expression to be evaluated after the plot axes are set up but before any plotting takes place. This can be useful for drawing background grids.

panel.last

An expression to be evaluated after plotting has taken place but before the axes, title and box are added.

legend

A list of additional arguments to be passed to graphics::legend(); names of the list are used as argument names. If NULL, no legend is displayed.

Value

she() is called for its side-effects: it results in a graphic being displayed (invisibly returns object).

Details

If samples are taken along a gradient or stratigraphic section, breaks in the curve may be used to infer discontinuities.

This assumes that the order of the matrix rows (from \(1\) to \(n\)) follows the progression along the gradient/transect.

References

Buzas, M. A. & Hayek, L.-A. C. (1998). SHE analysis for biofacies identification. Journal of Foraminiferal Research, 1998, 28(3), 233-239.

Hayek, L.-A. C. & Buzas, M. A. (2010). Surveying Natural Populations: Quantitative Tools for Assessing Biodiversity. Second edition. New York: Columbia University Press.

See also

Other diversity measures: heterogeneity(), occurrence(), plot_diversity, plot_rarefaction, profiles(), rarefaction(), richness(), similarity(), simulate(), turnover()

Author

N. Frerebeau

Examples

## Data from Conkey 1980, Kintigh 1989
data("cantabria")

## SHE analysis
she(cantabria)