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Diversity Profiles

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

Diversity Profiles

Usage

profiles(object, ...)

# S4 method for class 'matrix'
profiles(
  object,
  alpha = seq(from = 0, to = 4, by = 0.04),
  color = NULL,
  symbol = FALSE,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes,
  panel.first = NULL,
  panel.last = NULL,
  legend = list(x = "topright"),
  ...
)

# S4 method for class 'data.frame'
profiles(
  object,
  alpha = seq(from = 0, to = 4, by = 0.04),
  color = NULL,
  symbol = FALSE,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes,
  panel.first = NULL,
  panel.last = NULL,
  legend = list(x = "topright"),
  ...
)

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()

alpha

A numeric vector giving the values of the alpha parameter.

color

A vector of colors (will be mapped to the rownames of object). If color is a named a named vector, then the colors will be associated with the rownames of object. Ignored if set to FALSE.

symbol

A specification for the line type (will be mapped to the rownames of object). If symbol is a named a named vector, then the line types will be associated with the rownames of object. Ignored if set to FALSE.

xlab, ylab

A character vector giving the x and y axis labels.

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

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

Details

If the profiles cross, the diversities are non-comparable across samples.

References

Tóthmérész, B. (1995). Comparison of Different Methods for Diversity Ordering. Journal of Vegetation Science, 6(2), 283-290. doi:10.2307/3236223 .

See also

Other diversity measures: diversity(), evenness(), heterogeneity(), occurrence(), plot.DiversityIndex(), plot.RarefactionIndex(), rarefaction(), richness(), she(), similarity(), simulate(), turnover()

Author

N. Frerebeau

Examples

## Replicate fig. 1 of Tóthmérész 1995
spc <- matrix(
  data = c(33, 29, 28, 5, 5, 0, 0, 42, 30, 10,
           8, 5, 5, 0, 32, 21, 16, 12, 9, 6, 4),
  nrow = 3, byrow = TRUE, dimnames = list(c("Z", "B", "C"), NULL)
)

profiles(spc, color = color("bright"))