plot.abc: Plot function for Abundance and Biomass Comparison Method...

In forams: Foraminifera and Community Ecology Analyses

Plot function for Abundance and Biomass Comparison Method objects.

Description

This function is a customizable plot for the abundance and biomass lines from the ABC object.

Usage

## S4 method for signature 'abc'
plot(x, xlim = c(0, ceiling(log(length(x@abc$Accum.Abund)))),
     ylim = c(0, 100), yaxp = c(0, 100, 10), lty.bio = 'dotted',
     lty.abu = 'solid', lwd = 2, col.bio = 'black', col.abu = 'black',
     xlab = expression('Species Rank'~(Log[e]~Scale)),
     ylab = 'Cumulative Dominance %', leg = TRUE, W = TRUE, col.pol = '#f5f5f5',
     ...)

Arguments

x	an object of class abc.
xlim	the x limits (x1, x2) of the plot, defaults from 0 to the maximum value of x (in a log scale).
ylim	the y limits (x1, x2) of the plot, defaults to c(0, 100)
yaxp	a vector of the form c(y1, y2, n) giving the coordinates of the extreme tick marks and the number of intervals between tick-marks, defaults to c(0, 100, 10).
lty.bio	line type of the biomass curve, defaults to "dotted".
lty.abu	line type of the abundance curve, defaults to "solid".
lwd	the line width, a positive number, defaulting to 2.
col.bio	the line color of the biomass curve, defaulting to "black".
col.abu	the line color of the abundance curve, defaulting to "black".
xlab	a label for the x axis, defaults to expression('Species Rank'~(Log[e]~Scale)).
ylab	a label for the y axis, defaults to "Cumulative Dominance %".
leg	logical; if TRUE draws a legend at the bottomright part of the plotting area, defaults to TRUE.
W	logical; if TRUE draws the W statistics value at the topleft part of the plotting area, defaults to TRUE.
col.pol	the polygon filling color, defaults to "#f5f5f5".
...	other graphical parameters, see par for details.

Details

The plot produces a two lines plot with a ln abscissa and uses the axis function, so a complete customization (i.e. side) of the axes is not possible at this moment.

Note

For more details on other graphic prameters such as line and box types see par and plot.default.

Author(s)

Rodrigo Aluizio

References

Warwick, R.M. (1986). A new method for detecting pollution effects on marine macrobenthic communities. Marine Biology 92 (4), 557-562.

Warwick, R.M., & Clarke, K.R. (1994). Relearning the ABC: taxonomic changes and abundance/biomass relationships in disturbed benthic communities. Marine Biology 118 (4), 739-744.

Examples

data(NB)
MyABC <- abc(NB)
plot(MyABC)

forams documentation built on Aug. 24, 2023, 5:11 p.m.