forams (version 2.0-6)

plot.abc: 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 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.

Author

Rodrigo Aluizio

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.

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)