mefa (version 2.0-1)

plot.mefa: Plotting Methods for Object of Class 'mefa'

Description

Various methods for plotting objects of class 'mefa'.

Usage

## S3 method for class 'mefa':
plot(x, stat = 1:4, type = c("bar", "rank"),
trafo = c("none", "log", "ratio"), ylab = NULL, xlab = NULL, show = TRUE, ...)
## S3 method for class 'mefa':
boxplot(x, stat = 1:4, ylab = NULL, xlab = NULL, show = TRUE, \dots)
## S3 method for class 'mefa':
image(x, segm=NULL, trafo=c("none", "log", "bins", "prab"), 
probs = seq(0, 1, 0.05), ordering = TRUE, reverse = TRUE, ylab = NULL, 
xlab = NULL, show = TRUE, ...)

Arguments

x

an object of class 'mefa'.

stat

numeric, to determine which characteristic to plot. 1: number of species in samples (default), 2: total number of indiwiduals in samples, 3: number of occurrences per taxa, 4 number of individuals per ta

type

character, "bar" produces barchart (default), "rank" ranked curves based on the characteristic defined by stat.

trafo

character, transformation of the plotted variable. "none": no transformation (default), "log": logarithmic transformation (base 10), "ratio": normalizes values by the maximum and rescales to the [0, 1] interval (usef

ylab, xlab

character to overwrite default label for the y and x axes. If NULL, than default labels are returned on the plot.

segm

if NULL the x$xtab matrix is used for plotting. Otherways, this defines the segment (one element in x$segm) for plotting (can be numeric or character with the name of the segment).

probs

numeric vector of probabilities with values in [0, 1] (passed internally to qvector).

ordering

logical, if TRUE (default) the samples-by-taxa matrix is ordered by row and columns sums, if FALSE row and columns are not rearranged.

reverse

logical, if the values to plot should be reversed (TRUE, default, original zero values are lightly, while higher values are strongly coloured) or not (FALSE). This is related to col argument of the generic function <

show

logical, produce a plot (TRUE) or not (FALSE). FALSE can be useful, if the returned plotted values are reused (e.g. the matrix returned invisibly image can be used by

...

further arguments to pass to plotting functions. See especially zlim and col arguments of the generic function image, and arguments for the generic function

Value

• All methods produce a plot if show = TRUE, and return the plotted values if show = FALSE without plotting them.

encoding

UTF-8

Details

plot returns barchart, or ranked curve of summary statistics (number of species, individuals in samples, number of occurrences or abundence of taxa) based on the x$xtab matrix of the 'mefa' objects. These walues are basically returned by summary.mefa.

boxplot returns box-and-whiskers plots for the summary statistics based on matrices for each segments in x$segm.

image creates a grid of colored rectangles with colors corresponding to the values in the segment defined by the argument segm. If ordering = TRUE, the ordering of the segment will be based on the x$xtab matrix and not on the matrix for the segment itself. This is due to better comparison among segments.

References

Sólymos{Solymos} P. 2008. mefa: an R package for handling and reporting count data. Community Ecology 9, 125--127.

http://mefa.r-forge.r-project.org/

See Also

image, plot, boxplot, filled.contour, par, heat.colors, heat.colors, topo.colors, terrain.colors, rainbow

Examples

data(DOLINAcounts, DOLINAsamples, DOLINAtaxa)
x <- mefa(stcs(DOLINAcounts), DOLINAsamples, DOLINAtaxa)
## Histograms
par(mfrow=c(2,2))
plot(x, 1)
plot(x, 2)
plot(x, 3)
plot(x, 4)
par(mfrow=c(1,1))
## Ranked curves
par(mfrow=c(2,2))
plot(x, 1, type="rank")
plot(x, 2, type="rank")
plot(x, 3, type="rank")
plot(x, 4, type="rank")
par(mfrow=c(1,1))
## Boxplot for segments
par(mfrow=c(2,2))
boxplot(x, 1)
boxplot(x, 2)
boxplot(x, 3)
boxplot(x, 4)
par(mfrow=c(1,1))
## Image (levelplot)
## comparing all and the segments
par(mfrow=c(1,3))
image(x, trafo = "bins", main = "All segments")
image(x, segm = 1, trafo = "bins", main = dimnames(x)$segm[1])
image(x, segm = 2, trafo = "bins", main = dimnames(x)$segm[2])
par(mfrow=c(1,1))