plot.CAP: Draws cummulative abundance profiles

Description Usage Arguments Author(s) References See Also Examples

View source: R/plot.CAP.R

Description

Create plots used to inspect one or more cumulative abundance profiles.

Usage

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## S3 method for class 'CAP'
plot(x, sizes=NULL, species=NULL, plots=NULL, switchAxes=FALSE, 
                   add=FALSE, drawAxes = TRUE, xlab="", ylab="", type="s",...)
## S3 method for class 'stratifiedvegdata'
plot(x, sizes=NULL, species=NULL, plots=NULL, switchAxes=FALSE, 
                   add=FALSE, drawAxes = TRUE, xlab="", ylab="", type="s",...)

Arguments

x

An object returned from function CAP or an object of class stratifiedvegdata (see documentation for function stratifyvegdata).

sizes

A vector containing the size values associated to each size class. If NULL the y-axis will be defined using the size class order in x.

species

A vector of strings indicating the species whose profile is to be drawn. If NULL all species are plotted.

plots

A vector indicating the plot records whose profile is to be drawn. Can be a character vector (for plot names), a numeric vector (for plot indices) or a logical vector (for TRUE/FALSE selection). If NULL all plot records are plotted.

switchAxes

A flag indicating whether ordinate and abscissa axes should be interchanged.

add

A flag indicating whether profiles should be drawn on top of current drawing area. If add=FALSE a new plot is created.

drawAxes

A flag indicating whether axes should be drawn.

xlab

String label for the x axis.

ylab

String label for the y axis.

type

Type of plot to be drawn ("p" for points, "l" for lines, "s" for steps, ...).

...

Additional plotting parameters.

Author(s)

Miquel De Cáceres, Forest Science Center of Catalonia

References

De Cáceres, M., Legendre, P. & He, F. (2013) Dissimilarity measurements and the size structure of ecological communities. Methods in Ecology and Evolution 4: 1167-1177.

See Also

CAP

Examples

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## Load stratified data
data(medreg)

## Check that 'medreg' has correct class
class(medreg)

## Create cumulative abundance profile (CAP) for each plot
medreg.CAP = CAP(medreg)

## Draw the stratified data and profile corresponding to the third plot
plot(medreg, plots="3")
plot(medreg.CAP, plots="3")

## Look at the plot and CAP of the same plot
medreg[["3"]]
medreg.CAP[["3"]]

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
[1] "stratifiedvegdata" "list"             
                               1    2    3    4    5 6 7
Pine trees                   0.0 12.5  0.0  0.0  0.0 0 0
Quercus trees                0.0  0.0 12.5 12.5 12.5 0 0
Tall shrubs and small trees  0.0 25.0 62.5 25.0  0.0 0 0
Scrubs and small shrubs      0.0 50.0  0.0  0.0  0.0 0 0
Grass                       37.5  0.0  0.0  0.0  0.0 0 0
                                1     2    3  4    5 6 7
Pine trees                   12.5  12.5  0.0  0  0.0 0 0
Quercus trees                37.5  37.5 37.5 25 12.5 0 0
Tall shrubs and small trees 112.5 112.5 87.5 25  0.0 0 0
Scrubs and small shrubs      50.0  50.0  0.0  0  0.0 0 0
Grass                        37.5   0.0  0.0  0  0.0 0 0

vegclust documentation built on Sept. 17, 2017, 5:03 p.m.