isopam (version 3.2)

plot.isotab: Plot species fidelities to clusters

Description

Function to plot isotab results. Based on equalised phi values according to Tichý & Chitrý (2006), the method visualises how closely how many species are associated with clusters.

Usage

# S3 method for isotab
plot(x, labels = FALSE, text.size = 15, title = NULL,
       phi.min = "isotab", p.max = "isotab", ...)

Value

Prints and returns (invisibly) an object of class ggplot.

Arguments

x

Object of class isotab.

labels

Logical. Whether the bars should be labeled with species names. You may need to enlarge the figure height to accommodate these names (or decrease text.size).

text.size

Text size

title

Optional text string with title

phi.min

Threshold of equalized phi determining which species are shown. Applies only to species passing the criterion defined by p.max. If phi.min = "isotab" (the default) the threshold used by isotab is applied. Use phi.min = 0 to remove the filter.

p.max

Threshold of Fisher's p determining which species are shown. Applies only to species passing the criterion defined by phi.min. Note that this value relates to frequencies rather than phi. If p.max = "isotab" (the default) the threshold used by isotab is applied. Use p.max = 1 to remove the filter.

...

Other arguments (ignored)

Author

Sebastian Schmidtlein

Details

The thresholds are explained in isotab.

References

Tichý, L., Chytrý, M. (2006): Statistical determination of diagnostic species for site groups of unequal size. Journal of Vegetation Science 17: 809-–818.

See Also

isopam, isotab

Examples

   ## load data to the current environment
   data(andechs)
     
   ## call isopam with the default options
   ip <- isopam(andechs)
       
   ## calculate fidelities
   it <- isotab(ip)
   
   ## plotting
   plot(it)

   ## show species labels
   plot(it, labels = TRUE)

   ## show all species
   plot(it, phi.min = 0)