BiodiversityR (version 1.5)

ordisymbol: Add Other Graphical Items to Ordination Diagrams

Description

Functions to add some other graphical itmes to ordination diagrams than provided within vegan by ordihull, ordispider, ordiarrows, ordisegments, ordigrid, ordiellipse, ordicluster and lines.spantree.

Usage

ordisymbol(ordiplot, y, factor, col=1, rainbow=T, legend=T,...)
ordibubble(ordiplot,var,...)
ordicluster2(ordiplot, cluster, mingroups=1, maxgroups=nrow(ordiplot$sites),...)
ordinearest(ordiplot, dist,...)
ordivector(ordiplot, spec, lty=2,...)

Arguments

ordiplot

An ordination graph created by ordiplot (vegan).

y

Environmental data frame.

factor

Variable of the environmental data frame that defines subsets to be given different symbols.

var

Continous variable of the environmental dataset or species from the community dataset.

col

Colour (as points).

rainbow

Use rainbow colours.

legend

Add the legend (you need to click in the graph where the legend needs to be plotted).

cluster

Cluster object.

mingroups

Minimum of clusters to be plotted.

maxgroups

Maximum of clusters to be plotted..

dist

Distance matrix.

spec

Species name from the community dataset.

lty

Line type as specified for par.

...

Other arguments passed to functions points, symbols, ordihull or

Value

• These functions add graphical items to an existing ordination diagram.

Details

Function ordisymbol plots different levels of the specified variable in different symbols and different colours (if rainbow option was selected). When you opt to add the legend, then you need to click in the ordination graph to indicate the position of the legend. Function ordibubble draws bubble diagrams indicating the value of the specified continuous variable. Circles indicate positive values, squares indicate negative values. Function ordicluster2 provides an alternative method of overlaying information from hierarchical clustering on an ordination diagram than provided by function ordicluster. The method draws convex hulls around sites that are grouped into the same cluster. You can select the minimum and maximum number of clusters that are plotted (i.e. the range of clustering steps to be shown). Function ordinearest draws a vector from each site to the site that is nearest to it as determined from a distance matrix. When you combine the method with lines.spantree using the same distance measure, then you can evaluate in part how the minimum spanning tree was constructed. Function ordivector draws a vector for the specified species on the ordination diagramme and draws perpendicular lines from each site to a line that connects the origin and the head of species vector. This method helps in the biplot interpretation of a species vector as described by Jongman, ter Braak and van Tongeren (1995).

References

Jongman, R.H.G, ter Braak, C.J.F & van Tongeren, O.F.R. (1987). Data Analysis in Community and Landscape Ecology. Pudog, Wageningen. Kindt, R. & Coe, R. (2005). Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies. http://www.worldagroforestry.org/resources/databases/tree-diversity-analysis

Examples

library(vegan)
data(dune)
data(dune.env)
Ordination.model1 <- rda(dune)
plot1 <- ordiplot(Ordination.model1, choices=c(1,2), scaling=2)
ordisymbol(plot1,dune.env,"Management",legend=FALSE)
## Make sure you click in the graph to show where the legend should be placed
## In case that you choose option of legend=TRUE
plot2 <- ordiplot(Ordination.model1, choices=c(1,2), scaling=1)
distmatrix <- vegdist(dune, method='bray')
cluster <- hclust(distmatrix, method='single')
ordicluster2(plot2, cluster)
ordinearest(plot2,distmatrix,col=2)
ordivector(plot2,"Agrsto",lty=2)