ordisymbol {BiodiversityR}R Documentation

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,...)
ordihull.centroids(ordmod, ordiplot, groups, draw = c("lines", "polygon"), 
    show.groups, return.outliers=F, return.index=F, ...)
ordispider.centroids(ordmod, ordiplot, groups, w = weights(ordiplot, "sites"), 
    show.groups, return.outliers=F, return.index=F,...) 
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).
ordmod Constrained ordination model that provides constrained ordination axes (provided by rda, cca or capscale).
groups Factor giving the groups for which the graphical item is drawn (as in ordihull and ordispider).
draw Use either lines or polygons (as in ordihull).
show.groups Show only given groups. This can be a vector, or TRUE if you want to show items for which condition is TRUE (as in ordihull and ordispider).
w Weights used to find the average within group (as in ordispider).
return.outliers Return the sites that are not closest to their own centroid.
return.index Return results of a test whether sites are closest to their own centroid (TRUE) or not.
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 arrows.

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.

Functions ordihull.centroid and ordispider.centroid have the same behaviour as their vegan equivalents (ordihull and ordispider), except that hulls and spiderplots are only drawn for those sites that are closest to their own group centroid. The function thus allows to identify multivariate outliers. Optionally details about the outliers are provided. The function only returns results for ordination methods that provide constrained ordination axes.

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).

Value

These functions add graphical items to an existing ordination diagram.

Author(s)

Roeland Kindt (World Agroforestry Centre) and Jari Oksanen (ordinearest)

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/treesandmarkets/tree_diversity_analysis.asp

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)

[Package BiodiversityR version 1.2 Index]