ordisymbol {BiodiversityR} | R Documentation |
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
.
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,...)
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 . |
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).
These functions add graphical items to an existing ordination diagram.
Roeland Kindt (World Agroforestry Centre) and Jari Oksanen (ordinearest
)
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
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)