Theory, Examples & Exercises
Section: Ordination analysis
plot- if called on the result of ordination (e.g.
cca), it draws ordination diagram with setting relevant for given method; high-level plotting function, which can be combined with low-level plotting functions (
pointsetc. described below). Draws species and site labels if the number of items displayed is relatively low.
ordiplot- an alternative high-level plottig function to
plot- draws complete ordination diagrams without labels, which can be added by low-level plotting functions (
biplot- high-level plotting function suitable only for unconstrained and linear ordination methods (PCA and tb-PCA); draws species scores as arrows indicating the direction of increasing species abundance. If used with unimodal methods (like CA) or constrained ordination (RDA, CCA), an error is returned.
points- adds points to the ordination diagram (low-level plotting function, adds points to ordination diagram created by
plot). Has argument
select- logical vector indicating which elements should be displayed (the same for
text- similar to
pointsabove, adds the text labels for sites/species.
orditorp- adds labels onto existing ordination diagram, so as they are readable (they don't overlap). Has arguments
priority(which species/sites will be given priority to draw the text instead of only point) and
select(logical vector - which species/sites should be drawn).
ordilabel- adds the labels which look like stickers; also has
ordipointlabel- creates new ordination diagram and adds both points and labels (for species or sites) in a way to minimize their overlap (uses iteratively optimizing algorithm and can be rather slow). Can be stored in an object further editable interactively by the function
orditkplot- produces editable and clickable ordination diagrams, which can be exported, saved into R and also reedited again. Check blogpost of Gavin Simpson to see how to use it.
ordispider- creates spiderplot by connecting individual members of the group with the group centroid.
ordihull- draws envelope (convexhull) around the group of samples (possibly also color-filled polygon).
ordiellipse- similar to envelopes - clouds of points within the group are encircled by ellipse.
ordiarrows- draws arrows connecting the groups of samples (visualizing e.g. development of composition in time or in space).
scores- function extracting site or species scores from the ordination object. All functions drawing ordination diagrams are using scores extracted by this function. Note that the way how scaling is implemented in vegan package was recently reworked - read the blog post of Gavin Simpson for more details.
ordirgl- draws 3D ordination diagram, using functionality of
orglspider- adds spiders to 3D ordination diagram created by
BiodiversityR) - calculates broken-stick model for PCA axes. Function can be
ordicenter- adds labels to centroids of groups onto ordination diagrams. Similar to
label = TRUE, but does not draw spider plot. Arguments and use are analogous to
ordihull. Definition here.
orglhull- adds 3D convexhulls wrapping groups of samples (possibly transparent). Custom function not in
library (geometry). Definition here.
vegan3d- the reason according to this message from Jari Oksanen is that these function caused troubles with running or even installing
veganon some platforms, so to separate them was good for stability of