Theory, Examples & Exercises
- Constrained ordination
An important component of unconstrained ordination analysis is visualization of results (this doesn't apply so much in case of constrained ordination, when we are more interested in explained variance and results of significance test). R is notoriously not good in drawing ordination diagrams with complex information, because these usually needs manual adjustment, which is not easy in R. Generally, if you need ordination diagram with interpretation focused on individual species or samples (with appropriate labels), R may not produce satisfying results - you may consider using CANOCO 4.5 with CanoDraw for Windows or CANOCO 51). However, R can still draw nice ordination diagrams, if the focus is on overall pattern of samples, grouping of samples into clusters or projecting linear or surface response of environment onto ordination space (even three dimensional) - few examples are below.