Unconstrained ordinations in vegan: an online Shiny app

The R package “vegan”, written and maintained by Jari Oksanen, Gavin Simpson and others, contains the whole set of functions needed for unconstrained ordination (and many other things) in R. I also experimented with other packages (“labdsv” by Dave Roberts or “ade4” by Stephane Dray et al.), but “vegan” is unbeatable when it comes to ordinations. One a little annoying thing in “vegan” is the naming convention of various ordination functions. It’s relatively easy to get used to that PCA (principal component analysis) and CA (correspondence analysis), respectively, are calculated by “rda” and “cca”, respectively, which, if one also supplies environmental variables, also calculate constrained versions (RDA aka redundancy analysis and CCA aka canonical correspondence analysis). DCA (detrended correspondence analysis) is calculated by “decorana”, which also makes sense, if you know the history of the method and the fact that first program written by Mark Hill in Fortran to calculate DCA was called exactly in this way (and in fact the “decorana” function in R is based on the original Fortran code ported into R by Jari). Somewhat harder is to remember that NMDS (non-metric multidimensional scaling) is calculated by a function called “metaMDS”, and the definite killer for me is PCoA (principal coordinate analysis), calculated by “cmdscale”. When you are teaching these to students, it may get a bit frustrating, so some handouts come handy. That’s partly why I got this idea: an interactive online tool, which would allow using few example community ecology dataset, analyse them by a set of standard ordination methods, draw resulting ordination diagram, print summary output, and mainly – show also the R code which was used to do all that. The result is here, welcome to click through!

Previously I used Shiny apps to play with visualisation of random drift, and I got quite hooked on the concept of a dynamic website with R running behind. In the case of this project, it got more complex, and I spent the whole day learning various Shiny hacks (e.g. how to modify dynamically also the clickable menu at the left panel). Although the result is far from perfect (and perhaps will stay like that for a while), it’s functional. You may choose one of the datasets (short description and the link to the website with details will appear), then choose one of six ordination methods, transform or not the community data, and decide what to display in the ordination diagram. The figure above shows the PCA on a simulated community dataset structured by one long gradient, and a lovely horse-shoe artefact which PCA chronically produces on datasets with many zeros.

Don’t get me wrong – this is not an attempt to provide an online, clickable alternative interface to “vegan”, I have no intention to do something like this. But I think that Shiny apps are a great teaching aid and visualisation tool. If you have a new R package and want to show how it works, a small Shiny example may be much better than a long online tutorial (at least as an appetiser with the aim to hook users actually to try the package).

Welcome to play, and thanks for any feedback!

2 thoughts on “Unconstrained ordinations in vegan: an online Shiny app

  1. Shan-Hua Yang

    Thank you very much for providing it. It’s very helpful to see what do results look like.
    Also, the website “Analysis of community ecology data in R” is very clear and easy to understand the meanings of different methods. Thank you for your introduction!


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