Theory, Examples & Exercises
- Constrained ordination
This website is currently undergoing reconstruction (see details here). Since spring semester 2017, I will use this website for teaching the class Numerical Methods in Community Ecology, which will be based on R and which is also the main reason for this (slow) reconstruction.
This website is focused on an analysis of multivariate community ecology data, i.e. data with many descriptors (usually species) and samples (usually plots/sites/traps etc). Since I am vegetation ecologist, the website descriptions, and elaborated examples are heavily biased toward analysis of vegetation data; still, I think that also other ecological fields (e.g. zoologists or microbiologists) may find the website useful. The aim is not a comprehensive on-line source of information about multivariate analysis (there are much more useful websites for this, see Links to other study materials). I focus mostly on preparing useful working examples of analyses with real datasets and elaborated solutions of individual exercises. The secondary aim of the website is to provide insight into the theoretical background of established methods and links to recent developments in multivariate analysis and analysis of diversity. This is not to say that I try to keep pace with all the new and fancy analytical methods, more likely just those I found useful, promising or interesting (in my purely subjective and desperately biased view).
From time to time, I use this website as teaching materials for my class Numerical Methods in Community Ecology or some of the R workshops. For that reason, parts of the website are locked, namely those with class exercises and their solutions. Also, the website is constantly under construction, with major development and changes done during or before the semester when I teach some of the classes. In the remaining time, the website could serve as a source of on-line information about different aspects of community data analysis in R.
This wiki contains a short overview of relevant theory, real community datasets and example R scripts. Although these R scripts could be copied directly into the R command line, I strongly recommend you to avoid copy-paste action and instead to type the script by yourself - this is the best way how you will get familiar with the logic of R, although at the beginning the typing may feel annoying. This website also provides several working examples and datasets with real or simulated ecological data - you may use them to get more familiar with a method or problem. Each working example has (or should have soon) a solution link - but please, try to resist clicking it immediately, and instead push hard to find the solution by yourself. Sometimes the link to hints is provided - if you struggle with a search for the solution, hints may help.
If you need to print the website, export the website into pdf using the export button located at the right margin of the website among page tools. Or, you may use the print function of the browser (works fine in Firefox, Chrome, and IE as far as I know). This will print the current page without buttons/links and stuff around.
If you need to get to previous pages, you can find them in Trace line in the website header. There is also a useful button Backlinks in the right vertical menu, which shows the other available wiki pages which link to the currently opened page.
Not important (or too much detail) information is sometimes provided as a footnote, with a link in a text which looks like this:1). By hovering the mouse over it, you can see its content without clicking on it. By clicking on it, you get down the page, and if you want to get back to the original place, click again on the [number] in front of the footnote.
In the beginning, I was writing this website in Czech, since I used it as a teaching material for my class taught at Masaryk University, Brno, Czech Republic. Eventually, I made it bilingual to make it useful also to international students in the class. For some time I kept updating both Czech and English version of it, but I am no longer able to do it; the Czech version started to lag behind the English one, including outdated and not functional scripts and links. I decided to send the Czech version into the museum of out-of-date websites; now all links to the original Czech version redirect directly to their English equivalents, without any redirection message. Sorry for the inconvenience if that bothers you.