User Tools

Site Tools


Analysis of community ecology data in R

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.

David Zelený


This website is focused on multivariate analysis of community ecology data. 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 the field of (mostly) multivariate analysis. 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).

Time to time, this website will be used as teaching material for class Numerical Methods in Community Ecology or some of the R workshops. In that case, parts of the website, mostly those uncovering the solution of the exercises, may be temporarily blocked. Also, the website is constantly under construction, with major development and changes done during or before the semester when I teach the NumEcol class. In the remaining time, the website could serve as a source of on-line information about different aspects of community data analysis in R.

How to use this website

This wiki contains some instant 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 solution by yourself. Sometimes link to hints is provided - if you struggle with search for solution, hints may help.

Export button creating pdf of the website.

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 an 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 detail) information is sometimes provided as a footnote, with a link in 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.

This is a footnote! I guess this information (that it's a footnote) is really not important, that's why it's a footnote…
en/start.txt · Last modified: 2017/02/22 08:15 by David Zelený