Presentations and Tutorials
Here are handouts for a presentation (pdf) given by Cajo ter Braak when introducing Canoco 5 at Wageningen University on 5th February 2013. The presentation focuses on existing users of the older (4.0 and 4.5) CANOCO versions. Handouts for new Canoco 5 users are here.
Cajo ter Braak also offered a 45-minute hands-on tutorial after the presentation, using these materials. This tutorial refers to data available after installing Canoco 5 on your computer.
These brief videos will demonstrate the software use, using recorded screen actions with Petr Šmilauer' commentary.
Canoco 5 tour for novices
|1 - Importing data
|2 - First analysis
|3 - Analysis notebook
|4 - Constrained ordination
These articles will clarify or describe in more detail selected topics about statistical or visualization methods available in Canoco 5.
In the pdf sub-folder of Canoco 5 installation folder, you can find two articles:
- article in terBraak_et_Smilauer_2015_Topics_constr_unconstr.pdf deals with constrained ordination, but also with a defense of the detrending in unimodal unconstrained methods
- article in terBraak_et_al_2017_dc-CA_preprint.pdf provides basic information about the dc-CA method, introduced in Canoco 5.10.
Bugs and features
For an overview of issues that we found in the latest released Canoco 5 version, as well as those fixed in the preceding minor versions, click here: Canoco 5 Issues. If you want to report any issues missing in the list, please send us a message.
You can find the present errata to both 5.1 and 5.0 manual versions here. Main differences of the Canoco 5.1 manual as compared with Canoco 5.0 manual are listed in the pdf\manual-changes.html file of the Canoco installation folder (typically, this is C:\Program Files\Canoco5 folder).
Canoco 5 manual that comes with your software licence is the place for you to start. We suggest you begin with section 1.1, read and exercise the contents of Chapter 2 (experienced Canoco 4.x users might start at section 2.9), and then read all or selected parts of Chapter 3. Chapters 4, 5, and 7 are of referential nature, although they also contain introductions to working with various parts of user interface. You may find useful to read selected (or all) parts of Chapter 6, where available example projects, build around real-world datasets and research problems are described. Each section is supported by a project where the described analyses and graphs are already present, so that you can examine the required analysis setup, but also do your own experiments with the same data. To open example projects, use the File | Open project menu command and locate the Canoco 5 Application | Samples shortcut at the left side of the opening dialog box (not present under Windows XP and takes various forms in later Windows versions).
Unimodal Models booklet contains many of the seminal papers that introduced the ideas and methods, on which the Canoco software is based. Starting as a doctoral thesis of Cajo Ter Braak, his later papers were added. As from version 5.10, this booklet comes as pdf Unimodal_Models.pdf in the Canoco/pdf folder. The numbering of pages in the pdf agrees with those mentioned in the Canoco 5 manual. You find in the pdf folder also the paper Topics in constrained ordination(terBraak_et_Smilauer_2015_Topics_constr_unconstr.pdf) and a preprint of a paper
on double constrained ordination (terBraak_et_al_2017_dc-CA_preprint.pdf).
From the multitude of books published on the subject of multivariate analysis and covering also the methods available with Canoco 5, we would recommend particularly two:
For those in need of lighter reading, the P. Šmilauer & J. Lepš (2014) Multivariate Analysis of Ecological Data using Canoco 5, published by Cambridge University Press is recommended. This book describes the methods with examples refering to Canoco 5, unlike the first edition (published in 2003).
Another introductory booklet for ordination (but also classification, regression, spatial analysis) is R.H.G. Jongman, C.J.F. Ter Braak & O.F.R. Van Tongeren (1995), Data Analysis in Community and Landscape Ecology, also available from the Cambridge University Press. The 1987 edition would be sufficient for most readers and it is freely available from here.
More heavy reading (literally) is the P. Legendre & L. Legendre (2012) Numerical Ecology, published at Elsevier Press. Please note the publication year, using the third edition is essential for some of the newer development (e.g. the analysis including spatial information, such as the PCNM method also implemented in Canoco 5).
If you have support questions
If you have problems with installing the Canoco 5 software or it does not behave as expected from its documentation, you are entitled to a free support. Please contact the software distributor (Microcomputer Power) for this. If they are unable to handle your issue properly, they will pass it on to software authors.
For Canoco 5 related technical and statistical questions, the licensed owners of Canoco 5 are invited to join a subscription-based web discussion board, moderated by Petr Šmilauer, co-author of the Canoco 5 (and earlier 4.x versions).
To join this group, go to the following web page:
and click the [Register] link in the upper left corner of the page, then confirm the registration statement by clicking the I agree button, and then fill the required details on the following page, confirming them subsequently with the Submit button at the page bottom. Please make sure that you correctly specify the license number provided by the software distributor (as given on your install disc envelope or on your manual' cover). Without this number, your membership will not be approved.
On the other hand, the specification of your birthday comes from the platform itself and we could not avoid the form asking for it. We recommend that you immediately set its use to "Completely hide birthday from public viewing" (at the following line of the form), so that even the administrator will not see it (we do not care about your age and do not send birthday presents either :-).
Once you submit the page, your subscription request will wait for the administrator (Petr Smilauer) approval and he will inform you by a personal welcome e-mail once it is confirmed, so that you know you can log into the group, read existing support questions and their answers and eventually ask your own questions.
A general list about ordination methods and other methods of multivariate statistical analysis is the ORDNEWS mailing list. Please see the page http://ordination.okstate.edu/ordnews.htm for all the fine details about how to subscribe, how to post and what (not) to do in the list correspondence.
To remove user-account specific settings of Canoco 5 and reset program behaviour to the state immediately after its installation, you can download and execute following small utility named C5CleanReg.
This is an executable file and you do not need to install it in any special way, simply store it in any folder and execute from there. Please note that to remove Canoco 5 custom settings, Canoco 5 cannot be running at the time you execute this utility. If it does, C5CleanReg warns you and does not proceed until you close Canoco 5 application.