Demo 2: Specifying ordination

Specifying the CCA ordination by Canoco for Windows

1. From the Canoco for Windows submenu in the Start / Programs menu (see point 3 of Importing data), select now the Canoco for Windows item. Upon startup, the Tip of the Day appears, unless you already switched this feature off. Click the Close button to proceed. The Canoco for Windows workspace is now empty. To define a new analysis, we must create a new project. We can do that quickly using the New project button in the Canoco toolbar. This button is marked in the snapshot below.
   
   

   The New project button on the Canoco for Windows toolbar

   
   
2. After you clicked the New project button, new Project View and Log View windows are created and the Project Setup Wizard is automatically started (because we must first define our new project).
    
3. A canonical correspondence analysis (CCA) attempts to explain species data by environmental data. We must therefore specify on the first Project Setup Wizard page, that we want to analyze both species data (the primary data) and environmental data (the explanatory data) and that we want to do a direct gradient analysis. Review the settings and make them same as on the snapshot below. Then click the Next button at the bottom of the Project Setup Wizard page.
   
   

   The Available Data page of the Project Setup Wizard

   
   
4. On the next page, you must specify two input data files and as well as the file where the ordination results will be stored (the Canoco solution file). The other fields (used for covariables or supplementary environmental variables data sets) are disabled, based on our choices in the previous wizard page. You can either type the names of your data files straight into the edit fields or, alternatively, you can use the corresponding Browse buttons to find where the data files are. You should fill-in the fields as in the snapshot below, except when your Canoco for Windows installation directory is not C:\Canoco.
    
   
   The Data Files page of the Project Setup Wizard
    
   
5. After clicking the Next button, a wizard page appears where the type of the analysis can be specified. Select the CCA option here. You can also try the ? button in the upper right corner of the Project Setup Wizard page. If you click it, your mouse cursor changes to a question mark and you can click particular labels (say CCA) to get specific information about its meaning. To get an explanation of this whole wizard page, click the Help button at the bottom of the wizard page.
    
6. In the next wizard page, the scaling of the ordination scores must be selected. Keep the default values here, as they come handy in a first analysis. You may wish to review the choice after reading the Help text.
    
7. The next wizard page offers us the possibility to apply a transformation to the species data. In our case, the species values are roughly on a logarithmic scale. So we keep the default of no transformation, and proceed to the next page.
    
8. This page (titled Data Editing Choices and illustrated by the snapshot below) is the core page for any necessary adjustments to your datasets. After checking the appropriate boxes, you can remove particular samples, species, or environmental variables from the analysis, change their weights or make them supplementary (passive). In addition, you can extend the explanatory variables with interactions terms (powers and products of the original environmental variables). To keep our demo simple, we do not check any of the boxes and skip in that way a number of Setup Wizard pages.
   
   

   The Data Editing Choices page of the Project Setup Wizard

   
   
9. The next page allows us to do Forward selection of environmental variables. Beside manual forward selection, which you may know from CANOCO 3.x, there is Automatic Forward Selection which provides a quick summary of both the marginal and the conditional effects of the individual explanatory variables (see The Package). In this demo, we keep the default (Do not use forward selection) and proceed to the next page using the Next button.
   
10. The next page (titled Global Permutation Test) makes Monte Carlo permutation tests easily accessible. We will demonstrate the simplest permutation test available in Canoco for Windows. In this page, select the last option on the left of the page (Both above tests) and leave the number of permutations and the permutation type choices at their default values. Compare your choices with those in the snapshot below.
    
    

    Global Permutation Test page of the Project Setup Wizard

    
     
11. On the next wizard page, keep the default settings. In this page, you can departure from the simplest permutation method (unrestricted permutation). In analyses with covariable data, you can also specify the block structure of your sampling/experimental design, so that samples from different blocks are not exchanged in the permutations. See The Package 
     
12. Given the simple options selected in this demo, the final page appears now. Note however, that you might go back through your choices and modify them as needed. You can do so also after the ordination analysis is completed, to iteratively improve or extend your analytical approach. Click the Finish button now.
     
13. A file-save box (titled Canoco Project) appears and you must specify a name for the file where the project will be saved. Save the file tutorial.con into the directory C:\Canoco\Samples, as illustrated in the snapshot below.
    
    

    Saving a Canoco project in a file

    
    
14. After clicking the OK button, your project is saved and you are back in the Canoco for Windows workspace with in the foreground the Project View window and the Log View window in the background.
    
    

    The Canoco for Windows workspace with Project View and Log View

    
    
15. Click the Analyze... button in the Project View. The progress of the calculations (including the Monte Carlo permutations) is reported in a pop-up window. After this window disappears, you are back in the Canoco for Windows workspace, with the Log View filled with the summary results of the analysis. To inspect the ordination summary, switch to the Log View by clicking in its window. Alternatively, press the F3 key or click Switch toolbar button.
     
16. In the Log View, you can see the result of the Monte Carlo permutation test, the ordination summary and additional information, all described in detail in the Canoco for Windows manual. You can scroll through the Log View using the scrollbar on the righthand side. 
    
    

    The Log View brought to the foreground

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