CAFCA - Manual

1. Select Primary Analysis in the Run menu.

2. Click 1 (From an ASCII file) and OK in the dialog.

   

3. Select PLANTB.INP from the example data on your distribution disk and click Load File.

   

4. Enter 'Plant' (without quotation marks!), for example, as a name for your data matrix in the next dialog box.

   

5. The file with the data matrix selected in step 3 does not contain names for the taxa. CAFCA will notice that and will prompt you for a file that contains a separate list of names for the taxa concerned. Click button 1 (Copy from an ASCII file) in theNamelist for taxa dialog box.

   

   Nota Bene:If, on the other hand, the ASCII file with your data matrix already contains names for your taxa, like in the following example,

   / This is an example of an ASCII file containing a data matrix,
   / representing the distribution of character states
   / over all terminal taxa.
   Aus
   2020110011
   Bus
   1120110011
   Cus
   1010110021
   Dus
   1020121111
   Eus
   1120031111
   / You may start the inputfiles for CAFCA with comments, 
   / i.e. text preceded by either a # / \ * " ' ; or !
   / and you may add closing comments as well, like this one.
   / You can add names for the terminal taxa.
   / Names for taxa may contain {}()[]-+._
   / and integers 01234567789 when enclosed by alphabetic characters.
   / Spaces in names are not allowed and replaced by _ when reading inputfiles.
   

   then CAFCA will not bother you with steps 5 and 6, as the names for the taxa are extracted from the input file, together with the data matrix.

6. Select PLANT.NMS from the example data on your distribution disk and click Read File.
   

7. Click Read-from-ASCII-file in the No (correct) partition vector present dialog box.

   

8. In the next file selector box select PLANTB.CPV from the example data on your distribution disk and click Read File

   

   Nota Bene:CAFCA runs it analyses on binary (0/1) expressions of the data matrix. If the data-file (step 3) already contains binary expressions of the multi-state characters in the data matrix, as in this case, CAFCA computes the multi-state expression of the data by means of the partition vector and renames the binary expression by adding the letters 'deltaB' to the name given previously (step 4). CAFCA notifies you with the following message box.

   

   If, on the other hand, your data matrix contains multi-state characters and already has a multi-state expression when read in (as is the case with the file PLANT.ASC in the examples folder) than steps 7 and 8 will be skipped as CAFCA can now compute the partition vector from the data matrix itself. You will get the following message box instead.

   

9. Click No in the dialog presenting you the option for separate columns for character states in polytypic taxa .

10. Click No in the Do you want to edit your data dialog.
    

11. Click No in the Data matrix needs clipping ? dialog box.

    

12. Click No in the Taxon on the outgroup node dialog box.

    

13. Take all defaults in the CAFCA Parameters dialog boxes. Then click OK.

    

    

    The analysis will now start running. Its progress can be followed on the screen..

    

    If for whatever reason you want to stop this run, use the Interrupt menu (see chapter 2).
    When the elapsed time message appears the analysis is finished

    

14. Now select All Results from the Print menu.

    

15. You can either print your data to file, and use your favourite word processor to open, edit and print the output of a CAFCA run, or you could print from within CAFCA. If you choose the first option you should click button 3 (File) and OKin the dialog.

    

    In the following file save box you can enter a name for the file where the output will be written to.

    

16. Sending a file to a (appletalk connected) [laser]printer from within CAFCA is now reasonably up to standards.
    So, if you do want to send your output to a printer directly, click button 2 (Printer) in the Select Print Device dialog box.

    

17. You will get a standard Macintosh Page Setup dialog box...

    

18. ...followed by a standard Macintosh Print dialog, depending on the (type of) printer you did select in the Chooser.

    

19. After printing your results on a printer or to file, select Save & Resume in the Output-File menu if you want to save your results in a CAFCA.IO file, to be used later on, eventually.
    Click OK in the Output for PlantB will be saved to OutputFile dialog box if you really want to save your results.

    

20. CAFCA will continue by asking you to select a volume and folder in which to save the outputfile.

    

    If you have never saved any data to an OutputFile before, you can click any file within the folder of your choice. CAFCA won't use this file but it will use this folder to write its outputfile (CAFCA.IO) to.

21. CAFCA will notify you of its discovery that there is no OutputFile system present yet in this folder by means of the following dialog. Click OK.

    

22. CAFCA will start writing the output of this primary analysis of PLANTdeltaB to its OutputFile. The results of several analyses can be written to the same OutputFile. This file can be recognised by the name CAFCA.IO The results of the separate analyses can be found and retrieved from this file-system by their own name, PLANTdeltaB in this particular case.

    

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© M. Zandee 1996.