- Click in the menu. You get the following message.
If you skipped step 12 and 13 () in the primary analysis, your data will still be present in the workspace and CAFCA starts a secondary analysis with step 4 from this tutorial.
- Select an Outputfile system () in the next file select box.
- Click Second in the next dialog box. Note that you may have many files in your OutputFile system in stead of just one as shown in this particular example
- All the elements from the primary analysis on Second that are needed to run a secondary analysis are now loaded into the workspace.
- Click () in the next dialog box.
- Remember that two minimum step cladograms were selected by CAFCA. Because a secondary analysis is restricted to only one cladogram at the time the following dialog appears next.
Click (= cladogram # 2) in this dialog box, and then .
- The next two dialogs are for setting the CAFCA parameters to be used in this secondary analysis. The main point to consider here is the maximum number of cladograms that will be retained in memory for each of the nodes to be analysed. If this number is too high, a combinatorial explosion may occur when all equally parsimonious possibilities for each node are combined to give all possible full resolutions for the original cladogram, and consequently, memory will be swamped. Another remedy against this combinatorial explosion is provided by RQ as a selection criterion for cladograms, because it offers more resolving power and is therefore more restrictive than the CI (minimum steps).
- After the parameters are set the secondary analysis will start running. You can follow its progress on a sequence of screens, each showing a primary analysis on each separate node that constitutes a polytomy.
If for whatever reason you want to stop this run, use the menu.
- The solutions resulting from these restricted primary analyses are combined and merged (with each other and with the resolved part of the old cladogram) to form better resolved cladograms. The new cladogram is evaluated (table 4.6) with respect to the complete data matrix (table 4.1)
- When the secondary analysis is finished you can print the results by selecting from the menu. In the following dialog you must select option 2 (Secondary analysis).
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