Changes for PDAP:PDTREE for version 1.08

Enhancements

• Added support for correcting the degrees of freedom on screen 9. This change reflects that this screen reports p-values, which are calculated from the t-statistic reported for the regression. If you have set verbose mode, you will be asked about this each time to enter screen 9. Otherwise, the program will now ask exactly once for each tree during a session. The command to manually change the degrees of freedom has also been added to the menu for this screen. Note that:
  • the raw t and F statistics are correct and unchanged in this version.
  • the DOS version of PDAP never reported a p-value for the t statistic and therefore needs no updating.
  • if you use the "Felsenstein correlation" calculator for a tree and two characters to generate a p-value, it will always treat polytomies in the most conservative way: subtract one degree of freedom for each branch collapsed into a polytomy. Because of the contexts that this calculator is likely to be used, it is not practical to ask the user for each tree that contains polytomies.

Bug Fixes

• Pagel's branch length transform 'broke' polytomies in trees loaded from PDI files. The problem was caused by the PDI file reader retaining zero length branches that PDAP uses to represent polytomies. The reader now collapses zero length branches into Mesquite-style polytomies.
• Column 9 of the FIC file incorrectly duplicated column 8 (raw node heights) instead of reporting the corrected node heights.
• An problem with the variance of contrasts returned by as a "number for tree", for example in a tree legend has been fixed. The number was incorrectly calculated and was different from the value displayed on screen 9 of the PDAP:PDTREE diagnostic charts, which is correct. The discrepancy has been fixed.
• The log10 character transform was incorrectly reporting some data as nonpositive.
• The unassigned branch length checker was reporting problems with generated trees, such as the Yule trees in Part 6 of the guided tour. The only unassigned branch length was in the branch below the root. Since PDAP never uses this branch, the checker is now set to ignore it.
• Problems in saving large (493 tip) trees to a PDI file have been fixed.
• The guided tour files have been updated and no longer report being of an older version.