[Adephylo-commits] r79 - in pkg: . R

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2008-12-03 14:20:30 +0100 (Wed, 03 Dec 2008)
New Revision: 79

Modified:
   pkg/R/proximities.R
   pkg/TODO
Log:
ppca is now ok. Code was ok, but symmetrization was not done in proxTips when requested. 


Modified: pkg/R/proximities.R
===================================================================
--- pkg/R/proximities.R	2008-12-03 10:40:14 UTC (rev 78)
+++ pkg/R/proximities.R	2008-12-03 13:20:30 UTC (rev 79)
@@ -50,7 +50,7 @@
 
     ## re-symmetrize
     if(symmetric){
-        D <- 0.5 * (D + t(D))
+        res <- 0.5 * (res + t(res))
     }
 
     ## set the output

Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-12-03 10:40:14 UTC (rev 78)
+++ pkg/TODO	2008-12-03 13:20:30 UTC (rev 79)
@@ -62,8 +62,8 @@
 
 # TESTING:
 ==========
-* test distTips a little more (see Abouheif with an outgroup, otherwise seems ok) -- done (TJ)
-* test ppca: are results identical to those with previous implementation?
+o test distTips a little more (see Abouheif with an outgroup, otherwise seems ok) -- done (TJ)
+o test ppca: are results identical to those with previous implementation? -- done (TJ)