[Adephylo-commits] r38 - pkg

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

Author: jombart
Date: 2008-11-26 15:10:34 +0100 (Wed, 26 Nov 2008)
New Revision: 38

Modified:
   pkg/TODO
Log:
Updated TODO.


Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-11-26 14:04:46 UTC (rev 37)
+++ pkg/TODO	2008-11-26 14:10:34 UTC (rev 38)
@@ -8,7 +8,8 @@
 # and all detected bugs
 #
 # please add a "-- done" or "-- fixed" tag when
-# you achieved something
+# you achieved something, and replace the 
+# initial star "*" with a "o"
 #
 # Inside a given section, priority goes decreasing.
 #
@@ -35,15 +36,16 @@
 
 # NEW IMPLEMENTATIONS:
 =====================
-* plot methods from phylobase ('old' version) -- done (TJ)
-* implement a pathTwoTips method, which has to go fast to find shortest path between two tips - done (TJ): is now sp.tips.
-* basic stuff existing in phylog objects (while option=TRUE), e.g. distance to the root for tips, etc.
+o plot methods from phylobase ('old' version) -- done (TJ)
+o implement a pathTwoTips method, which has to go fast to find shortest path between two tips - done (TJ): is now sp.tips.
+o basic stuff existing in phylog objects (while option=TRUE), e.g. distance to the root for tips, etc.
 * proximities between OTUs like Abouheif, etc.
-* distances between OTUs (like sum of branch lengths) -- done (TJ)
-* dummy vectors indicating class of related OTUs (like in orthogram) -- done (TJ)
+o distances between OTUs (like sum of branch lengths) -- done (TJ)
+o dummy vectors indicating class of related OTUs (like in orthogram) -- done (TJ)
+* add a orthobasis method for objects inheriting phylo4.
 * orthogram
 * ppca
-* put some datasets from ade4
+* migrate some (all ?) datasets from ade4 to adephylo (lizards, mjrochet, ...)
 
 
 
@@ -62,7 +64,7 @@
 # LONG TERM
 ==========================
 ==========================
-* re-implement all phylogenetic methods from ade4 in adephylo
+* re-implement all relevant phylogenetic methods from ade4 in adephylo
 * implement several phylogenetic proximities
 * implement an orthobasis for phylogenies
 * write a comprehensive tutorial, going through adephylo, ade4, ape, phylobase, etc.