[Picante-commits] r36 - / pkg/man

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

Author: skembel
Date: 2008-03-03 00:24:49 +0100 (Mon, 03 Mar 2008)
New Revision: 36

Modified:
   TODO
   pkg/man/phylosignal.Rd
Log:
Updated TODO and cleaned up documentation. Passes check cleanly now!

Modified: TODO
===================================================================
--- TODO	2008-03-02 23:06:54 UTC (rev 35)
+++ TODO	2008-03-02 23:24:49 UTC (rev 36)
@@ -3,13 +3,18 @@
 General notes: Many functions are untested or outright broken. Do not use any of these functions for 'real' analysis without getting in touch with a project developer first.
 
 TODO
--fix trait data input - currently most want a vector with names, should handle/check lack of names and allow data.frames (single or multiple columns).
+====
+For 0.1
+-------
+-fix trait data input - currently most functions expect a vector with names, should handle/check lack of names and allow data.frames (single or multiple columns).
 -fix null models - most assume presence-absence data but don't check
--fix null models - implement heavy lifting in C code - see BB's email for a start
--standardize use of null model functions
+-standardize use of null model functions (combine all into one function)
+-standardize species distance metrics (combine all into one function)
 -clean up/hide utility functions
--fix Kcalc - new version doesn't work with non-ultrametric trees
--phylosignal currently broken
+
+For 0.2
+-------
+-implement null model heavy lifting in C code - see BB's email for a start
 -implement contrib index and similar
 -qr on comdist as option
--fix .Rd files to pass CMD CHECK (etc.)
+-trait gradient analysis and contrast diagnostics functions from DDA

Modified: pkg/man/phylosignal.Rd
===================================================================
--- pkg/man/phylosignal.Rd	2008-03-02 23:06:54 UTC (rev 35)
+++ pkg/man/phylosignal.Rd	2008-03-02 23:24:49 UTC (rev 36)
@@ -13,7 +13,7 @@
   \item{x}{ Trait vector (same order as phy\$tip.label) }
   \item{phy}{ phylo object }
   \item{reps}{ Number of randomizations }
-  \item{reps}{ Additional arguments passed to pic }
+  \item{...}{ Additional arguments passed to pic }
 }
 \value{
  Data frame with columns...