[adegenet-commits] r151 - pkg

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

Author: jombart
Date: 2008-07-09 23:41:37 +0200 (Wed, 09 Jul 2008)
New Revision: 151

Modified:
   pkg/ChangeLog
   pkg/TODO
Log:
Updated the ChangeLog and TODO


Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2008-07-08 09:23:05 UTC (rev 150)
+++ pkg/ChangeLog	2008-07-09 21:41:37 UTC (rev 151)
@@ -1,3 +1,36 @@
+			CHANGES IN ADEGENET VERSION 1.2-0
+
+
+NEW FEATURES
+
+	o implement different levels of ploidy in genind / genpop
+	objects. Make necessary adaptations throughout the package.
+
+	o put some stop where needed when ploidy!=2 is not handled.
+
+	o implement a "sep" argument in df2genind.
+
+	o implement accessor for genind/genpop: nLoc.
+
+	o implement "scaleGen" for genind/genpop, which allows for
+	different types of scaling.
+
+	o added several coercion methods, from genind/genpop to
+	data.frame, matrix and ktab objects.
+
+	o implemented propTyped, a function giving the proportion of
+	non-missing data in different ways.
+
+
+
+BUG FIXES
+
+	o missing data indicated in summary corrected (loci with more
+	alleles had more weight in the computations).
+
+
+
+
 			CHANGES IN ADEGENET VERSION 1.1-3
 
 

Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-07-08 09:23:05 UTC (rev 150)
+++ pkg/TODO	2008-07-09 21:41:37 UTC (rev 151)
@@ -26,19 +26,16 @@
 
 # CODE ISSUES:
 ==============
-* fix missing data indication in summaries -- done (TJ)
 
+
 # DOCUMENTATION ISSUES:
 =======================
 *
 
+
 # NEW IMPLEMENTATIONS:
 =====================
-* implement different levels of ploidy in genind / genpop objects.
-  - put some stop where needed when ploidy!=2 is not handled -- done (TJ)
-  - adapt intput functions to different degree of ploidy -- done (TJ)
-  - adapt genind2df -- done (TJ)
-  - look for other functions to adapt -- done (TJ)
+* 
 
 
 # TESTING:
@@ -53,7 +50,6 @@
 * in spca, when nfposi=0, the returned object actually contains what corresponds to nfposi=1. Comes from multispati in ade4. To correct in ade4.
 * use spcaIllus to illustrate global.rtest and local.rtest
 * check all examples and look for possible improvements
-* Implement "sep" argument in df2genind -- done(TJ)
 * Implement a method to merge different markers for the same individuals
 * Build accessors for marker names, indiv names, pop names, spatial coords, ... -- done in part (nLoc) (TJ)
 * Return a spatial object from monmonier (class sp?)
@@ -71,8 +67,9 @@
 * export to geneticsBase -- same thing
 * see where code needs tuning, and use C/C++
 * implement global.rtest and local.rtest for genind/genpop objects
-* Implement method "scale" for genind / genpop objects -- done (TJ)
 * Implement dudi wrappers for genind / genpop objects -- one step (automatic coercion as data.frames) (TJ)
 * Check the formulae provided for Reynolds (consistent with Felsenstein's
 formulae, not straightforward reading the original article)
-* Implement wrappers for spatial function (Moran's I, Mantel's correlogram, etc.).
\ No newline at end of file
+* Implement wrappers for spatial function (Moran's I, Mantel's correlogram, etc.).
+
+