[adegenet-commits] r213 - pkg

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

Author: jombart
Date: 2008-12-04 22:57:06 +0100 (Thu, 04 Dec 2008)
New Revision: 213

Modified:
   pkg/TODO
Log:
Try to add a 'branches' directory


Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-11-28 17:00:41 UTC (rev 212)
+++ pkg/TODO	2008-12-04 21:57:06 UTC (rev 213)
@@ -9,6 +9,8 @@
 #
 # please add a "-- done" or "-- fixed" tag when
 # you achieved something
+# '*' indicates stuff to do
+# 'o' indicates done stuff
 #
 # Inside a given section, priority goes decreasing.
 #
@@ -26,31 +28,53 @@
 
 # CODE ISSUES:
 ==============
-* fix bug 1.2-2.01 (read.structure issue) -- fixed: was due to the default of "onerowperind" argument.
-* fix bug 1.2-2.02 (read.genetix issue) -- fixed: was due to an error in the data file (wrong nloc); now read.genetix corrects that automatically and issues a warning. (TJ)
-* fix bug 1.2-2.03 (monmonier issue) -- fixed: was a non-detected code 2 due to intersection check with previously drawn segment (was not always removed). (TJ)
+o fix bug 1.2-2.01 (read.structure issue) -- fixed: was due to the default of "onerowperind" argument.
+o fix bug 1.2-2.02 (read.genetix issue) -- fixed: was due to an error in the data file (wrong nloc); now read.genetix corrects that automatically and issues a warning. (TJ)
+o fix bug 1.2-2.03 (monmonier issue) -- fixed: was a non-detected code 2 due to intersection check with previously drawn segment (was not always removed). (TJ)
 * fix request 1.2-2.04 (implement adjusted heretozygosity in summary)
-* fix bug 1.2-2.05 (monmonier is such a pain is the ass)
-* !! comment the if(DEBUG) in monmonier when it is fixed -- fixed, done and done (TJ)
+o fix bug 1.2-2.05 (monmonier is such a pain is the ass) -- fixed, done and done (TJ)
+o !! comment the if(DEBUG) in monmonier when it is fixed -- done
+* make the package work after all changes (pass the check)
 
+
 # DOCUMENTATION ISSUES:
 =======================
 * make a tutorial for the sPCA -- done (TJ)
+* explain new changes inside the tutorial (handling of AFLP/RAPD...)
 
 
 # NEW IMPLEMENTATIONS:
 =====================
-* color plot for the sPCA results, based on RGB representation of Cavalli-Sforza -- done(TJ)
-* loadingplot for plotting loadings of one axis -- done (TJ)
-* adegenetTutorial function which opens the online tutorials -- done (TJ)
-* allow for the use of na.replace and scaleGen in spca function -- done (TJ)
-* add rupica dataset -- done (TJ)
-* enable reading data from URL (import2genind, read.[...]).
+o color plot for the sPCA results, based on RGB representation of Cavalli-Sforza -- done(TJ)
+o loadingplot for plotting loadings of one axis -- done (TJ)
+o adegenetTutorial function which opens the online tutorials -- done (TJ)
+o allow for the use of na.replace and scaleGen in spca function -- done (TJ)
+o add rupica dataset -- done (TJ)
+o enable reading data from URL (import2genind, read.[...]).
+* implement handling of presence/absence data
+* add a type argument to genind/genpop objects
+* make all the required subsequent changes in the package:
+- class definition and checks
+- constructors
+- basic methods
+- spca
+- distances
+- propShared
+- input/output
+- HWE
+- Fstat
+- old2new
+- scaleGen
+- genind2genpop
+- gstat.randtest
+- propTyped
+- hybridize
+- repool
 
 
 # TESTING:
 ==========
-* 
+* test reading from url files.
 
 
 
@@ -63,12 +87,12 @@
 * 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?)
-* implement classical Fst sensu Weir 1996
+* implement classical Fst sensu Weir 1996 ? Or wait for EP to do it...
 * Implement different levels of ploidy in:
 - hybridize
 - read.structure
 - propShared
-* Permit specification of a matrix of spatial weights in spca (email A. Piotti).
+o Permit specification of a matrix of spatial weights in spca (email A. Piotti) -- done (TJ)
 *
 
 
@@ -79,7 +103,7 @@
 * 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 dudi wrappers for genind / genpop objects -- one step (automatic coercion as data.frames) (TJ)
+o 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.).