[adegenet-commits] r255 - in pkg: . R man

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

Author: jombart
Date: 2009-01-27 18:12:16 +0100 (Tue, 27 Jan 2009)
New Revision: 255

Modified:
   pkg/R/handling.R
   pkg/TODO
   pkg/man/seppop.Rd
Log:
Updated TODO, added selpopsize


Modified: pkg/R/handling.R
===================================================================
--- pkg/R/handling.R	2009-01-27 16:49:38 UTC (rev 254)
+++ pkg/R/handling.R	2009-01-27 17:12:16 UTC (rev 255)
@@ -481,10 +481,10 @@
 #############
 # selpopsize
 #############
-setGeneric("selpop", function(x, ...) standardGeneric("selpop"))
+setGeneric("selpopsize", function(x, ...) standardGeneric("selpopsize"))
 
 ## genind method ##
-setMethod("selpop", signature(x="genind"), function(x,pop=NULL,nMin=10){
+setMethod("selpopsize", signature(x="genind"), function(x,pop=NULL,nMin=10){
 
     ## misc checks
     checkType(x)

Modified: pkg/TODO
===================================================================
--- pkg/TODO	2009-01-27 16:49:38 UTC (rev 254)
+++ pkg/TODO	2009-01-27 17:12:16 UTC (rev 255)
@@ -11,6 +11,7 @@
 # you achieved something
 # '*' indicates stuff to do
 # 'o' indicates done stuff
+# '*o*' indicates partly done stuff
 #
 # Inside a given section, priority goes decreasing.
 #
@@ -30,18 +31,18 @@
 ==============
 * fix request 1.2-2.04 (implement adjusted heretozygosity in summary)
 
+
 # DOCUMENTATION ISSUES:
 =======================
-* make a tutorial for the sPCA -- done (TJ)
 * explain new changes inside the tutorial (handling of AFLP/RAPD...)
 
 
 # NEW IMPLEMENTATIONS:
 =====================
 
-* implement handling of presence/absence data
-* add a type argument to genind/genpop objects
-* make all the required subsequent changes in the package:
+*o* implement handling of presence/absence data -- mostly done, but mostly issues a (fair) error (TJ)
+o add a type argument to genind/genpop objects -- done (TJ)
+o make all the required subsequent changes in the package: -- all done, some checks cannot harm (TJ)
 - class definition and checks
 - constructors
 - basic methods
@@ -58,6 +59,8 @@
 - propTyped
 - hybridize
 - repool
+o select genotypes by population sample size -- done <selpopsize> (TJ)
+o import SNPs from sequence data -- done <DNAbin2genind> (TJ)
 
 
 # TESTING:
@@ -73,7 +76,12 @@
 * use spcaIllus to illustrate global.rtest and local.rtest
 * check all examples and look for possible improvements
 * 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)
+*o* Build accessors for:
+- marker names
+- indiv names
+- pop names/factor -- done <pop> (TJ) 
+- spatial coords
+- nb of loci -- done <nLoc> (TJ) 
 * Return a spatial object from monmonier (class sp?)
 * implement classical Fst sensu Weir 1996 ? Or wait for EP to do it...
 * Implement different levels of ploidy in:
@@ -90,7 +98,6 @@
 * export to geneticsBase -- same thing
 * see where code needs tuning, and use C/C++
 * implement global.rtest and local.rtest for genind/genpop objects
-
 * 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.).

Modified: pkg/man/seppop.Rd
===================================================================
--- pkg/man/seppop.Rd	2009-01-27 16:49:38 UTC (rev 254)
+++ pkg/man/seppop.Rd	2009-01-27 17:12:16 UTC (rev 255)
@@ -1,6 +1,6 @@
 \encoding{UTF-8}
 \docType{methods}
-\name{seploc}
+\name{seppop}
 \alias{seppop}
 \alias{seppop-methods}
 \alias{seppop,ANY-method}