#######################
#
# adegenet TODO list
#
#######################
#
# please list here all intended modifications
# and all detected bugs
#
# please add a "-- done" or "-- fixed" tag when
# you achieved something
# '*' indicates stuff to do
# 'o' indicates done stuff
# '*o*' indicates partly done stuff
#
# Inside a given section, priority goes decreasing.
#
# Delete fixed things each new release.
#
# T.J. 2008
#
######################



# FOR NEXT STABLE VERSION
=========================
=========================

# CODE ISSUES:
==============
* fix request 1.2-2.04 (implement adjusted heretozygosity in summary)


# DOCUMENTATION ISSUES:
=======================
* explain new changes inside the tutorial (handling of AFLP/RAPD...)


# NEW IMPLEMENTATIONS:
=====================

o allow genind2df to export alleles on separate columns -- done


# TESTING:
==========


# LOW PRIORITY / MINOR ISSUES
===========================
===========================
* 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
* Implement a method to merge different markers for the same individuals
*o* Build accessors for:
- marker names -- done <locNames> (TJ)
- 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:
- hybridize - done (TJ)
- read.structure



# LONG TERM
==========================
==========================
* import from pegas
* import from geneticsBase -- wait for geneSet to be stable
* 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.).


