#######################
#
# adegenet TODO list
#
#######################
#
# please list here all intended modifications
# and all detected bugs
#
# please add a "-- done" or "-- fixed" tag when
# you achieved something
#
# Inside a given section, priority goes decreasing.
#
# Delete fixed things each new release.
#
# T.J. 2008
#
######################



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

# 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:
==========
* 



# LOW PRIORITY / MINOR BUGS
===========================
===========================
* 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?)
* implement classical Fst sensu Weir 1996
* Implement different levels of ploidy in:
- hybridize
- read.structure
- propShared


# LONG TERM
==========================
==========================
* 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
* 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.).