#######################
#
# adegenet TODO list
#
#######################
#
# please list here all intended modifications
# and all detected bugs
#
# please add a '-- done' or '-- fixed' tag when
# you achieved something, and replace the 
# initial star '*' (to do) with a 'o' (done).
#
# Inside a given section, priority goes decreasing.
#
# Delete fixed things each new release.
#
# T. Jombart, 2008
#
######################



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

# CODE ISSUES:
==============
o make a working package that passes the check -- done (TJ)

# DOCUMENTATION ISSUES:
=======================
* make a vignette


# NEW IMPLEMENTATIONS:
=====================
o plot methods from phylobase ('old' version) -- done (TJ)
o implement a pathTwoTips method, which has to go fast to find shortest path between two tips - done (TJ): is now sp.tips.
o basic stuff existing in phylog objects (while option=TRUE), e.g. distance to the root for tips, etc.
o proximities between OTUs like Abouheif, etc. -- done (TJ)
o distances between OTUs (like sum of branch lengths) -- done (TJ)
o dummy vectors indicating class of related OTUs (like in orthogram) -- done (TJ)
o add a orthobasis method for objects inheriting phylo4 or phylo. -- done(TJ)
o orthogram and multivariate orthogram; use Stephane's version -- done (SD, TJ)
o ppca -- done (TJ)
o migrate datasets from ade4 to adephylo: -- done (TJ)
- carni19.Rd -- done
- carni70.Rd -- done
- lizards.Rd -- done
- maples.Rd -- done
- mjrochet.Rd -- done
- palm.Rd -- done
- procella.Rd -- done
- tithonia.Rd -- done
- ungulates.Rd -- done
o build an orthobasis from treePart dummy variables -- done (TJ)
o move gearymoran inside adephylo -- done, is now abouheif.moran. (TJ)



# TESTING:
==========
o test distTips a little more (see Abouheif with an outgroup, otherwise seems ok) -- done (TJ)
o test ppca: are results identical to those with previous implementation? -- done (TJ)



# LOW PRIORITY / MINOR ISSUES
===========================
===========================
* draw a rectangle around legend in table.phylo4d


# LONG TERM
==========================
==========================
o re-implement all relevant phylogenetic methods from ade4 in adephylo -- done (TJ)
o implement several phylogenetic proximities -- done (TJ)
o implement an orthobasis for phylogenies -- done (TJ)
* write a comprehensive tutorial, going through adephylo, ade4, ape, phylobase, etc.
o new plotting / summary for ppca objects. Maybe move actual plot to a scatter method, and make a plot similar to other plots. -- done (TJ)
o make a summary method for ppca. -- done (TJ)

