0.9-7
======================

* Uploaded on R-Forge 2013 - 09 - 19

* updated dependency from igraph0 to igraph

0.9-6
======================

* Uploaded on R-Forge 2013 - 03 - 18

* Updated maize centromere positions according
  to maizeGDB, version 2
  
* Fixed bug in add.individuals

* Added option in codeGeno to code by a reference
  allele for each marker 
  
* Option to supply user-specified values instead 
  of the MAF to correct in function kin for 
  ret="realized" and ret="realizedAB" (thanks to
  Yvonne Badke for this suggestion)    
  
* Fixed bug in crossVal when committing a TS
  


0.9-5
======================

* Uploaded on R-Forge 2013 - 03 - 15

* Added warning in case of large entries in the
  inverse covariance matrix of crossVal

* Return original alleles in write.beagle, not
  only "A" and "B" by default in the marker file
  
* Added summary method for LDmat and LDdf  

* Fixed bugs in write.beagle and codeGeno (counting
  number of missing values with Beagle)

* Include lowest category for r2 and dist breaks
  in LDDist and plot.LDdf
  
* changed function .path.package to path.package   



0.9-4
======================

* Uploaded on CRAN 2012 - 09 - 20

* Bug fix in create.gpData() to get full compatibility
  with write.plink() and other functions

* In plot functions and LDDist and LDMap the format
  "png" is now available for graphic files. For fileType = "pdf"
  the option oneFile is added.

* new class 'GenMap' for marker maps

* generic plot functions for classes LDdf and LDmat. Decision 
  can be made between "dist" and "map" respectively and for both 
  "neighbour"

* search for duplicated IDs in create.gpData()

* fixed bug in print.report feature of codeGeno
  when non-numeric coded genotypes were used

* Included citation file


0.9-3
======================

* Uploaded on CRAN 2012 - 05 - 24

* Included default value for gpData$covar$family to
  avoid an error when running write.plink without
  family information, replaced error by a warning
  (on R-Forge since 2012 - 03 - 28)

* Included addtional 'print.report' argument for
  function codeGeno to generate (optionally) a report
  to decode original coding scheme, and count number
  of missing values per SNP

* Bug fix in codeGeno using family imputing, polymorphic
  families were identified partly incorrect

* Bug fix in predict.gpMod, when using BLUP and marker
  effects (on R-Forge since  2012-05-04)

* Renamed return argument in gpMod: predicton -> prediction

* Added argument 'ld.window' to function pairwiseLD
  (on R-Forge since  2012-05-07)

* Changed dependency: igraph -> igraph0
  (on R-Forge since  2012-05-10)

* Improved color key representation for plotGenMap
  (on R-Forge since 2012-05-22)

* Report of mean values for the diagonal/off-diagonal in
  summary.relationshipMatrix



0.9-2
======================

* Uploaded on CRAN 2012 - 03 - 22

* updated vignette, replace LDmaize.pdf by LDmaize.png

* proof-reading of the manual

* minor updates in the demos

