# NEWS
#--------------------------------------------------------------------------
# What: What are the news for GeneticsPed?
# Time-stamp: <2007-09-20 00:49:16 ggorjan>
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1.1.0
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+ 2007-09-12 Gregor Gorjanc

    o Added prune function for pruning/trimming the pedigree. It does not
      work on pedigree, but assumes a data.frame with defined structure.
      Adaption needed.

    o We depend on genetics package since gpLong2Wide and hwp assume that
      input is of genotype class.

    o Added two utility functions (gpLong2Wide and hwp) for work with
      gpi(). There is also a separate help page for them.

    o Internal fixes in gpi
      - no need to transpose inputs for Fortran call anymore
      - check that there are no NA values in gp and hwp

+ 2007-04-25 Gregor Gorjanc

    o Version bump to follow BioC releases.

0.1.4
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+ 2007-04-19 Gregor Gorjanc

    o Added internal .get* functions for retrieving slot values and use of
      it.

+ 2007-04-18 Gregor Gorjanc

    o R CMD check should now fail also when R error (usually call to
      stop()) occurs in unit testing.

    o Added unit tests for sort, examples in help page and clarified sort
      help page.

+ 2007-04-?? Dave Henderson

    o Implemented sort by pedigree information only.

0.1.3
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+ 2007-04-06 Gregor Gorjanc

  o New small dataset Falconer5.1.

  o Added sex(), sex<-(), ascendantSex() and ascendantSex<-()
    functions.

  o Added some more tests for relationshipAdditive, inverseAdditive and
    inbreeding.

0.1.2
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+ 2007-04-01 Gregor Gorjanc

    o Now we are more rigorous for value of ascendantSex argument in
      Pedigree(). It must accord to values in sex column, if that one is
      passed of course.

    o MASS added to depends due to use of fractions() in many places in
      documnetation.

    o Added vignette on quantitative genetic (animal) model and
      model.matrix.Pedigree() functions for educational
      purposes.

    o Created data directory and added pedigree example Mrode2.1 and
      Mrode3.1.

    o Added unit tests for genetic relationship matrices that should test
      all related functions - mainly against Mrode's book examples -
      runit.genRelMatrix.R.

    o Added arguments sort and names to inverseAdditive(),
      relationshipAdditive() and inbreeding().

    o Reworked core for relationshipAdditive() into vectorized form.

    o Added geneFlowT(), geneFlowTinv(), geneFlowM() and mendelianSamplingD()
      functions.

+ 2007-03-02 Gregor Gorjanc

    o Registration of native routines - src/register.cc.

    o Added gpi() function.

0.1.1
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+ ?
    o Temporarily removed unknown funcs, due to planned move to BioC and
      change to S4.

    o All depends are now in gdata --> removing ggmisc.

+ 2006-03-29 Gregor Gorjanc

    o codeUnit to get internal codes for subject and ascendants if factors
      are used.

    o Handled unused levels in nlevels.pedigree and summary.pedigree now
      produces a simple summary

    o Started to implement checks in check.pedigree and friends

    o Proper factor handling

+ 2006-03-16 Gregor Gorjanc

    o Playing around with NA/unknown representation - it is very likely
      that I messed up some things with factors --> subject to changes.

0.1.0
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    o Initial version

