NEWS

GeneticsPed 1.1.0

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.

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.

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.

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.

? 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.