Changes in version 4.6.3 (2023-12-10)                  

    o   Header in package overview help file

                 Changes in version 4.6.2 (2023-01-06)                  

    o   Changed parallel execution in A.mat to use cluster instead of forking

                 Changes in version 4.6.1 (2019-12-18)                  

    o   Updated code to address changes in behavior of "class" in base R

                  Changes in version 4.6 (2018-01-28)                   

    o   Fixed error in reference manual regarding shrinkage option for A.mat

    o   Changed normalization of A in Yang/Mueller shrinkage method

                  Changes in version 4.5 (2017-06-12)                   

    o   Two shrinkage options now in A.mat

    o   Removed "reduce" and heterogeneous error options

                  Changes in version 4.4 (2015-10-28)                   

    o   Modified GWAS plot functionality to play nice with RStudio

    o   kin.blup returns predicted values, averaged over the fixed effects

    o   kin.blup allows specification of heterogeneous error variance

                  Changes in version 4.3 (2014-03-06)                   

    o   Old-style vignettes are no longer allowed on CRAN, so they have been moved to http://potatobreeding.cals.wisc.edu/software.

                  Changes in version 4.2 (2013-06-18)                   

    o   shrink=FALSE is now the default in A.mat

    o   Only return imputed markers in A.mat when impute=TRUE

                  Changes in version 4.1 (2012-12-21)                   

    o   Replaced function GWA with GWAS for association mapping.  Improvements include (1) P3D is now optional, (2) multiple phenotypes handled, (3) Manhattan and qq plots are generated, (4) uses data frame for input.

    o   Changed default to reduce=FALSE in kin.blup

                  Changes in version 4.0 (2012-09-18)                   

    o   kinship.BLUP is no longer being improved.  It has been replaced by kin.blup, which has a more intuitve interface.

    o   Shrinkage estimation functionality has been added to A.mat, which is beneficial at low marker density.

                  Changes in version 3.8 (2012-05-17)                   

    o   Fixed error regarding imputation of monomorphic markers in A.mat.

                  Changes in version 3.7 (2012-04-10)                   

    o   Improved handling of positive semi-definite kinship matrix in mixed.solve.

                  Changes in version 3.6 (2012-04-03)                   

    o   Improved error handling in mixed.solve.

                  Changes in version 3.5 (2012-02-14)                   

    o   Labels now transfer from input to output with mixed.solve.

                  Changes in version 3.4 (2012-02-06)                   

    o   Additional features for A.mat.

                  Changes in version 3.3 (2012-02-01)                   

    o   Improved handling of missing genotype data in A.mat.

    o   Removed impute function.  Imputation is now done through A.mat.

                  Changes in version 3.2 (2012-01-24)                   

    o   Parallel computation enabled for GWA, A.mat, and kinship.BLUP.

    o   Missing genotypic data permitted for GWA.

                  Changes in version 3.1 (2012-01-05)                   

    o   Fixed error in regression coefficient for adjusted A.mat.

                  Changes in version 3.0 (2012-01-04)                   

    o   Major changes to A.mat.  Read the help manual.

                  Changes in version 2.8 (2011-12-17)                   

    o   Added NEWS file

    o   Updated A.mat to calculate both the raw and adjusted UAR models.

                  Changes in version 2.7 (2011-12-02)                   

    o   Updated mixed.solve to handle missing observations.

    o   Updated A.mat to handle missing alleles.

                  Changes in version 2.5 (2011-11-23)                   

    o   rrBLUP manuscript is published.  Included CITATION file.