NEWS

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rrBLUP 4.6.3 (2023-12-10)

• Header in package overview help file

rrBLUP 4.6.2 (2023-01-06)

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

rrBLUP 4.6.1 (2019-12-18)

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

rrBLUP 4.6 (2018-01-28)

• Fixed error in reference manual regarding shrinkage option for A.mat
• Changed normalization of A in Yang/Mueller shrinkage method

rrBLUP 4.5 (2017-06-12)

• Two shrinkage options now in A.mat
• Removed "reduce" and heterogeneous error options

rrBLUP 4.4 (2015-10-28)

• Modified GWAS plot functionality to play nice with RStudio
• kin.blup returns predicted values, averaged over the fixed effects
• kin.blup allows specification of heterogeneous error variance

rrBLUP 4.3 (2014-03-06)

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

rrBLUP 4.2 (2013-06-18)

• shrink=FALSE is now the default in A.mat
• Only return imputed markers in A.mat when impute=TRUE

rrBLUP 4.1 (2012-12-21)

• 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.
• Changed default to reduce=FALSE in kin.blup

rrBLUP 4.0 (2012-09-18)

• kinship.BLUP is no longer being improved. It has been replaced by kin.blup, which has a more intuitve interface.
• Shrinkage estimation functionality has been added to A.mat, which is beneficial at low marker density.

rrBLUP 3.8 (2012-05-17)

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

rrBLUP 3.7 (2012-04-10)

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

rrBLUP 3.6 (2012-04-03)

• Improved error handling in mixed.solve.

rrBLUP 3.5 (2012-02-14)

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

rrBLUP 3.4 (2012-02-06)

• Additional features for A.mat.

rrBLUP 3.3 (2012-02-01)

• Improved handling of missing genotype data in A.mat.
• Removed impute function. Imputation is now done through A.mat.

rrBLUP 3.2 (2012-01-24)

• Parallel computation enabled for GWA, A.mat, and kinship.BLUP.
• Missing genotypic data permitted for GWA.

rrBLUP 3.1 (2012-01-05)

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

rrBLUP 3.0 (2012-01-04)

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

rrBLUP 2.8 (2011-12-17)

• Added NEWS file
• Updated A.mat to calculate both the raw and adjusted UAR models.

rrBLUP 2.7 (2011-12-02)

• Updated mixed.solve to handle missing observations.
• Updated A.mat to handle missing alleles.

rrBLUP 2.5 (2011-11-23)

• rrBLUP manuscript is published. Included CITATION file.