NEWS

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polyBreedR 0.46

• improved VCF parsing of model params for gbs(model.file=FALSE)

polyBreedR 0.45

• G_mat has option for allele matching (AM) coefficient
• Updated CDF1 analysis in madc

polyBreedR 0.44

• G_mat has option for reference allele frequency

polyBreedR 0.43

• impute_L2H was missing mean/mode imputation for CSV input
• changed default n.mark to 100 for impute_L2H

polyBreedR 0.42

• new option "model.fit" in gbs function
• check_ploidy accepts VCF input

polyBreedR 0.41

• Generalized data input for madc

polyBreedR 0.40

• OFP20 option in madc

polyBreedR 0.39

• Changed impute_PO to impute_LA to allow for other methods eventually (MAPpoly)

polyBreedR 0.38

• Added chunk.size option to gbs
• exception handling in impute_L2H

polyBreedR 0.37

• Vignette 3

polyBreedR 0.36

• PolyOrigin option moved to impute_PO
• GT2DS has multicore option
• internal changes for impute_L2H

polyBreedR 0.34

• GT2DS function has diploidize option
• impute_L2H has PolyOrigin ("PO") option
• madc function
• vcf2csv function

polyBreedR 0.33

• updates to gbs function
• fr2vcf renamed to array2vcf, now with options for both long and wide format
• created impute_L2H function
• update_alias removes leading zeros in progeny id

polyBreedR 0.32

• handling of missing AD in gbs

polyBreedR 0.31

• fr2vcf function

polyBreedR 0.30

• minor bug in impute

polyBreedR 0.29

• modified dart_tag to become dart2vcf
• new functions gbs, impute, write_vcf

polyBreedR 0.28

• new function array2VCF for storing SNP array data in VCF

polyBreedR 0.27

• dart_tag function has option to output B allele dosage
• update_alias can be used to update file

polyBreedR 0.26

• Added dart_tag function
• updated potato_V3array_map.csv with REF column for dart_tag
• fixed readXY bug due to changes in tidyr
• fixed slight bug in merge_impute

polyBreedR 0.25

• Moved functions for stage-wise analysis to R package StageWise

polyBreedR 0.24

• Fixed naming conflict in Stage2

polyBreedR 0.23

• Changes to multi-trait functionality

polyBreedR 0.22

• Completed multi-trait functionality for Stage2 and predict_MME

polyBreedR 0.21

• Changed name of argument in predict_MME to mask
• Conditioning of kernel matrices in Stage2

polyBreedR 0.20

• Changes in Stage2

polyBreedR 0.19

• Added cross-validation to Vignette 3 and predict_MME

polyBreedR 0.18

• Completed Vignette 3 for genomic selection.
• Modifications to Stage1, Stage2_prep, Stage2
• Added function dart_tag

polyBreedR 0.17

• Updated sparse matrix handling for stage wise analysis

polyBreedR 0.16

• Added PSD to Omega in Stage2

polyBreedR 0.15

• Major revisions to functions for two-stage analysis

polyBreedR 0.14

• Major revisions to functions for two-stage analysis

polyBreedR 0.13

• Removed some poor markers from V3array_model
• Fixed error with trim_ped

polyBreedR 0.12

• Changed G_coeff to G_mat
• Added several new functions for genomic selection

polyBreedR 0.11

• Options for axis limits in GvsA