NEWS

Changes in 1.17
* fixed error with read-geno H matrix calculation when founders are not included in pedigree

Changes in 1.16
* Revised gain function to work for phenotypic and BLUP selection. See details.
* Changed reliability calculation in blup to include contribution of fixed effects for markers and heterosis. This required two additional slots in class blup_prep. 

Changes in 1.15
* In read_geno, fourth column of ped now fully controls individuals in H matrix 

Changes in 1.14
* Stage1 returns residuals from the BLUE and BLUP models as separate columns
* blup now able to return marker effects with H matrix

Changes in 1.13
* fixed error in the routine for multiple expt per env
* summary.var has new option for separate.loc
* Stage1 argument env allows to analyze only subset of environments
* Stage1 returns both plot and entry H2 for asreml

Changes in 1.12
* GWAS "DM" option modified so that now only the random effect is standardized. The effect itself still includes the fixed (heterosis) portion.

Changes in 1.11
* dominance function is now scaled to population, not just var component

Changes in 1.10
* Added support for multi-population/multi-ploidy analysis
* Fixed error in Stage1 related to multiple experiments per env

Changes in 1.09
* changed read.csv to fread in read_geno

Changes in 1.08
* summary.var and dominance functions now work for multi-trait

Changes in 1.07
* coerce_dpo updated to account for changes to the Matrix package

Changes in 1.06
* Duplicate values removed from pheno2.csv, updated Vignette2
* max.iter option in Stage1

Changes in 1.05
* Added function remove_spatialtrend

Changes in 1.04
* Added desired gains index option
* Changed name of argument "coeff" to "merit" in gain function
* Fixed error for multi-trait + multi-expt/env option in Stage1
* Pairwise option for multiple traits in Stage2
* Updated Vignette3

Changes in 1.03
* predict.geno allows marker effects model to be subset of geno variable

Changes in 1.02
* Handles positive semi-definite D matrix
* Additive covariates allowed in Stage2

Changes in 1.01
* Eliminated "fixed" output from Stage2, replaced with "params"
* New function "dominance" for reporting dominance parameters 

Changes in 1.00
* fixed bug in blup for AM/DM when using list of blup_prep inputs

Changes in 0.95
* corrected missing heterosis in dominance marker effect blups

Changes in 0.94
* Changed dgeMatrix call due to Matrix package update

Changes in 0.93
* Fixed bug encountered with missing environment and multiple traits

Changes in 0.92
* Added max.iter argument to Stage2, to control maximum number of ASReml-R iterations.
* Upon lack of convergence, Stage2 now terminates instead of prompting user.

Changes in 0.91
* Fixed bug for GWAS with non.add="none" option

Changes in 0.90
* Updated README, preparing for submission

Changes in 0.28
* Updated Vignette 3, including wheat dataset

Changes in 0.27
* renamed output blue to blues in Stage1
* changed internal representation for class_var and class_prep
* blup now accepts list of class_prep objects as input for multi-trait prediction
* use inbreeding command instead of summary for class_geno object
* changed dominance argument in Stage2 with non.add

Changes in 0.26
* Updated vignette dataset
* Stage2 returns factor loadings instead of uniplot (now public function)
* renamed index.weights index.coeff in blup function

Changes in 0.25
* directional dominance
* modified variance partitioning
* corr function
* gain function, restricted index
* summary method for class_geno
* multiple expt per env in Stage1

Changes in 0.20
* blup_prep now inverts MME instead of V if #id < #obs. This led to changes in class_prep.
* Modified numerical conditioning of G in read_geno. Function arguments changed.
* Option to use A matrix from pedigree file in read_geno
* Removed/renamed duplicate genotypes in vignette dataset

Changes in 0.17
* Fixed error for vcov=NULL in blup_prep

Changes in 0.16
* Partitioning of covariance
* summary correlation matrix interpreted differently

Changes in 0.15
* Dropping of environments in Stage2 now works
* blup_prep now works even with one environment

Changes in 0.14
* Added min.minor.allele argument to read_geno

Changes in 0.13
* multi-trait functionality completed and Vignette 3 added
* changed argument for blup from index.coeff to index.weights
* AIC returned in Stage1 with asreml solver

Changes in 0.12
* Improved analysis and reporting for fixed effects markers 

Changes in 0.11
* Handling of missing environments in Stage 1

Changes in 0.10
* Removed g.resid x loc from Stage 2

Changes in 0.09
* Improved handling of missing environments in Stage1
* Fixed handling NA in genotype data

Changes in 0.08
* blup returns marker effects with proper scale 
* blup returns sum of random and fixed effects for marker effects
* Added predict method to class_geno

Changes in 0.07
* Modified NAMESPACE for asreml

Changes in 0.06
* Stage1 and Stage2 multi-trait completed
* Changed summary output to proportion of variance
* Monomorphic markers removed with read_geno

Changes in 0.05
* Added SpATS option to Stage 1 and updated vignette
* {-1,0,1} coding allowed for diploids in read_geno

Changes in 0.04
* Changed scaling of index coefficients