NEWS

Changes in 1.13
* fitQTL now returns CI for the additive and digenic effects

Changes in 1.12
* Updated convert_polyorigin to handle PolyOrigin version 2

Changes in 1.11
* Fixed numerical underflow error in BayesCI, and now only first/last marker returned

Changes in 1.10
* Fixed h2 output for binary traits

Changes in 1.09
* fixed bug in phased_parents for diploids

Changes in 1.08
* fixed error in convert_rabbit regarding parental haplotype naming

Changes in 1.07
* new function haplo_match to match up haplotypes between two phased parent files

Changes in 1.06
* null model for scan1 did not include the covariate; fixed now

Changes in 1.05
* Removed NA before running BGLR to avoid NA for DIC

Changes in 1.04
* Fixed error introduced in 1.02 for fitQTL

Changes in 1.03
* No longer assumes first column in phenotype file is named "id"

Changes in 1.02
* Matrix objects cast to base matrix class to prevent error with BGLR
* Fixed error with dominance=1 in fitQTL

Changes in 1.01
* Separate tmp directories used in scan1 to prevent problems with parallel execution on some machines

Changes in 1.00
* Added epistasis to IBDmat
* Renamed cofactor argument to covariate for scan1

Changes in 0.99
* Changed function name to convert_polyorigin
* Renamed polyorigin slot as "input"
* Proportion of variance computed based on clone rather than plot average


Changes in 0.98
* Updated documentation
* Fixed scan1_summary plot's flip and threshold arguments
* Fixed set_params output. The help does not save it in a par1 object anymore

Changes in 0.97
* Added read_rabbit function for diploids

Changes in 0.96
* Added outstem option to read_polyancestry
* New arguments for fitQTL to allow multiple QTL and epistasis
* Added kinship matrices to diallel_geno class, computed in read_data, for faster fiTQTL
* Renamed qtl1 as runBGLR
* Changed set_params to return results for each genetic variance component
* Changed scan1 and set_params to call fitQTL for better code stewardship

Changes in 0.95
* Updated scan1_summary for default statistic as deltaDIC
* Added marker position in fine_map
* Replaced LODthresh with DIC_thresh
* Added alpha parameter for DIC_thresh
* Fixed all the notes for R checking
* Updated vignette in terms of deltaDIC

Changes in 0.94
* Changed default value for dominance in read_data to 4
* Updated vignette

Changes in 0.93
* Added new cofactor functionality to fitQTL
* Removed Gprep function
* Added n.core option for IBDmat

Changes in 0.92
* Modified permutation test to preserve relationship between phenotypes and fixed effects
* Modified cofactor functionality in scan1 to include additive x additive epistasis
* Modified scan1_summary so that either DIC or LOD can be used

Changes in 0.91
* Updates to fine_map
* Switched from mclapply to parLapply for Windows compatibility

Changes in 0.90
* Added constraint that sum of qtl effects (for each order) is zero
* Inclusion of CI for fitQTL is now optional

Changes in 0.89
* Changed R2 to r2

Changes in 0.88
* Modified haplo_switch to become fine_map
* Added bioRxiv citation

Changes in 0.87
* Modified haplo_unique to become haplo_cluster

Changes in 0.86
* Removed valents_summary
* Added digenic model to LODthresh 
* Updated potato dataset

Changes in 0.85
* Modified haplo_freq plot, now returns frequency of individuals
* Fixed read_polyancestry to handle degenerate case of 1 pop with 1 chrom
* Added functions phased_parents and haplo_unique

Changes in 0.84
* Added function valents_summary

Changes in 0.83
* Added polygenic effect to fitQTL

Changes in 0.82
* Check whether marker is valid in set_params
* Updated recommendation for set_params

Changes in 0.81
* Added function BayesCI
* cM no longer optional 

Changes in 0.80
* modified interface for set_params 
* merged Amat and Dmat into IBDmat
* fitQTL returns residuals 
* fitQTL returns Bayesian CI
* Changed color scheme for fitQTL plots
* Dominance plot from fitQTL has dom above diagonal, add + dom below diagonal

Changes in 0.79
* Cosmetic change to scaling of GCA

Changes in 0.78
* Fixed bug in read_polyancestry
* explicitly set stringsAsFactors = T when reading phenofile
* Fixed tmp directory issue

Changes in 0.77
* Changed terminology from "haplotype.pairs" to "diplotypes"
* Added functions to get and plot diplotype dosage
* Added function to create input files from PolyOrigin output file
* Changed formatting of output for fitQTL
* BGLR output files now put in tmp directory

Changes in 0.76
* Adjusted frequency in haplo_freq by ploidy

Changes in 0.75
* Can now include multiple markers in haplo_plot
* Fixed labeling error in fitQTL plot for diploids
* Fixed error with dominance effects for diploids

Changes in 0.74
* scan1 output now includes all markers, not just bins
* Added function haplo_freq
* Changed name of haplotypes function to haplo_get

Changes in 0.73
* Corrected error with names for digenic effects

Changes in 0.72
* Corrected error introduced in v0.71

Changes in 0.71
* Fixed documentation for set_params

Changes in 0.70
* Changed terminology from allele to haplotype
* Added function haplo_switch
* Changed name of dosage to haplotypes
* Changed name of plot_dosage to haplo_plot
* Added marker binning to reduce run time
* Both cM and bp positions can be used
* Added trigenic and quadrigenic dominance
* Added parallel execution in read_data
* Changed linear model
* Removed "population" from pedigree input file

Changes in 0.63
* Fixed error with peak position units in scan1_summary

Changes in 0.62
* Fixed error with plot_dosage for S1 individuals
* Removed default option for "distance" argument in plotting

Changes in 0.61
* Changed "distance" to "position" in plot_dosage and scan1_summary

Changes in 0.60
* Repository is public
* Removed option to disable dominance in read_data
* Removed qqplot and dominance option from set_params
* Changed reporting of dominance variance to be proportion of total variance
* Added LODthresh function 
* Removed two markers from the vignette dataset due to discordance with new reference genome
* Changed display of R2 results to percent instead of proportion
* Removed deltaDIC from scan1_summary
* fitQTL returns h2 and d2 as named vector instead of list
* Changed sign of phenotype data
* Changed indiv to id