Changes in version 1.13 o fitQTL now returns CI for the additive and digenic effects Changes in version 1.12 o Updated convert_polyorigin to handle PolyOrigin version 2 Changes in version 1.11 o Fixed numerical underflow error in BayesCI, and now only first/last marker returned Changes in version 1.10 o Fixed h2 output for binary traits Changes in version 1.09 o fixed bug in phased_parents for diploids Changes in version 1.08 o fixed error in convert_rabbit regarding parental haplotype naming Changes in version 1.07 o new function haplo_match to match up haplotypes between two phased parent files Changes in version 1.06 o null model for scan1 did not include the covariate; fixed now Changes in version 1.05 o Removed NA before running BGLR to avoid NA for DIC Changes in version 1.04 o Fixed error introduced in 1.02 for fitQTL Changes in version 1.03 o No longer assumes first column in phenotype file is named "id" Changes in version 1.02 o Matrix objects cast to base matrix class to prevent error with BGLR o Fixed error with dominance=1 in fitQTL Changes in version 1.01 o Separate tmp directories used in scan1 to prevent problems with parallel execution on some machines Changes in version 1.00 o Added epistasis to IBDmat o Renamed cofactor argument to covariate for scan1 Changes in version 0.99 o Changed function name to convert_polyorigin o Renamed polyorigin slot as "input" o Proportion of variance computed based on clone rather than plot average Changes in version 0.98 o Updated documentation o Fixed scan1_summary plot's flip and threshold arguments o Fixed set_params output. The help does not save it in a par1 object anymore Changes in version 0.97 o Added read_rabbit function for diploids Changes in version 0.96 o Added outstem option to read_polyancestry o New arguments for fitQTL to allow multiple QTL and epistasis o Added kinship matrices to diallel_geno class, computed in read_data, for faster fiTQTL o Renamed qtl1 as runBGLR o Changed set_params to return results for each genetic variance component o Changed scan1 and set_params to call fitQTL for better code stewardship Changes in version 0.95 o Updated scan1_summary for default statistic as deltaDIC o Added marker position in fine_map o Replaced LODthresh with DIC_thresh o Added alpha parameter for DIC_thresh o Fixed all the notes for R checking o Updated vignette in terms of deltaDIC Changes in version 0.94 o Changed default value for dominance in read_data to 4 o Updated vignette Changes in version 0.93 o Added new cofactor functionality to fitQTL o Removed Gprep function o Added n.core option for IBDmat Changes in version 0.92 o Modified permutation test to preserve relationship between phenotypes and fixed effects o Modified cofactor functionality in scan1 to include additive x additive epistasis o Modified scan1_summary so that either DIC or LOD can be used Changes in version 0.91 o Updates to fine_map o Switched from mclapply to parLapply for Windows compatibility Changes in version 0.90 o Added constraint that sum of qtl effects (for each order) is zero o Inclusion of CI for fitQTL is now optional Changes in version 0.89 o Changed R2 to r2 Changes in version 0.88 o Modified haplo_switch to become fine_map o Added bioRxiv citation Changes in version 0.87 o Modified haplo_unique to become haplo_cluster Changes in version 0.86 o Removed valents_summary o Added digenic model to LODthresh o Updated potato dataset Changes in version 0.85 o Modified haplo_freq plot, now returns frequency of individuals o Fixed read_polyancestry to handle degenerate case of 1 pop with 1 chrom o Added functions phased_parents and haplo_unique Changes in version 0.84 o Added function valents_summary Changes in version 0.83 o Added polygenic effect to fitQTL Changes in version 0.82 o Check whether marker is valid in set_params o Updated recommendation for set_params Changes in version 0.81 o Added function BayesCI o cM no longer optional Changes in version 0.80 o modified interface for set_params o merged Amat and Dmat into IBDmat o fitQTL returns residuals o fitQTL returns Bayesian CI o Changed color scheme for fitQTL plots o Dominance plot from fitQTL has dom above diagonal, add + dom below diagonal Changes in version 0.79 o Cosmetic change to scaling of GCA Changes in version 0.78 o Fixed bug in read_polyancestry o explicitly set stringsAsFactors = T when reading phenofile o Fixed tmp directory issue Changes in version 0.77 o Changed terminology from "haplotype.pairs" to "diplotypes" o Added functions to get and plot diplotype dosage o Added function to create input files from PolyOrigin output file o Changed formatting of output for fitQTL o BGLR output files now put in tmp directory Changes in version 0.76 o Adjusted frequency in haplo_freq by ploidy Changes in version 0.75 o Can now include multiple markers in haplo_plot o Fixed labeling error in fitQTL plot for diploids o Fixed error with dominance effects for diploids Changes in version 0.74 o scan1 output now includes all markers, not just bins o Added function haplo_freq o Changed name of haplotypes function to haplo_get Changes in version 0.73 o Corrected error with names for digenic effects Changes in version 0.72 o Corrected error introduced in v0.71 Changes in version 0.71 o Fixed documentation for set_params Changes in version 0.70 o Changed terminology from allele to haplotype o Added function haplo_switch o Changed name of dosage to haplotypes o Changed name of plot_dosage to haplo_plot o Added marker binning to reduce run time o Both cM and bp positions can be used o Added trigenic and quadrigenic dominance o Added parallel execution in read_data o Changed linear model o Removed "population" from pedigree input file Changes in version 0.63 o Fixed error with peak position units in scan1_summary Changes in version 0.62 o Fixed error with plot_dosage for S1 individuals o Removed default option for "distance" argument in plotting Changes in version 0.61 o Changed "distance" to "position" in plot_dosage and scan1_summary Changes in version 0.60 o Repository is public o Removed option to disable dominance in read_data o Removed qqplot and dominance option from set_params o Changed reporting of dominance variance to be proportion of total variance o Added LODthresh function o Removed two markers from the vignette dataset due to discordance with new reference genome o Changed display of R2 results to percent instead of proportion o Removed deltaDIC from scan1_summary o fitQTL returns h2 and d2 as named vector instead of list o Changed sign of phenotype data o Changed indiv to id