Changes in version 1.6 (2023-12-07)                   

Bug fixes

  - Corrected (minor) bugs in manhattan plot / qqplot functions

                 Changes in version 1.5.9 (2022-12-22)                  

New features

  - Default argument max.dist = 500e3 in LD.thin

Bug fixes

  - Corrected bug in ld clump, thanks to valgrind and Pr Ripley <3

                 Changes in version 1.5.8 (2022-12-09)                  

New features

  - new function LD.clump

                 Changes in version 1.5.7 (2020-09-24)                  

Implementation details

  - Corrected return; to return() as requested by the CRAN

  - Improved code for snp_hash.h (from gaston.utils)

New features

  - Argument EM in logistic-mm-aireml

                 Changes in version 1.5.6 (2020-02-26)                  

Bug fixes

  - Corrected bug in gwas lmm wald (PQL) (was sending back NaNs only :/
    )

                 Changes in version 1.5.5 (2019-04-02)                  

Bug fixes

  - Corrected naugthy bug in logistic regression (in case of 20
    iterations, still compute covariance matrix!!!) (bug introduced
    in 1.5.4)

New features

  - Started to write an FAQ

                 Changes in version 1.5.4 (2018-07-15)                  

New features

  - New functions SNP.rm.duplicates and set.dist

  - Argument 'by = ' in SNP.match

Implementation details

  - Re-enabled TBB

  - Improved logistic regression code / small improvements in
    association.testa

                 Changes in version 1.5.3 (2018-01-30)                  

Implementation details

  - Cast in log() function (fix compilation error on solaris)

  - Modified plot thinning in qqplot.pvalues

                 Changes in version 1.5.2 (2018-01-24)                  

Implementation details

  - Remove some compilation warnings (-Wreorder)

  - Temporarily disable TBB (UBSAN test) + function setThreadOptions

                        Changes in version 1.5.1                        

New features

  - Improved functions association.test / random.pm

  - cbind : now keep p, mu, sigma

  - rbind : now handles alleles longer than 1

  - New functions qqplot.pvalue, manhattan

  - New functions SNP.duplicated, SNP.match

  - New functions lmm.restricted.likelihood,
    lmm.profile.restricted.likelihood

Implementation details

  - Vignette in knitr

                  Changes in version 1.5 (2017-05-25)                   

New features

  - VCF files support

  - Computation of the Dominance Matrix (DM)

  - New functions test.snps test.inds which.snps which.inds

  - Faster optimization with the diagonalization trick

  - Auto set the #threads when loaded

                 Changes in version 1.4.9 (2016-11-29)                  

New features

  - Modification of rbind, cbind to handle bed.matrices with different
    column names in @ped, @snps

  - A new test in association.test

  - Minor changes in GRM and LD.thin

                 Changes in version 1.4.8 (2016-11-05)                  

Bug fixes

  - Corrected bug in set.stats (stats for chr Y)

  - Finally removed CompQuadForm from dependence list !

New features

  - Minor modifs in read vcf, rbind, set.genomic.sex

  - New function merge.inds (function finally not exported)

  - New functions (short cuts) is.autosome, is.chr.x, is.chr.y,
    is.chr.mt

                 Changes in version 1.4.7 (2016-10-20)                  

Bug fixes

  - Corrected (minor) bug in association.test (handling of monomorphic
    SNPs in some tests)

New features

  - New function LD.plot (LDheatmap dependence removed)

  - Handling NAs in select.snp select.inds

  - Added chr X, Y, MT support / modified set.stats, set.genomic.sex
    accordingly

  - Added which.snps argument in LD.thin and GRM

  - rbind and cbind now check individuals ids / snp ids ; rbind check
    reference alleles and perform reference inversions / strand flips if
    needed.

  - Integrated code from CompQuadForm / removed dependence

  - Minor modifications of the vignette (update description of modified
    functions)

                 Changes in version 1.4.6 (2016-07-11)                  

Implementation details

  - Modified Imports/Depends fields to remove a warning about
    RcppParallel

  - Modified VCF handling functions to follow the new interface of
    WhopGenome (patch by Tomas Kalibera and Ulrich Wittelsbuerger)

New features

  - New functions logistic.mm.aireml, score.variance.linear,
    score.variance.logistic, score.fixed.linear, score.fixed.logistic

  - New argument get.P in lmm.aireml

  - New features and arguments in association.test

  - Minor modifications of the vignette (illustration of
    association.test)

                 Changes in version 1.4.5 (2016-03-30)                  

Bug fixes

  - corrected a bug in method 'show'

Implementation details

  - better handling of constraints in AIREML methods

  - faster implementation of GRM

New features

  - new function genomic.sex

                  Changes in version 1.4 (2016-02-10)                   

New features

  - introduced option gastion.auto.set.stats / updated vignette
    accordingly

  - added 'hz' in ped stats

  - new function reshape.GRM

  - as.bed.matrix no longer is a method, but a function

  - minor modifs in read.vcf

Implementation details

  - matrix4 now uses uint8_t array instead of char array (induced many
    small changes in the C++ code).

                 Changes in version 1.3.1 (2015-12-15)                  

Bug fixes

  - fixed an (intermittent) bug (?!) in kinhsip matrix computations

                         Changes in version 1.3                         

Bug fixes

  - corrected bug in HWE chi square (monomorphic SNP)

New features

  - select.snps and select.inds (negative indices, presence of NAs)

                  Changes in version 1.2 (2015-11-10)                   

Improvements

  - kinship matrix is now in single precision (faster)

  - various minor changes

                  Changes in version 1.1 (2015-10-03)                   

Corrections

  - corrected C++ code (compilation errors on some distributions)