Changes in version 1.1.6 (2026-05-12)                  

  - Remove superheat as dependency.

                 Changes in version 1.1.5 (2025-08-23)                  

Bug fixes:

  - Tests updated to comply with dependencies recent changes.

                 Changes in version 1.1.4 (2024-01-29)                  

Bug fixes:

  - Minor corrections on documentation and synthetic.cross.

                 Changes in version 1.1.3 (2022-11-28)                  

Improvements:

  - Tests have been improved.

Bug Fixes:

  - Fixed RM data frame exported by match.G2A in which combinations of
    row and columns were being replicated.

                 Changes in version 1.1.2 (2022-11-22)                  

Improvements:

  - Added a NEWS.md file to track changes to the package.

  - Small internal changes for better integration with ASRgwas.

  - Enabled qc.filtering to finish calculations when a single marker is
    left.

  - Code synthetic.cross will leave only one of the records if
    duplicated in the pedigree.

  - Code kinship.diagnostics will leave only one of the records if
    duplicated in the kinship matrix.

Bug Fixes:

  - Now kinship.diagnostics with clean = TRUE will not crash if there is
    nothing to remove.

                        Changes in version 1.1.1                        

Improvements:

  - Small internal changes for better integration with ASRgwas.

                        Changes in version 1.1.0                        

New Features:

  - The function snp.pruning for marker pruning based has been added.

  - The function synthetic.cross for obtaining the genotypes of
    offspring off of a set of crosses has been added.

  - The function snp.recode for marker recoding has been added.

  - The function H.matrix, which is a simplification of H.inverse, has
    been added.

  - In kinship.diagnostics, an option to determine the proportion of
    data points to use for plotting has been added to improve processing
    time.

  - Two new filters for markers have been added to qc.filtering, one
    based on inbreeding and one based on the observed heterozygosity
    (suggested by Simon Nadeau).

  - An option to draw group-dependent ellipses has been added to both
    snp.pca and kinship.pca.

  - Now the markers map can be passed to qc.filtering and will also be
    filtered.

Improvements:

  - Relevant attributes of an object (such as INVERSE) are preserved
    after using full2sparse and sparse2full.

  - Now qc.filtering can better deal with markers with all samples
    missing. These markers are removed first thing when the function is
    called.

  - Plot generation in match.G2A processing time has been reduced by a
    factor of ~3.

  - The recoding section of qc.filtering has been put into another
    function (snp.recode). The arguments related to recoding in the
    first have not been removed, but if used will generate a stop
    suggesting the usage of the latter. Consequently, the M.recode
    output has been removed.

  - More message control with message = TRUE/FALSE has been added to
    several functions.

  - Some internal linear algebra has been changed to improve processing
    time.

  - Error handling has been improved in G.inverse to provide more
    informative messages to the user.

  - Help files have been reviewed and improved.

Bug Fixes:

  - Now the colNames attribute is correctly assigned in full2sparse.