Changes in version 2.4.1 (2023-03-22)                  

  - Fixed minor native routine registration issue.
  - Drop defunct CI services.
  - Update link to paper.

                 Changes in version 2.4.0 (2021-12-08)                  

  - Add FWD() function for performing forward regressions.

                 Changes in version 2.3.0 (2021-10-05)                  

  - Add segments() function for finding non-overlapping segments based
    on a summary statistic.
  - preprocess(): Add nCores parameter.
  - findRelated(): Map indices to sample names for matrix inputs.
  - getG(): Add impute parameter.
  - getG(): Impute by mean instead of 0 if center = FALSE.
  - getG(): Use preprocess() internally for better performance.
  - as.BGData(): Read genetic distances in .bim file as double instead
    of integer.

                 Changes in version 2.2.0 (2020-08-02)                  

  - Follow [Bioconductor S4 practices][1].
      - If you have used new() to create BGData instances, please use
        the BGData() constructor function instead.
      - If you have used @ to access the slots of BGData instances,
        please use the geno(), pheno(), and map() accessors instead.
  - BGData():
      - Do not create dimnames for geno as this object is likely shared.
      - Check if geno has row names before creating pheno stub.
      - Check if geno has column names before creating map stub.
      - Rename IID in pheno stub to sample_id.
      - Rename mrk in map stub to variant_id.
      - Change format of rownames for pheno stub to a sequence starting
        with sample_ and rownames for map stub to a sequence starting
        with variant_ if geno does not have dimnames.
  - as.BGData():
      - Force column classes when loading .fam and .bim files.
      - Force FID and IID columns to be of type character when loading
        alternate phenotype files.
      - Do not make assumptions about the structure of dimnames of a
        BEDMatrix object if it is passed without .fam and .bim file
        unless they are NULL.
  - Add validity tests for BGData objects:
      - Check if number of rows of geno matches number of rows of pheno.
      - Check if number of columns of geno matches number of rows of
        map.
      - Warn if the row names of pheno do not match the row names of
        geno.
      - Warn if the row names of map do not match the column names of
        geno.
  - Add preprocess() function for fast centering, scaling, and
    imputation.
  - GWAS(): Return number of records used for each variant and allele
    frequencies in rayOLS.
  - Update citation instructions.
  - Use inherits(., *) instead of class(.) == * (R4 compat).

                 Changes in version 2.1.0 (2019-01-25)                  

  - Add chunkedMap() function.
  - Improve error handling in chunkedMap() and chunkedApply().
  - summarize(): Improve performance.
  - GWAS(): Improve performance of rayOLS method.
  - GWAS(): Fix bug when computing p-values for methods other than
    rayOLS, lsfit, or SKAT when i is used to subset samples.
  - GWAS(): Fix wrong results in lsfit method when covariates with
    missing values are used.
  - as.BGData(): Fix bug loading .fam and .bim files when path contains
    the word bed.

                 Changes in version 2.0.0 (2018-08-24)                  

Breaking Changes

  - Rename bufferSize to chunkSize.
  - Remove nTasks parameter from chunkedApply() and methods based on it.
  - Remove crossprods function.

Other Changes

  - Change chunking strategy to improve parallelism: instead of loading
    a subset of chunkSize in the main process, load a subset of
    chunkSize in the each fork. That way nTasks is not necessary anymore
    and the same code can be used for one core and multiple cores.
  - Add findRelated() function for use with matrices and symDMatrix
    objects.
  - Add orderedMerge() function that allows for phenotypes to be easily
    merged into a BGData object.
  - Performance improvements in getG() function: use single shared
    memory matrix to collect results.
  - Performance improvements in rayOLS method in GWAS() function.
  - getG_symDMatrix(): Support version 2 of symDMatrix package.
  - getG_symDMatrix(): Add chunkSize parameter.
  - getG_symDMatrix(): Add minVar parameter.
  - as.BGData(): Use rownames of BEDMatrix object as rownames for pheno,
    and colnames of BEDMatrix object as rownames for map.
  - Include process ID in verbose output if nCores > 1.

Bug Fixes

  - getG_symDMatrix(): Fix scaling error when scale = FALSE.
  - getG_symDMatrix(): Compute block indices correctly for out-of-order,
    non-sequential indices.
  - getG_symDMatrix(): Do not include centers and scales in attributes
    anymore because the influence of j and minVar is difficult to
    retain.

                 Changes in version 1.0.0 (2017-05-11)                  

Initial release.