Chanegs in version 1.0.2 (2026-04-28)
  o 2026-04-28
  o Added stringr to DESCRIPTION.
  o Removed curly braces from the documentation of the cALD(), LD.heat.map() and LD.sign.test() functions.
  o Update URLs in the vignette.
  o Resubmitted for unarchiving from CRAN.

Changes in version 1.0.1 (2020-10-08)
  o 2020-10-08
  o Resubmitted for unarchiving from CRAN.

Changes in version 1.0.0 (2020-04-10)
  o 2020-04-10
  o Included options for users to specify the directory into which files should be written for
    cALD(), LD.heat.map(), LD.sign.test() and LDwrap().
  o Changed cat() messages to warning messages() in LD.heat.map(), LD.sign.test() and LDWrap().
  o Renamed the reportVector parameter in cALD to saveVector.
  o Submission to CRAN.

Changes in version 0.10.5.9000 (2020-02-21)
  o 2020-02-21
  o Changes to documentation in advance of CRAN submission.

Changes in version 0.10.4.9000 (2019-10-17)
  o 2019-10-17
  o Updated the vignette to include recommendations on locus order.

Changes in version 0.10.3.9000 (2019-10-15)
  o 2019-10-15
  o Updated LDWrap() and parseGenotypes() to to streamline parsing and processing of 'untyped data'.

Changes in version 0.10.2.9000 (2019-10-14)
  o 2019-10-14
  o Updated LDWrap() and parseGenotypes() to reject single-locus genotype files.
  o Additional updates to LDWrap() to support text files.

Changes in version 0.10.1.9000 (2019-10-08)
  o 2019-10-08
  o Updated LDWrap() to accomodate tab-delimited text (.txt or .tsv) format files.

Changes in version 0.10.0.9000 (2019-10-05)
  o 2019-10-05
  o Updated package DESCRIPTION.
  o Updated LD.heat.map() to account for locus pairs with no LD values.
  o Added the parseGenotypes() function to support column-formatted genotype data.
  o Updated LDWrap() to incorporate parseGenotypes().
  o Updated the citations to reflect recent publications.
  o Updated the Vignette.

Changes in version 0.9.1.9000 (2019-08-01)
   o Removed notes regarding gap::LDkl() from ReadMe and Vignette documents.
   o Updated documentation for LDWrap() to reflect current data requirements.

Changes in version 0.9.0.9000 (2019-07-26)
   o Added the trimAlleles() function to LDWrap() to enable the truncation of
     colon-delimited allele names to a specified number of fields.
   o When a positive trunc value is provided to LDWrap(), the generated files
     include the truncation level in their filenames.
   o Updated the documentation for cALD()'s vectorPrefix parameter.
   o Updated the ReadMe.md and Vignette documents to reflect these changes.
   o Thanks to K. Osoegawa for suggesting the above improvements.
   o Added a user notification to LDWrap() for instances when famData is not defined.
   o Corrected a typo in the LD.heat.map documentation.
   o Reformatted NEWS to function under R version 3.6.0.
   o Updated DESCRIPTION file.

Changes in version 0.8.5.9000 (2019-07-12)
   o Addressed a Warning being generated by LD.heat.map().
   o Shortened an example on the LD.heat.map() Help Page.
   o Updated the message delivered by LD.heat.map() when different loci are
    included in specified phased and unphased LDWrap() outputs.

Changes in version 0.8.4.9000 (2019-11-07)
   o Added the phasedData and unphasedData parameters to LD.heat.map(), allowing
    users to identifify specific LDWrap() output files to be used to generate
    heatmaps.
   o Modified the LD.heat.map() Vignette and function documentation to reflect
    these changes.
   o Modified the 6-21-2019 NEWS entry for grammar and accuracy.

Changes in version 0.8.3.9000 (2019-03-07)
   o Corrected the citation for the publication describing this package in the
    LD.heat.map(), LD.sign.test() and LDWrap() functions.
   o Expanded the package name in the GitHub ReadMe document.
   o Added the note about the LDkl() function in the gap package to the ReadMe
    and moved this note higher in the vignette.

Changes in version 0.8.2.9000 (2019-06-21)
  o Added phasedLabel and unphasedLabel to LD.heat.map(), allowing users to
   specify the labels associated with the upper and lower half of each plot.
  o Modified the LD.heat.map() Vignette and function documentation to reflect
   these changes, and to cite a publication describing this package.
  o Happy Summer Solstice!

Changes in version 0.8.1.9000 (2019-02-28)
  o Added the color parameter to LD.heat.map(), allowing color or grey-scale
   heat-map plots to be generated.
  o Added the color parameter to the Vignette and LD.heat.map() documentation.
  o Added keywords to the LD.heat.map() documentation.
  o Modified the LDWrap() Vignette to make it clear that ambiguous allele and
   genotype data cannot be included in LDWrap() data files.
  o Removed example non-ggplot heat-map code.

Changes in version 0.8.0.9000 (2019-02-27)
  o Added the LD.heat.map() function to generate heat maps of LD values from
   the LD data exported from LDWrap().
  o Updated the ReadMe.md and Vignette documents to reflect the changes to
   LDWrap() and the addition of the LD.heat.map() function.

Changes in version 0.7.0.9000 (2019-02-06)
  o Added a Reference to the documentation of LDWrap() and LD.sign.test().
  o Added the extractLoci() function to LDWrap() to automate the processing of
   locus information from haplotype datasets, accommodating non-HLA data.

Changes in version 0.6.3.9000 (2018-09-24)
  o Modified Vignette to reflect the limitations of LDkl in the gap package
   and the availability of an updated gap package on GitHub.
  o Modified ReadMe.md document to include devtools installation instructions.
  o Thanks to L. Creary for identifying both issues.
  o Modified Description to mention sign tests.

Changes in version 0.6.2.9000 (2018-06-28)
  o Modified cALD(), LDWrap() and LD.sign.test() so that output files are
   always written to the working directory.

Changes in version 0.6.1.9000 (2018-06-27)
  o Updated LDWrap() documentation to include caveats regarding the analysis of
   unusual and truncated allele names.
  o Added package versioning to the README.md document.

Changes in version 0.6.0.9000 (2018-06-06)
  o Added the LD.sign.test() function.
  o Updated documentation to reflect this addition.
  o Corrected a typo in 5-18-2018 News entry.

Changes in version 0.5.0.9000 (2018-05-18)
  o Modified LDWrap() to avoid calling cALD() for locus pairs in which at least
   one locus is monomorphic. In these cases, the *LD_results.csv file identifies
   which loci were monomorphic for that locus pair.
  o Updated documentation to reflect this.

Changes in version 0.4.2.9000 (2018-05-12)
  o Streamlined the integration of cALD() into LDWrap().

Changes in version 0.4.1.9000 (2018-05-11)
  o Updated the Vignette and ReadMe file to correct versioning, punctuation and
   spelling errors, and elaborate on documentation for cALD()'s report of the
   number of haplotypes.

Changes in version 0.4.0.9000 (2018-05-08)
  o Added the number of haplotypes evaluated to the values returned by cALD(),
   and thereby to the content of the *LD_results.csv file generated by LDWrap().
  o Updated the documentation to reflect this.

Changes in version 0.3.0.9000 (2018-05-03)
  o Revised drb1.dqb1.demo so that it represents phased DRB1~DQB1 data pulled
   directly from hla.hap.demo.
  o Added README.Rmd and README.md files for GitHub.
  o Added NEWS.
  o Added Vignette.
  o Changed LDWrap() notification for input data lacking required columns, to
   reflect the data source as either a data frame or a file.
  o Removed the passFile parameter from cALD(), and updated documentation.

Changes in version 0.2.1.9000 (2018-04-30)
  o Added dataset documentation files.

Changes in version 0.2.0.9000 (2018-04-28)
  o Added *Rd files for each function.
  o Added hla.hap.demo and drb1.dqb1.demo datasets.

Changes in version 0.1.0.9000 (2018-04-27)
  o Created package that includes the exported LDWrap() and cALD() functions,
   and the internal writeVector() function.
