                 Changes in version 1.0.1 (2020-10-16)                  

    o   2020-10-08

    o   Resubmitted for unarchiving from CRAN.

                 Changes in version 1.0.0 (2020-04-15)                  

    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                     

    o   2020-02-21

    o   Changes to documentation in advance of CRAN submission.

                     Changes in version 0.10.4.9000                     

    o   2019-10-17

    o   Updated the vignette to include recommendations on locus order.

                     Changes in version 0.10.3.9000                     

    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                     

    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                     

    o   2019-10-08

    o   Updated LDWrap() to accomodate tab-delimited text (.txt or .tsv) format files.

                     Changes in version 0.10.0.9000                     

    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                      

    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                      

    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                      

    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                      

    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                      

    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                      

    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                      

    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                      

    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                      

    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                      

    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                      

    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                      

    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                      

    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                      

    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                      

    o   Streamlined the integration of cALD() into LDWrap().

                     Changes in version 0.4.1.9000                      

    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                      

    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                      

    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                      

    o   Added dataset documentation files.

                     Changes in version 0.2.0.9000                      

    o   Added *Rd files for each function.

    o   Added hla.hap.demo and drb1.dqb1.demo datasets.

                     Changes in version 0.1.0.9000                      

    o   Created package that includes the exported LDWrap() and cALD() functions,
	and the internal writeVector() function.
