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.