Changes in version 1.3.8 (2012-12-15) Bug fixes o Regenerate broken PDF files in inst/doc. Changes in version 1.3.7 (2012-08-14) Enhancements o Improve descripiton of last examples in manual page for HWE.test(). Other Changes o Correct warnings issued by recent versions of R CMD CHECK. Changes in version 1.3.6 (2011-02-02) o Add missing 'locus<-', 'gene<-', and 'marker<-' functions to NAMESPACE file. o Update Greg's email address to greg@warnes.net Changes in version 1.3.5 (2011-01-17) o Fix warning messages from R CMD check Changes in version 1.3.4 (2008-08-20) o Fix bug in makeGenotypes that caused it to ignore the 'sep' argument when determining which columns contain genotypes & add a corresponing regression test Changes in version 1.3.3 (2008-04-30) o Correct 'obsolete' use of '$'. R no longer permits '$' to be used to extract named elements from vectors (just lists). o Remove the power.casectl() function, which was based on invalid assumpations. It has been marked depreciated. Please use the functions in the Bioconductor package 'GeneticsDesign' instead. Changes in version 1.3.2 (2007-11-20) o Fix bug in handling of assignment of NA value(s) to elements of an existing genotype object. o Fix warning messages from R CMD CHECK o Correct documentation error by swapping definitions of kp and alpha arguments of power.casectl(). Changes in version 1.3.1 o fixes in genotypeOrder to ensure all genotype/haplotype combinations are used. o genotypeOrder<- is now exported Changes in version 1.3.0 (2007-08-08) o A note is now displayed on startup: The R-Genetics project has developed an set of enhanced genetics packages that will shortly replace 'genetics'. Please visit the project homepage at http://rgenetics.org for more information. o binsearch() has been moved to the gtools package o New function groupGenotype to create groups/levels based on genotype names o Added some internal utility functions (.genotype2Haplotype, .genotype2Allele, and .matchGenotype) o Genotype class gets additional slot genotypeOrder (and genotype() function gets additional argument with the same name) in order to enable predefined order of genotypes in other functions e.g. summary o Added order, sort and %in% methods for genotype and haplotype classes. o Fixed genotype() with allow.partial.missing=FALSE when 'alleles' argument is passed o There is no more warning in genotype() if 'a1' or 'a2' have NA value(s) and 'alleles'' argument is specified, since NA is NA anyway o Fixed documentation of power.casectrl() o added gtools to Depends as needed by expectedGenotypes(); the latter now gives sorted genotypes according to order of given alleles o print.HWE.test() wasn't displaying the observed vs expected genotype frequency table. Fixed. Changes in version 1.2.1 (2006-12-12) o Update Greg's email address o Fixed a bug in function allele.number, as pointed out by Chris Wallace Changes in version 1.2.0 (2005-11-09) o Add R^2 to HWE and LD estimates o Correct bug in denominator of Heterozygosity calculation, as identified by Christopher Calrson o Fix handling of the 'type' and 'what' arguments for plot.genotype() o Misc bug fixes in package imports/dependencies/etc. o Add expectedGenotypes() and plot.genotypes() contributed by Gregor GORJANC o Fix bug in heterozygote when more than one allele.name is provided o Return NA and issue a warning if diseq() called on a marker with only one observed allele. Changes in version 1.1.2 (2004-12-23) o Remove debugging code that printed intermediate values (sometimes a lot of them). o Ensure that allele.freq table reported by summary.genotype has the same ordering as allele.names table. Changes in version 1.1.1 (2004-11-15) o Make it clear that the Yates continuty correction is applied *only* when simulate.p.value=FALSE, so that the reported test statistics for simulate.p.value=FALSE and simulate.p.value=TRUE will differ. o Attempt to fix/clarify HWE diseq. computations & synchronize documentation. o Updated to use a namespace and to work with the lastest gregmisc bundle, which was previously a package. Changes in version 1.1.0 (2004-09-21) o Add namespace support o R/diseq.R: Restore ability to show Observed vs. Expected table by adding "table" option for the 'show' parameter. o Updates to power.casectrl. (including renaming from power.casectl) o Update to work with gregmisc now that it has been converted from a package to a bundle. Changes in version 1.0.4 (2004-05-26) o Updated to remove warnings in R CMD check for R 1.9.1. Changes in version 1.0.2 o Fixed Heterozygosity (H) and PIC calculations in summary.genotype. (Bug report from Gerard Tromp . o Added experimental, undocumented, and untested function hapmcmc for imputing haplotypes and related functions. (Code submitted by David Duffy ). Changes in version 1.0.1 (2003-06-04) o Fixed mislabeling of rows/columns in LDtable o Extended LDtable to resize text to fit box area, and to allow selection of which statistics are displayed, and which statistic is used for coloration. o Extended LDtable to allow all columns & rows to be shown o Added a larger example to plot.LD.data.frame documentation o Changed the name of some function parameters to be more clear and/or consistent o Added summary.LD.data.frame and print.LD.data.frame o Fixed a bug in genotype() when reorder="no", such as when called by haplotype(). Changes in version 1.0.0 (2003-05-28) o New functions to estimate and test linkage disequilibrium (LD): LD, LD.genotype, LD.data.frame o New functions to display LD results print.LD, print.LD.data.frame, plot.LD.data.frame, LDtable, LDplot o Various bug-fixes and corrections Changes in version 0.6.8 (2003-04-07) o Added HWE.chisq which performs the Chi-Square test for Hardy-Wienberg Equilibrium. o Modified HWE.exact to return an object of class 'htest'. o Modified HWE.test to use HWE.exact by default for 2-allele genotypes, and HWE.chisq otherwise. Changes in version 0.6.7 o Added 'HWE.exact()', an exact test for Hardy-Wienberg Equilibrium for two alleles. Code contributed by David Duffy o Added 'gregorius()', which computes the probability of observing all alleles with a given frequency in a sample of a specified size.