Update LICENSE
Upstream changes:
genetics 1.3.8 - 2012-12-14
---------------------------
Bug fixes:
- Regenerate broken PDF files in inst/doc.
genetics 1.3.7 - 2012-09-14
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Enhancements:
- Improve descripiton of last examples in manual page for HWE.test().
Other Changes:
- Correct warnings issued by recent versions of R CMD CHECK.
genetics 1.3.4 - 2008-08-20
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- Fix bug in makeGenotypes that caused it to ignore the 'sep' argument
when determining which columns contain genotypes & add a corresponing
regression test
genetics 1.3.3 - 2007-04-29
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- Correct 'obsolete' use of '$'. R no longer permits '$' to be used
to extract named elements from vectors (just lists).
- 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.
genetics 1.3.2 - 2007-11-20
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- Fix bug in handling of assignment of NA value(s) to elements of an
existing genotype object.
- Fix warning messages from R CMD CHECK
- Correct documentation error by swapping definitions of kp and alpha
arguments of power.casectl().
genetics 1.3.1
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- fixes in genotypeOrder to ensure all genotype/haplotype combinations
are used.
- genotypeOrder<- is now exported
genetics 1.3.0
--------------
- 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.
- binsearch() has been moved to the gtools package
- New function groupGenotype to create groups/levels based on genotype
names
- Added some internal utility functions
(.genotype2Haplotype, .genotype2Allele, and .matchGenotype)
- 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
- Added order, sort and %in% methods for genotype and haplotype classes.
- Fixed genotype() with allow.partial.missing=FALSE when 'alleles' argument
is passed
- 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
- Fixed documentation of power.casectrl()
- added gtools to Depends as needed by expectedGenotypes(); the latter now
gives sorted genotypes according to order of given alleles
- print.HWE.test() wasn't displaying the observed vs expected genotype
frequency table. Fixed.
genetics 1.2.1
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- Update Greg's email address
- Fixed a bug in function allele.number, as pointed out by Chris
Wallace
Classes and methods for handling genetic data. Includes classes to
represent genotypes and haplotypes at single markers up to multiple
markers on multiple chromosomes. Function include allele frequencies,
flagging homo/heterozygotes, flagging carriers of certain alleles,
estimating and testing for Hardy-Weinberg disequilibrium, estimating
and testing for linkage disequilibrium, ...
