CVS commit: pkgsrc/math/R-genetics

[Mark Davies <markd%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   markd
Date:           Tue Oct 14 07:38:26 UTC 2008

Modified Files:
        pkgsrc/math/R-genetics: Makefile distinfo

Log Message:
Update R-genetics to 1.3.4

genetics 1.3.4 - 2008-08-20
---------------------------

- 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
---------------------------

- 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
---------------------------

- 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
--------------

- 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
--------------

- Update Greg's email address

- Fixed a bug in function allele.number, as pointed out by Chris
  Wallace


To generate a diff of this commit:
cvs rdiff -r1.3 -r1.4 pkgsrc/math/R-genetics/Makefile
cvs rdiff -r1.2 -r1.3 pkgsrc/math/R-genetics/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.