r-cran-genetics 1.3.8-1 / usr / lib / R / site-library / genetics / NEWS

genetics 1.3.8 - 2012-12-14
---------------------------

Bug fixes:

- Regenerate broken PDF files in inst/doc.


genetics 1.3.7 - 2012-09-14
---------------------------

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 1.3.6 - 2011-02-01
---------------------------

- Add missing 'locus<-', 'gene<-', and 'marker<-' functions to
  NAMESPACE file.

- Update Greg's email address to greg@warnes.net


genetics 1.3.5 - 2011-01-17
---------------------------

- Fix warning messages from R CMD check


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

genetics 1.2.0
-------------

- Add R^2 to HWE and LD estimates

- Correct bug in denominator of Heterozygosity calculation, as
  identified by Christopher Calrson

- Fix handling of the 'type' and 'what' arguments for plot.genotype()

- Misc bug fixes in package imports/dependencies/etc.

- Add expectedGenotypes() and plot.genotypes() contributed by Gregor GORJANC

- Fix bug in heterozygote when more than one allele.name is provided

- Return NA and issue a warning if diseq() called on a marker with
  only one observed allele.


genetics 1.1.2
--------------

- Remove debugging code that printed intermediate values (sometimes
  a lot of them).

- Ensure that allele.freq table reported by summary.genotype has the
  same ordering as allele.names table.

genetics 1.1.1
--------------

- 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.

- Attempt to fix/clarify HWE diseq.  computations & synchronize
  documentation.

- Updated to use a namespace and to work with the lastest gregmisc
  bundle, which was previously a package.

genetics 1.1.0
--------------

- Add namespace support

- R/diseq.R: Restore ability to show Observed vs. Expected table by
  adding "table" option for the 'show' parameter.

- Updates to power.casectrl.  (including renaming from power.casectl)

- Update to work with gregmisc now that it has been converted from a
  package to a bundle.

genetics 1.0.4
--------------

- Updated to remove warnings in R CMD check for R 1.9.1.

genetics 1.0.2
--------------

- Fixed Heterozygosity (H) and PIC calculations in summary.genotype.
  (Bug report from Gerard Tromp <gtromp@cmb.biosci.wayne.edu>.

- Added experimental, undocumented, and untested function hapmcmc for
  imputing haplotypes and related functions. (Code submitted by David
  Duffy <davidD@qimr.edu.au>).


genetics 1.0.1
--------------

- Fixed mislabeling of rows/columns in LDtable

- 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.

- Extended LDtable to allow all columns & rows to be shown

- Added a larger example to plot.LD.data.frame documentation

- Changed the name of some function parameters to be more clear and/or
  consistent

- Added summary.LD.data.frame and print.LD.data.frame

- Fixed a bug in genotype() when reorder="no", such as when called by
  haplotype().


genetics 1.0.0
--------------

- New functions to estimate and test linkage disequilibrium (LD):
	LD, LD.genotype, LD.data.frame

- New functions to display LD results
	print.LD, print.LD.data.frame, plot.LD.data.frame, LDtable, LDplot

- Various bug-fixes and corrections


genetics 0.6.8
--------------

- Added HWE.chisq which performs the Chi-Square test for
  Hardy-Wienberg Equilibrium.

- Modified HWE.exact to return an object of class 'htest'.

- Modified HWE.test to use HWE.exact by default for 2-allele
  genotypes, and HWE.chisq otherwise.


genetics 0.6.7
--------------

- Added 'HWE.exact()', an exact test for Hardy-Wienberg Equilibrium for
  two alleles. Code contributed by David Duffy <davidD@qimr.edu.au>

- Added 'gregorius()', which computes the probability of observing all
  alleles with a given frequency in a sample of a specified size.