2008-08-20 19:06  warnes

	* DESCRIPTION, inst/NEWS: Bump version numer up and update NEWS
	  file

2008-08-20 19:04  warnes

	* R/makeGenotypes.R: Fix bug in makeGenoypes that caused it to
	  ignore 'sep' when identifying potential genotype columns

2008-04-30 01:23  warnes

	* man/depreciated.Rd: Add complete reference to GeneticsDesign
	  functions

2008-04-30 01:05  warnes

	* DESCRIPTION, inst/NEWS: Update for version 1.3.3

2008-04-30 00:54  warnes

	* R/genotype.R, R/locus.R: Replace obsolete (grr!) use of "$\" for
	  atomic vectors

2008-04-30 00:53  warnes

	* R/power.casectl.R, man/depreciated.Rd, man/power.casectl.Rd: Mark
	  power.casectl() as depreciated in favor of GeneticsDesign
	  functions

2007-11-20 20:30  warnes

	* R/expectedGenotypes.R: Add extra error checking to
	  expectedGenotypes()

2007-11-20 20:27  warnes

	* DESCRIPTION, inst/NEWS: Update NEWS and DESCRIPTION for genetics
	  1.3.2

2007-11-20 20:25  warnes

	* man/power.casectl.Rd: Fix documentation of kp and alpha arguments
	  to power.casectl()

2007-11-20 20:24  warnes

	* R/hapmcmc.R: Add set argument to hapshuffle

2007-11-20 20:23  warnes

	* R/power.casectl.plot.R: Add explicit variable definition to avoid
	  R CMD CHECK warning

2007-11-20 20:23  warnes

	* R/zzz.R: Package startup message states package is OBSOLETE

2007-11-20 20:20  warnes

	* R/genotype.R, tests/test.NA.R: Bug fix and regression test for
	  assignment of NA to element of existing genotype object

2007-09-12 10:41  ggorjan

	* DESCRIPTION, NAMESPACE, R/genotype.R, R/summary.genotype.R,
	  inst/NEWS, man/genotype.Rd: - fixes in genotypeOrder to ensure
	  all genotype/haplotype combinations
	  are used.
	  
	  - genotypeOrder<- is now exported

2007-08-21 14:37  warnes

	* ChangeLog, NEWS: Add softlinks into inst/ for ChangeLog and NEWS

2007-08-21 14:36  warnes

	* NEWS, inst/NEWS: Move Changelog (not in SVN) and NEWS to inst/

2007-08-21 14:35  warnes

	* inst/ChangeLog, inst/NEWS: Remove softlinks in inst, doesn't work
	  on windows

2007-08-20 18:30  warnes

	* inst/ChangeLog, inst/NEWS: Add softlinks in inst to NEWS and
	  ChangeLog so these will get installed.

2007-08-08 14:59  warnes

	* DESCRIPTION: Bump minor version number since Gregor added new
	  functions

2007-08-08 14:58  warnes

	* NEWS: Update NEWS file for new release

2007-08-08 14:56  warnes

	* DESCRIPTION: Update description for release, add credit to other
	  contributors

2007-08-08 14:51  warnes

	* R/zzz.R: Add note referring users to the R-Genetics project
	  homepage

2007-08-08 13:45  warnes

	* NAMESPACE, R/binsearch.R, man/binsearch.Rd: Move binsearch() to
	  the gtools package

2007-08-08 13:38  warnes

	* R/binsearch.R: Correct bug in binsearch. Elipses were omitted
	  from one cal to fun(). Bug reported by Matthew Walker
	  <m.g.walker@massey.ac.nz>

2007-07-25 07:32  ggorjan

	* NAMESPACE, NEWS, R/expectedGenotypes.R, R/genotype.R,
	  R/groupGenotype.R, R/order.genotype.R, R/summary.genotype.R,
	  man/expectedGenotypes.Rd, man/genotype.Rd, man/groupGenotype.Rd,
	  man/order.genotype.Rd: groupGenotype(), some utility funcs, ...

2007-07-18 16:57  ggorjan

	* NEWS, R/genotype.R: Fixed genotype() with
	  allow.partial.missing=FALSE when 'alleles'
	  argument is passed
	  
	  Example:
	  
	  ## Old
	  
	  > x <- c("C/C", "A/C", "A/A", NA, "C/B", "B/A", "B/B")
	  > alleles <- c("A", "B")
	  > genotype(x, alleles=alleles, allow.partial.missing=FALSE)
	  [1] NA "A/NA" "A/A" NA "B/NA" "B/A" "B/B"
	  Alleles: B A
	  Warning message: Found data values not matching specified
	  alleles. Converting to NA. in: genotype(x, alleles = alleles,
	  allow.partial.missing = FALSE)
	  
	  ## New
	  
	  > genotype(x, alleles=alleles, allow.partial.missing=FALSE)
	  [1] NA NA "A/A" NA NA "B/A" "B/B"
	  Alleles: B A
	  Warning message: Found data values not matching specified
	  alleles. Converting to NA. in: genotype(x, alleles = alleles,
	  allow.partial.missing = FALSE)
	  
	  > genotype(x, alleles=alleles, allow.partial.missing=TRUE)
	  [1] NA "A/NA" "A/A" NA "B/NA" "B/A" "B/B"
	  Alleles: B A
	  Warning message: Found data values not matching specified
	  alleles. Converting to NA. in: genotype(x, alleles = alleles,
	  allow.partial.missing = TRUE)

2007-07-18 16:32  ggorjan

	* NEWS, R/genotype.R: 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
	  
	  Here is the example:
	  
	  ## Old
	  
	  > x <- c("C/C", "A/C", "A/A", NA, "C/B", "B/A", "B/B")
	  > alleles <- c("A", "B", "C")
	  > x <- genotype(x, alleles=alleles, reorder="yes")
	  Warning message:
	  Found data values not matching specified alleles. Converting to
	  NA. in: genotype(x, alleles = alleles, reorder = "yes")
	  > x
	  [1] "C/C" "A/C" "A/A" NA "B/C" "A/B" "B/B"
	  Alleles: A B C
	  
	  ## New
	  
	  > x <- c("C/C", "A/C", "A/A", NA, "C/B", "B/A", "B/B")
	  > alleles <- c("A", "B", "C")
	  > x <- genotype(x, alleles=alleles, reorder="yes")
	  > x
	  [1] "C/C" "A/C" "A/A" NA "B/C" "A/B" "B/B"
	  Alleles: A B C

2007-07-18 14:22  ggorjan

	* NEWS, R/diseq.R, man/diseq.Rd: really fixed printing of Obs vs
	  Exp freqs

2007-07-18 12:51  ggorjan

	* R/expectedGenotypes.R, man/expectedGenotypes.Rd: sort produced
	  genotypes

2007-07-18 12:19  ggorjan

	* R/expectedGenotypes.R: rollback one part

2007-07-18 12:09  ggorjan

	* R/plot.genotype.R, man/plot.genotype.Rd: fixing S3 type of
	  documentation + minor fix

2007-07-18 12:08  ggorjan

	* man/genotype.Rd, man/locus.Rd, man/print.LD.Rd,
	  man/summary.genotype.Rd: fixing S3 type of documentation

2007-07-18 11:57  ggorjan

	* NEWS, man/power.casectl.Rd: Fixed documentation of
	  power.casectrl() to match its code

2007-07-18 11:49  ggorjan

	* DESCRIPTION, NEWS, R/expectedGenotypes.R: added gtools to Depends
	  as needed by expectedGenotypes() + some minor fixes

2007-06-17 01:27  warnes

	* man/power.casectl.Rd: Update with Michael's latest changes

2007-06-17 01:25  warnes

	* R/power.casectl.plot.R: Move old code from power.casectl.R to
	  power.casectl.plot.R

2007-06-17 01:24  warnes

	* R/power.casectl.R: Update with Michael's latest changes

2007-05-29 19:35  warnes

	* NEWS: Add display of observed vs expected table to
	  print.HWE.test()

2007-05-29 19:34  warnes

	* DESCRIPTION, man/HWE.test.Rd: Add display of observed vs expected
	  table to print.HWE.test()

2007-05-29 19:29  warnes

	* R/HWE.test.R: Add display of observed vs expected table to
	  print.HWE.test()

2006-12-05 18:22  warnes

	* man/undocumented.Rd: Remove typo/dupliucate alias entry for
	  ci.balance

2006-12-05 17:45  warnes

	* NEWS: Update NEWS file for 1.2.0 and 1.2.1

2006-11-14 22:20  ggorjan

	* trunk/GeneticsBase/DESCRIPTION, trunk/GeneticsBase/R/convert.R,
	  trunk/GeneticsBase/TODO.txt, trunk/GeneticsBase/data/ALZH.ped,
	  trunk/GeneticsBase/data/CAMP.ped,
	  trunk/GeneticsBase/data/CAMPZ.phe,
	  trunk/GeneticsBase/data/qtl.ped, trunk/GeneticsBase/data/qtl.phe,
	  trunk/GeneticsBase/data/xbat.ped,
	  trunk/GeneticsBase/data/xbat.phe,
	  trunk/GeneticsBase/man/fastGrid.Rd,
	  trunk/GeneticsBase/man/makeMarkerInfo.Rd,
	  trunk/GeneticsBase/man/makeTransTable.Rd,
	  trunk/GeneticsBase/man/makeTransTableList.Rd,
	  trunk/GeneticsBase/src/convert.c,
	  trunk/PopGenetics/R/HWE.test.data.frame.R,
	  trunk/PopGenetics/R/expectedGenotypes.R,
	  trunk/PopGenetics/R/plot.genotype.R,
	  trunk/PopGenetics/inst/doc/example_data.csv,
	  trunk/PopGenetics/man/expectedGenotypes.Rd,
	  trunk/PopGenetics/man/plot.genotype.Rd, trunk/fbat/DESCRIPTION,
	  trunk/fbat/data/CAMP.ped, R/HWE.test.data.frame.R,
	  R/expectedGenotypes.R, R/plot.genotype.R,
	  inst/doc/example_data.csv, man/expectedGenotypes.Rd,
	  man/plot.genotype.Rd: Removing executable property

2006-11-11 04:10  warnes

	* DESCRIPTION: Update version number

2006-11-11 04:09  warnes

	* DESCRIPTION, inst/doc/genetics_article.tex, man/HWE.exact.Rd,
	  man/HWE.test.Rd, man/LD.Rd, man/binsearch.Rd, man/ci.balance.Rd,
	  man/diseq.Rd, man/genotype.Rd, man/gregorius.Rd,
	  man/homozygote.Rd, man/locus.Rd, man/makeGenotypes.Rd,
	  man/print.LD.Rd, man/summary.genotype.Rd, man/write.pop.file.Rd:
	  Update my email address

2006-10-02 13:21  weiliang_qiu

	* DESCRIPTION: add the 'BioCViews' tag with 'Genetics' as the
	  keyword to the
	  DESCRIPTION file

2006-03-10 18:19  nj7w

	* R/write.pedigree.file.R: Fixed a bug in function allele.number,
	  as pointed out by Chris Wallace

2005-11-10 15:28  warnes

	* man/HWE.exact.Rd, man/HWE.test.Rd, man/LD.Rd, man/binsearch.Rd,
	  man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd,
	  man/gregorius.Rd, man/homozygote.Rd, man/locus.Rd,
	  man/makeGenotypes.Rd, man/print.LD.Rd, man/summary.genotype.Rd,
	  man/write.pop.file.Rd: Update my email address

2005-11-09 17:05  warnes

	* DESCRIPTION: Update version number and release date

2005-11-09 17:04  warnes

	* R/HWE.test.R, R/LD.R, R/ci.balance.R, R/diseq.R, man/diseq.Rd:
	  Add R^2 to HWE and LD estimates

2005-11-08 20:54  warnes

	* R/summary.genotype.R: Fix Heterozygosity correction, per
	  Christopher Carlson
	  <csc47@u.washington.edu>:
	  > My second question is with regard to the summary.genotype
	  > function. The value you return for Heterozygosity (Hu) appears
	  to be
	  > 2pq*(n/(n-1)), but with n as the number of individuals. I
	  believe
	  > that the proper correction is for n/(n-1) where n is the number
	  of
	  > chromosomes, not the number of individuals. For a reasonable
	  number
	  > of samples the difference is subtle, but it threw off my
	  Tajima's D
	  > estimates when I used Hu to calculate nucleotide diversity.

2005-10-04 23:43  warnes

	* DESCRIPTION, NAMESPACE, R/diseq.R, R/expectedGenotypes.R,
	  R/power.casectl.R, R/print.LD.R, R/zzz.R: Move all dependency
	  checking into DESCRIPTION and NAMESPACES.

2005-10-04 16:30  warnes

	* R/plot.genotype.R: Fix handling of the 'type' argument.

2005-10-04 16:28  warnes

	* R/plot.genotype.R: Correct the handling of the 'what' argument.

2005-10-04 15:17  warnes

	* DESCRIPTION: Forgot to increment version

2005-10-04 15:15  warnes

	* DESCRIPTION: Update email address, version number, and date.

2005-10-04 15:13  warnes

	* R/diseq.R: Return NA and issue a warning if diseq() called on a
	  marker with
	  only one observed allele.

2005-09-14 18:45  ggorjan

	* R/plot.genotype.R: Now plot percentage by default i.e. no need
	  for argument in function call.

2005-08-18 19:39  nj7w

	* R/genotype.R: Fix bug in heterozygote when more than one
	  allele.name is provided

2005-03-13 01:23  warnes

	* R/library.R, man/library.Rd: Remove old backport of library()
	  commanad that is no longer needed.

2005-03-12 21:57  warnes

	* R/summary.genotype.R: Change 'persons' to 'samples' so that we
	  aren't human-specific.

2005-03-12 21:54  warnes

	* DESCRIPTION, NAMESPACE, man/expectedGenotypes.Rd,
	  man/plot.genotype.Rd: Fixes to pass R CMD check after addition of
	  expectedGenotypes() and
	  plot.genotype().

2005-03-12 20:23  warnes

	* R/plot.genotype.R, man/plot.genotype.Rd: Add plot.genotype()
	  contributed by Gregor GORJANC

2005-03-12 20:22  warnes

	* R/expectedGenotypes.R, man/expectedGenotypes.Rd: Add
	  expectedGenotypes() contributed by Gregor GORJANC

2005-03-09 19:49  warnes

	* man/makeGenotypes.Rd: Add description of the use of the 'method'
	  argument, and an example
	  showing the use of 'method=as.genotype.allele.count'.

2005-03-02 18:14  nj7w

	* NAMESPACE: Fixed NAMESPACE file to import na.omit function
	  explicitly from stats package.

2004-12-23 01:34  warnes

	* R/HWE.test.data.frame.R, inst/doc/LD.pdf,
	  inst/doc/example_data.csv, inst/doc/genetics_article.pdf: Check
	  in some files that seem to have been overlooked in the past.

2004-12-23 01:21  warnes

	* NEWS: Update for 1.1.2 (and 1.1.1).

2004-12-23 01:14  warnes

	* DESCRIPTION: Update version number.

2004-12-23 01:08  warnes

	* R/diseq.R: Remove debugging code that printed intermediate values
	  (sometimes a
	  lot of them).

2004-11-22 14:35  warnes

	* man/LD.Rd: Fix typos.

2004-11-15 16:36  warnes

	* DESCRIPTION: Update version.

2004-11-15 16:22  warnes

	* R/summary.genotype.R: Ensure that allele.freq table has the same
	  ordering as allele.names.

2004-11-15 16:20  warnes

	* R/HWE.test.R: remove triplicate comment

2004-11-15 15:34  warnes

	* man/HWE.chisq.Rd: 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.

2004-10-13 16:21  warnes

	* R/diseq.R, man/diseq.Rd: Attempt to fix/clarify HWE diseq.
	  computations & synchronize documentation.

2004-09-21 21:45  warnes

	* DESCRIPTION, NAMESPACE, NEWS, R/power.casectl.R,
	  man/HWE.chisq.Rd, man/HWE.exact.Rd, man/HWE.test.Rd,
	  man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd,
	  man/homozygote.Rd, man/locus.Rd, man/power.casectl.Rd,
	  man/summary.genotype.Rd, man/undocumented.Rd: Updated to use a
	  namespace and to work with the lastest gregmisc
	  bundle (previously a package).

2004-09-17 18:46  warnes

	* man/HWE.chisq.Rd, man/HWE.exact.Rd, man/HWE.test.Rd, man/LD.Rd,
	  man/binsearch.Rd, man/ci.balance.Rd, man/diseq.Rd,
	  man/genotype.Rd, man/gregorius.Rd, man/homozygote.Rd,
	  man/library.Rd, man/locus.Rd, man/makeGenotypes.Rd,
	  man/power.casectl.Rd, man/print.LD.Rd, man/summary.genotype.Rd,
	  man/undocumented.Rd, man/write.pop.file.Rd: Comments were
	  incorrectly marked by '#' instead of '%'.

2004-09-16 22:15  warnes

	* R/power.casectl.R: Changes from Michael Man.

2004-09-16 21:33  warnes

	* man/diseq.Rd: Match changes to print.diseq revision 1.16, which
	  restored ability
	  to show Observed vs. Expected table by addition an additional
	  potential value for the 'show' parameter: "table".

2004-09-16 21:22  warnes

	* NAMESPACE: Add namespace.

2004-09-15 18:32  warnesgr

	* R/diseq.R: Restore ability to show Observed vs. Expected table by
	  addition an
	  additional potential value for the 'show' parameter: "table".

2004-07-02 15:57  warnesgr

	* R/power.casectl.R, man/power.casectl.Rd: Add power.casectl
	  provided by Micheal Man.

2004-05-25 19:40  warnesgr

	* DESCRIPTION, R/genotype.R, R/print.LD.R, man/HWE.test.Rd,
	  man/binsearch.Rd, man/genotype.Rd, man/locus.Rd,
	  man/makeGenotypes.Rd, man/undocumented.Rd: Many fixex.

2004-03-25 17:15  warnesgr

	* R/ci.balance.R, man/ci.balance.Rd: Remove unused '...' argument
	  from ci.balance.

2004-02-02 15:55  warnesgr

	* R/ci.balance.R, R/diseq.R, man/ci.balance.Rd: - Rename ci.balance
	  'conf' parameter to 'confidence', and add 'alpha'
	  parameter to remove R CMD check warning.
	  
	  - modify diseq.ci to pass confidence level to ci.balance.

2004-02-02 15:46  warnesgr

	* man/homozygote.Rd: remove extraneous period from argument to
	  carrier.genotype.

2003-12-02 18:41  warnesgr

	* R/genotype.R: - remove depreciated (and error prone) use of
	  codes().

2003-12-02 18:37  warnesgr

	* R/print.LD.R: - Fixed bug: "D" was being reported when only "D'"
	  was requested.

2003-11-24 17:32  warnesgr

	* man/write.pop.file.Rd: - Fix the last broken fix.

2003-11-24 17:22  warnesgr

	* man/write.pop.file.Rd: Changes to fix latex'ing problem.

2003-08-04 14:18  warnesgr

	* DESCRIPTION, NEWS: - Updated NEWS and DESCRIPTION for version
	  1.0.2

2003-08-04 13:48  warnesgr

	* R/summary.genotype.R: - Fixed a bug in Heterozygosity (H) and PIC
	  calcuations caused by
	  using allele count rather than allele proportions. Bug reported
	  by
	  Gerard Tromp <tromp@sanger.med.wayne.edu>.

2003-07-30 20:39  warnesgr

	* R/hapmcmc.R: - Added hapmcmc code submitted by David Duffy.

2003-06-06 09:27  warnesgr

	* man/binsearch.Rd, man/library.Rd, man/print.LD.Rd: - Fix
	  fuction/documententation argument mismatch.
	  - Fix lack of LF at the end of a couple of files.

2003-06-05 22:06  warnesgr

	* R/summary.genotype.R: - Added code to show number of alleles,
	  number of individuals
	  genotyped, heterogyosity, and poly. information content based on
	  code contribued by David Duffy.

2003-06-04 21:22  warnesgr

	* R/plot.LD.R: - Modified string size to only leave vertical space
	  for the number of
	  elements that will be printed.

2003-06-04 21:22  warnesgr

	* R/genotype.R: - Somehow the assigment of the haplotype function
	  got messed up. Fixed.

2003-06-04 21:21  warnesgr

	* man/print.LD.Rd: - Updated manual to match code
	  - Replaced 'T' with 'TRUE'

2003-06-04 21:20  warnesgr

	* R/print.LD.R: - summary functions should have 'object' as the
	  first parameter.

2003-06-04 20:26  warnesgr

	* DESCRIPTION, NEWS, TODO: Updates for release 1.0.1.

2003-06-04 20:20  warnesgr

	* R/plot.LD.R, R/print.LD.R, man/print.LD.Rd: - Fixed mislabeling
	  of rows/columns in LDtable
	  - Extended LDtable to handle resizing text to fit area
	  - Extended LDtable to allow slection of what 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 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

2003-06-03 12:59  warnesgr

	* R/LD.R: - LD.genotype needs to reject haplotype objects since
	  these are not
	  yet supported by the code.

2003-06-03 11:41  warnesgr

	* R/genotype.R: - Fix handling of allele names when reorder="no".
	  Apparently,
	  unique() on a matrix now returns a matrix with unique *rows*
	  removed,
	  instead of a vector of unique *elements*. The consequence in this
	  case was that genotype(...,reorder="no") was generating a list of
	  alleles that was a matrix instead of a vector.

2003-05-30 16:08  warnesgr

	* man/locus.Rd: - added documentation for "value" option.

2003-05-30 15:52  warnesgr

	* R/library.R, R/zzz.R: - library.pos will now always be defined.
	  Instead of conditionally
	  defining library.pos, a check is made in .First.lib to see
	  whether
	  the system library function has a pos argument. If not, it uses
	  library.pos instead of library to load dependencies.

2003-05-29 02:27  warnesgr

	* inst/doc/genetics_article.tex: - added ld to conclusion text

2003-05-29 02:23  warnesgr

	* inst/doc/genetics_article.tex: Updated for version 1.0.0

2003-05-29 02:22  warnesgr

	* DESCRIPTION, NEWS: - Updated for 0.7.0

2003-05-29 02:20  warnesgr

	* inst/doc/genetics_article.tex: - Final version to send to Fritz.

2003-05-29 01:55  warnesgr

	* inst/doc/example.R, inst/doc/genetics_article.tex,
	  inst/doc/make_example_data.R: - Add R code to generate and demo
	  genetics package

2003-05-29 00:36  warnesgr

	* R/locus.R: - All arguments are now optional.

2003-05-29 00:35  warnesgr

	* R/genotype.R: - Fix problem with NA's caused by grep bug in R <=
	  1.7.0.

2003-05-28 20:28  warnesgr

	* man/locus.Rd: - Add getmarker, getgene, locus<- , marker<-, and
	  gene<- functions.

2003-05-28 20:26  warnesgr

	* man/write.pop.file.Rd: - Add URL for LinkDos

2003-05-28 20:26  warnesgr

	* man/undocumented.Rd: - Add alias for to shortsummary function.

2003-05-28 15:09  warnesgr

	* man/LD.Rd: - Added "locus<-", "marker<-", "gene<-", as well as
	  "getgene", "getmarker"

2003-05-28 15:04  warnesgr

	* man/library.Rd: - renamed library() to library.pos(). Updated
	  text to correcty note
	  that the backport is from 1.8.0.

2003-05-28 15:01  warnesgr

	* R/write.pedigree.file.R: - Renamed write.pedigree to
	  write.pedigree.file.
	  - Added URL of LinkDos software.

2003-05-28 14:57  warnesgr

	* R/library.R, R/zzz.R: - Rename library to library.pos

2003-05-28 14:56  warnesgr

	* R/locus.R: - Added "locus<-", "marker<-", "gene<-", as well as
	  "getgene", "getmarker"

2003-05-27 21:18  warnesgr

	* R/print.LD.R, man/print.LD.Rd: - Added show.all argument
	  - Fixed code that omits blank row/column

2003-05-27 19:37  warnesgr

	* man/write.pop.file.Rd: - Add documentation for write.pop.file,
	  write.pedigree.file, write.marker.file.

2003-05-27 18:45  warnesgr

	* man/diseq.Rd, man/genotype.Rd, man/makeGenotypes.Rd,
	  man/summary.genotype.Rd: - Fix typos, update arguments to match
	  changes to code

2003-05-27 18:43  warnesgr

	* R/library.R, man/library.Rd: - Added temporary copy of library()
	  function. This copy will only be
	  installed if the global library() function does not define a
	  'pos'
	  argument. This code was backported from R-devel, and R 1.7.1 and
	  later will include it as part of base.

2003-05-27 18:41  warnesgr

	* R/write.pedigree.file.R, R/write.pop.file.R: - Add utility
	  functions to write pedigree, 'pop', and marker files
	  which are used to transfer data to genetics applications.

2003-05-27 18:36  warnesgr

	* R/zzz.R: - Use new library function to load MASS in search
	  position *3* before
	  loading gregmisc. This prevents the genotype dataset in MASS from
	  hiding the genotype function here.

2003-05-27 18:35  warnesgr

	* R/genotype.R: - fixed handling of genotype("") and similar
	  - improvements to "[<-.genotype", it now automatically converts
	  the
	  second argument to a genotype object.

2003-05-27 18:33  warnesgr

	* R/diseq.R: - Add call item to diseq.object giving original
	  function call
	  - Fixed bug in testing for 2 x 2 allele case

2003-05-27 18:32  warnesgr

	* R/plot.LD.R, R/print.LD.R, man/print.LD.Rd: - Add plot and print
	  methods for LD objects.

2003-05-27 18:30  warnesgr

	* R/LD.R: - Found and fixed bug in likelihood computation. The
	  count table
	  needed to be organized with high-frequency alleles in the upper
	  left
	  corner instead of the lower right corner.

2003-05-22 17:25  warnesgr

	* R/HWE.chisq.R, R/HWE.exact.R, R/HWE.test.R, R/LD.R,
	  R/binsearch.R, R/ci.balance.R, R/genotype.R, R/gregorius.R,
	  R/locus.R, R/makeGenotypes.R, R/plot.LD.R, R/print.LD.R,
	  R/summary.genotype.R, R/zzz.R: - Remove CVS Log tag, which was
	  eating up too much space. Just use
	  'cvs log' to get the comments if needed!

2003-05-22 16:22  warnesgr

	* R/LD.R, R/plot.LD.R, R/print.LD.R: - moved LD printing functions
	  to print.LD.R
	  - moved LD plotting functions to plot.LD.R
	  - fixed problems in print.LD.data.frame
	  - enhanced plot.LD.data.frame
	  - other small changes

2003-05-21 20:03  warnesgr

	* R/makeGenotypes.R: - Remove stray character that caused a syntax
	  error.

2003-05-21 20:03  warnesgr

	* R/summary.genotype.R: - Fix handling of genotype summary when
	  called from
	  summary.data.frame. Was broken by too-broad search and
	  replace... but the changes motivated enhancements. ;^)

2003-05-21 19:57  warnesgr

	* DESCRIPTION, R/zzz.R: - Added dependency on gregmisc package.

2003-05-21 19:46  warnesgr

	* R/LD.R, man/LD.Rd, man/print.LD.Rd: - Improvements to LD code and
	  documentation.

2003-05-20 16:46  warnesgr

	* R/makeGenotypes.R, man/makeGenotypes.Rd: - Reduce stringency for
	  considering a variable a genotype.

2003-05-20 16:43  warnesgr

	* R/LD.R, man/LD.Rd: - Add code & (incomplete) docs for linkage
	  disequilibrium

2003-05-16 18:39  warnesgr

	* DESCRIPTION, R/makeGenotypes.R, inst/doc/Rnews.sty,
	  inst/doc/genetics_article.tex, man/makeGenotypes.Rd: - Updated to
	  version 0.7.0
	  - Made changes to pass R CMD check

2003-05-16 15:50  warnesgr

	* R/makeGenotypes.R, man/makeGenotypes.Rd: - Added
	  makeGenotypes/makeHaplotypes to help convert variables in
	  dataframes to genotype/haplotype variables.

2003-04-07 20:30  warnesgr

	* R/diseq.R, man/diseq.Rd: - Flipped sign of D, D', r. Now D
	  matches sign given in Weir's book,
	  and r has the proper sign.

2003-03-07 14:52  warnesgr

	* R/HWE.exact.R, man/HWE.exact.Rd: - Modified HWE.exact to return
	  an object of class 'htest'
	  - Noted this change in the man file and added HWE.chisq to list
	  of
	  links and to example code.

2003-03-07 14:49  warnesgr

	* DESCRIPTION: - Updated version number to 0.6.7.

2003-03-07 14:47  warnesgr

	* man/HWE.test.Rd: - Added links to HWE.chisq, HWE.exact, genotype
	  to see also seciton.
	  - Slighlty modified example code.

2003-03-07 14:44  warnesgr

	* NEWS: - New file

2003-03-07 14:33  warnesgr

	* R/genotype.R, man/genotype.Rd: - Added nallele function to
	  compute the number of alleles.

2003-03-07 14:32  warnesgr

	* R/HWE.chisq.R, R/HWE.test.R, man/HWE.chisq.Rd, man/HWE.test.Rd: -
	  Created HWE.chisq, HWE.chisq.genotype and corresponding man page.
	  - Moved computation of Chisquare test for HWE from
	  HWE.test.genotype
	  to HWE.chisq.genotype.
	  - Added option (on by default) to compute the exact p-value using
	  HWE.exact.
	  This is on by default when nallele=2

2003-02-03 16:13  warnesgr

	* DESCRIPTION, inst/doc/genetics_article.tex, man/HWE.exact.Rd,
	  man/binsearch.Rd, man/gregorius.Rd: - Fixed typos and R CMD check
	  warnings.
	  - Updated version number
	  - Removed 'data' directory to fix new R CMD check warning.

2002-12-11 21:29  warnesgr

	* R/binsearch.R: - fixed typo

2002-12-11 21:07  warnesgr

	* R/binsearch.R, R/gregorius.R, man/binsearch.Rd, man/gregorius.Rd:
	  - Moved binsearch() into a separate file and added documentation.
	  - Simplified and documented binsearch() code.
	  - binsearch() now detects whether the function is increasing or
	  decreasing and acts accordingly.
	  - Updated gregorius() to use the modified binsearch.

2002-12-10 20:36  warnesgr

	* man/gregorius.Rd: - Updated title/description

2002-12-10 20:33  warnesgr

	* R/gregorius.R, man/gregorius.Rd: - Implemented gregorius()
	  function, replacing data frame gregorius.
	  - Re-created corresponding help page.

2002-12-02 17:23  warnesgr

	* man/gregorius.Rd: - Added cvs tags to header of gregorius.Rd

2002-12-02 17:13  warnesgr

	* data, data/00Index, data/gregorius.R, man/gregorius.Rd: - Added
	  data set (and documentation) 'gregorius' which contains
	  necessary samples sizes to detect alleles.

2002-12-02 16:16  warnesgr

	* man/HWE.exact.Rd: - Added HWE.exact.Rd.

2002-12-02 16:12  warnesgr

	* R/HWE.exact.R: - Now returnes only the computed P-value.

2002-12-02 15:40  warnesgr

	* R/HWE.exact.R: - Added code for HWE.exact, based on contributed
	  function by David
	  Duffy <davidD@qimr.edu.au>

2002-11-27 15:32  warnesgr

	* DESCRIPTION, R/HWE.test.R, R/diseq.R, R/genotype.R, TODO,
	  inst/doc/genetics_article.tex, man/HWE.test.Rd,
	  man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd, man/locus.Rd,
	  man/summary.genotype.Rd, man/undocumented.Rd: Correct spelling
	  errors and typos.

2002-11-13 20:18  warnesgr

	* DESCRIPTION: - Fix typo.

2002-11-12 19:59  warnesgr

	* DESCRIPTION, R/diseq.R, R/genotype.R: - Changes to remove
	  warnings generated by 'R CMD check'.

2002-11-12 19:58  warnesgr

	* man/HWE.test.Rd, man/ci.balance.Rd, man/diseq.Rd,
	  man/genotype.Rd, man/homozygote.Rd, man/locus.Rd,
	  man/summary.genotype.Rd, man/undocumented.Rd: - Changes to remove
	  warnings generated by 'R CMD check'.

2002-11-12 17:57  warnesgr

	* R/zzz.R: - diseq.ci now requires the combinat library instead of
	  boot.

2002-11-12 05:53  warnesgr

	* examples/test.ci.R: - Checkin of test.ci.R

2002-11-12 05:31  warnesgr

	* DESCRIPTION: - Bump version number

2002-11-12 05:31  warnesgr

	* R/genotype.R, R/locus.R, man/diseq.Rd, man/genotype.Rd,
	  man/homozygote.Rd: - Fix mismatches between documentation and
	  code that we generating
	  warning messages.

2002-11-11 22:56  warnesgr

	* R/diseq.R: - Added minval and maxval to ci.balnance call() in
	  diseq.ci()
	  - Fixed typo in output text.

2002-11-08 21:07  warnesgr

	* DESCRIPTION, R/genotype.R, R/summary.genotype.R, TODO,
	  man/HWE.test.Rd, man/genotype.Rd, man/homozygote.Rd,
	  man/locus.Rd, man/summary.genotype.Rd, man/undocumented.Rd: -
	  DESCRIPTION: Updated version number and date
	  - TODO: Updated todo list.

2002-11-08 19:54  warnesgr

	* tests, tests/ci.balance.R: Added tests for ci.balance() functon.

2002-11-08 19:53  warnesgr

	* R/ci.balance.R, R/diseq.R, man/ci.balance.Rd, man/diseq.Rd: -
	  Moved ci.balance() to a separate file and created a documenation
	  file for it.
	  - Modified ci.balance to better annotate when it uses boundary
	  values.
	  - Modified diseq.ci to better provide warning message when the
	  number of
	  alleles is greater than 3.

2002-11-08 17:20  warnesgr

	* R/HWE.test.R, R/diseq.R: - Added test for more than two alleles
	  to diseq.ci. If there are more
	  than two, generate a warning message indicating that confidence
	  intervals for values near 0 and 1 are ill-behaved. When
	  'correct=TRUE' use ci.balance to attempt to correct for this.
	  - Modified HWE.test to display warnings from diseq.ci.

2002-11-07 19:13  warnesgr

	* R/diseq.R: - Fixed code so that gentypes with some listed allele
	  not observed are
	  handled properly. For example, if we have "A/A", and "A/B", but
	  no
	  "B/B", or worse yet when we know that "A" and "B" allels are both
	  possible but we only see one.

2002-10-28 18:20  warnesgr

	* R/genotype.R: - Allow allele names to be specified for
	  as.genotype.allele.count().

2002-10-28 18:19  warnesgr

	* R/summary.genotype.R: - Fixed for syntax error in
	  summary.genotype()

2002-10-28 18:19  warnesgr

	* R/HWE.test.R, R/diseq.R: - Lots of changes to the disequlibrim
	  computation and confidence interval code.
	  - D, D', and R are now computed
	  - Overall values are reported *with sign* of the number of
	  alleles is 2
	  - Bootstrapping code is now more efficient
	  
	  - Changes to HWE.test() and print.hwe.test() corresponding to the
	  above changes

2002-10-24 21:43  warnesgr

	* DESCRIPTION, R/diseq.R, R/genotype.R, man/genotype.Rd: - Fixed
	  bug as.genotype.alllele.count() introduced when 'harmonizing'
	  methods
	  with generics.
	  - Added 'alleles' arguments to the as.genotype.alllele.count()
	  function.
	  - Added example code for as.genotype.alllele.count() to doc file.
	  - Added explicit mention of as.genotype.alllele.count() to doc
	  file.

2002-10-11 18:01  warnesgr

	* R/HWE.test.R, R/diseq.R, R/zzz.R: Updated version number.

2002-09-30 14:35  warnesgr

	* R/diseq.R: - Modified diseq() to retain sign on the overall
	  disequlibrium estimate
	  - Modified diseq.ci() to use percentile confidence intervals

2002-09-24 01:53  warnesgr

	* DESCRIPTION: - Updated version number
	  - Added 'computing disequilibrium' to description text.

2002-09-24 01:32  warnesgr

	* R/HWE.test.R, R/diseq.R, R/genotype.R, R/zzz.R, man/HWE.test.Rd,
	  man/diseq.Rd, man/genotype.Rd, man/summary.genotype.Rd: -
	  'Un-genericized' diseq()
	  - Moved documentation of diseq() and diseq from HWE.test.Rd to
	  diseq.Rd
	  - Cleaned up HWE.test.Rd and diseq.Rd
	  - Fixed broken class check in diseq() and diseq.ci()
	  - Removed allele.count.default() -- this will force the user to
	  explicitly call 'genotype' on the data to use allele.count().
	  - Added zzz.R to require package 'boot'

2002-09-24 00:02  WarnesGR

	* R/HWE.test.R, R/diseq.R, man/HWE.test.Rd: - Moved code that
	  computed D-hat to diseq() and diseq.genotype() in diseq.R.
	  - Added diseq.ci() to compute confidence interval for D-hat.
	  - Added code to call diseq() and diseq.ci() from HWE.test()
	  - Added arguments to HWE.test() and print.HWE.test() to control
	  these new features
	  - Added text to HWE.test.Rd documenting these new functions and
	  arguments

2002-09-23 20:08  warnesgr

	* R/genotype.R: - Added as.genotype.table()

2002-06-27 18:46  warnesgr

	* inst/doc/genetics_article.tex: - More revisions. Hopefully last
	  set before submission to publication
	  review.

2002-06-27 18:46  warnesgr

	* R/HWE.test.R, examples/HWE_Test.R: - Allow user to specify
	  parameters for the chisquare test.

2002-06-25 21:38  warnesgr

	* inst/doc/genetics_article.tex: - Fixed syntax errors
	  - Some reorganization

2002-06-19 11:17  warnesgr

	* man/locus.Rd: - Fixed typo in \seealso.

2002-06-19 10:34  warnesgr

	* inst/doc/genetics_article.tex: Much enhancement, including
	  addition of example section.

2002-06-19 00:13  warnesgr

	* R/HWE.test.R: - Fixed bug that caused 'Error: subscript out of
	  bounds' when a 2
	  allele genotype had 1/1 and 1/2 but not 2/2.

2002-06-18 20:42  warnesgr

	* DESCRIPTION: Updated version.

2002-06-18 20:41  warnesgr

	* R/genotype.R, man/summary.genotype.Rd: - Fixed a bug in
	  allele.count that resulted in infinite recuresion.
	  - Modified documentation to match changed code.

2002-06-18 19:38  warnesgr

	* DESCRIPTION, R/genotype.R, R/summary.genotype.R, man/HWE.test.Rd,
	  man/genotype.Rd, man/locus.Rd, man/summary.genotype.Rd: Changes
	  to fix problems reported by R CMD check.

2002-05-06 18:35  swietm

	* 7, TODO: Testing CVS functionality. Removed addewd characters to
	  TODO

2002-05-06 18:31  swietm

	* 7, TODO: This was a test to learn how to add and modify files
	  using CVS

2002-04-09 00:49  warneg

	* inst, inst/doc, inst/doc/Rnews.sty,
	  inst/doc/genetics_article.tex: - Initial checkin of article
	  sources

2002-04-08 23:24  warneg

	* DESCRIPTION, man/homozygote.Rd: First checkin after moving
	  repository from tuwein.

2002-04-08 23:23  warneg

	* man/genotype.Rd: - Noted that when the user specifies the alleles
	  non-matching elements
	  are converted to NAs.

2002-04-08 23:19  warneg

	* R/genotype.R: - Modified 'genotype' function so that when the
	  user specifies the
	  alleles non-matching elements are converted to NAs.

2002-02-21 03:09  warnes

	* R/genotype.R, man/genotype.Rd, man/undocumented.Rd: - Add
	  as.factor.genotype.

2002-02-14 12:55  warnes

	* DESCRIPTION: Rephrased description.

2002-02-14 12:55  warnes

	* R/HWE.test.R, R/genotype.R: Fixed bugs in [.genotype and
	  [.haplotype.
	  
	  - There was a serious typo that would have been cought had I just
	  done
	  R CMD check.
	  
	  - Revamped [.genotype and [.haplotype to work correctly and to
	  avoid
	  the overhead of calling genotype() or haplotype() when drop=T. I
	  think these finally work properly.

2002-02-14 12:48  warnes

	* man/HWE.test.Rd, man/genotype.Rd, man/undocumented.Rd: - Added
	  'keywords' to HWE.test
	  - Create undocumented.Rd to satisfy documentation requiremets for
	  objects not otherwise included in documentation
	  - Add 'alais' commands noting that 'genotype' and '[.haplotype'
	  are
	  documented here.

2002-02-14 12:37  warnes

	* man/genotype.Rd: - Small change to the example code.

2002-02-09 00:47  warnes

	* R/genotype.R: - Fixed the changes to "[.genotype" and
	  "[.haplotype". I was
	  incorrectly coping *all* of the attributes in the case of drop=T.
	  This caused mis-labeling of the underlying factor levels.

2002-02-07 17:08  warnes

	* man/genotype.Rd: Added examples related to two bugs,
	  - == with non-genotype/non-haplotype rhs, and
	  - [...,drop=T] .

2002-02-07 16:57  warnes

	* R/genotype.R: Fixed two bugs
	  
	  1) "[.genotype" and "[.haplotype" didn't have the 'drop'
	  argument, so
	  an error would be generated when used in a context that expected
	  it (like
	  lm(..., subset=something) ).
	  
	  I've implemented these so that drop=T not only drops unused
	  factor
	  levels, but also drops unused *allele* levels.
	  
	  2) "==.genotype" and "==.haplotype" didn't handle second
	  arguments that
	  weren't genotypes / haplotypes, so
	  x <- genotype( "A/B" )
	  x == "A/B"
	  would generate an error. Solved by converting the y argument to a
	  genotype / haplotype before the comparison.
	  
	  Note that if the lhs is a genotype this means
	  x == "A/B"
	  and
	  x == "B/A"
	  give the identical results.

2001-08-13 15:36  warnes

	* R/HWE.test.R: BUGFIX: Corrected problem where the allele order
	  was not consistent between
	  the first (Observed #) and second columns (Expected #) of the
	  HWE.test table. This caused incorrect values for Obs-Exp to
	  be calcuated, as well as incorrect D-hat estimates.
	  Fortunately, it did not effect the correctness of the test
	  statistic or p-value, since these were computed via the chisq
	  function.

2001-08-03 11:33  warnes

	* DESCRIPTION, man/genotype.Rd: Minor changes.

2001-06-28 19:26  warnes

	* R/chisq.test.R: Will let Fritz and Kurt negotiate any
	  changes/modifications to chisq.test.

2001-06-28 19:23  warnes

	* R/genotype.R: Minor change, mask off extra attributes when
	  calling print() to
	  dislplay genotype data.

2001-06-28 19:15  warnes

	* man/HWE.test.Rd: - Updated to match v1.4 of HWE.test.R.
	  
	  - Added CVS id and log fields to file.

2001-06-28 19:14  warnes

	* R/HWE.test.R: - Modified to use
	  chisq.test(...,simulate.p.value=T,B=10000) to use
	  simulated p-value so that assumptions underlying Chi-square
	  approximation need not hold. This particularly useful for small
	  sample sizes or when some allele pairs are not observed.
	  
	  - Now gives a table of observed counts, observed frequency,
	  expected
	  frequency, and disequilibrium statistic (D-hat) for each pair of
	  alleles in addition to the overall disequilibrium statistic
	  (D-hat).

2001-06-15 17:02  warnes

	* DESCRIPTION, R/HWE.test.R, R/chisq.test.R, R/genotype.R, TODO,
	  examples/Genomics.examples, man/HWE.test.Rd, man/genotype.Rd,
	  man/homozygote.Rd, man/locus.Rd, man/summary.genotype.Rd: -
	  Modified HWE.test to use chisq.test. Added a modified version of
	  chisq.test until the (minor) changes show up in ctest.
	  
	  - Fixed documentation links and alias omissions
	  
	  - Fixed getallele() to snag allele element or attribute if either
	  is
	  present. This makes it work for summary.genotype as well as for
	  genotype.

2001-06-13 20:00  warnes

	* R/summary.genotype.R: - Added "allele.names" attribute.

2001-06-13 17:03  warnes

	* R/HWE.test.R, man/genotype.Rd: - Updated HWE.test.R to not assume
	  that a summary.genotype object
	  contains the original genotype object.
	  
	  - Removed a duplicate link to "allele.names" from genotype.Rd.

2001-05-30 22:15  warnes

	* man/HWE.test.Rd: Added HWE.test.Rd to document HWE.test.

2001-05-30 22:12  warnes

	* R/HWE.test.R, R/genotype.R, R/locus.R, TODO,
	  examples/Genomics.examples, man/genotype.Rd, man/homozygote.Rd,
	  man/summary.genotype.Rd: Updated documentation mostly. Added
	  as.character.genotype().

2001-05-30 22:03  warnes

	* man/locus.Rd: Initial version of locus.Rd.

2001-05-29 17:42  warnes

	* man/summary.genotype.Rd: Updated to note that row for NA is only
	  present if the data contains
	  NA. Corresponds to revision 1.2 of summary.genotype.R.

2001-05-29 17:38  warnes

	* man/genotype.Rd, man/summary.genotype.Rd: Modified seealso().

2001-05-29 17:16  warnes

	* man/homozygote.Rd: Completed homozygote.Rd which documents
	  homozygote(), heterozugote(),
	  carrier(), allele(), and allele.cound().

2001-05-29 10:27  leisch

	* R/summary.genotype.R: add NA line only if NA's are present

2001-05-26 00:28  warnes

	* man/homozygote.Rd: Partially completed man/homozygote.Rd
	  containing documentation for
	  homozygote(), heterozygote(), carrier(), allele.count(), and
	  allele().

2001-05-26 00:26  warnes

	* R/genotype.R: Removed allele.ind() and added "any" parameter to
	  carrier(). When
	  more than one allele is selected, or when no alleles are slected
	  and
	  any=F, carrier() now acts as allele.ind() did.
	  
	  Modified allele.count() to have similar behavior.

2001-05-25 23:39  warnes

	* man/genotype.Rd: Added man/genotype.Rd to document genotype and
	  haplotype classes in
	  R/genotype.R.

2001-05-25 23:37  warnes

	* R/genotype.R, R/summary.genotype.R, man, man/summary.genotype.Rd:
	  Moved summary.genotype and print.summary.genotype into a separate
	  file
	  (R/summary.genotype.R). Added man/summary.genotype.Rd containing
	  documentation for summary.genotype.

2001-05-22 20:26  warnes

	* R/Gene.R, R/Genomics.R: classes defined in Gene.R substantially
	  rewritten and moved to locus.R.
	  
	  Contents of Genomics.R moved to genotype.R.

2001-05-22 20:23  warnes

	* examples/locus.example.R: Added more examples

2001-05-22 19:00  warnes

	* examples/locus.example.R: Initial checkin of test script for code
	  in locus.R.

2001-05-22 18:58  warnes

	* R/locus.R: - Renamed "location.X" to "as.character.X" to better
	  represent thier
	  function. (Note as.character isn't generic at the moment, so
	  these
	  functions must be called directly.)
	  
	  - added function getlocus() to grab the appropriate locus field
	  or
	  attribute from an arbitrary object.

2001-05-22 18:53  warnes

	* R/genotype.R: - Renamed "genotype.R" from "Genomics.R".
	  
	  - Added slot for "locus" into genotype class.
	  
	  - Made allele.count, allele.ind, heterozygote, homozygote, and
	  carrier
	  return objects with the same class and created print.X routines.
	  This enabled the next item..
	  
	  - Made "locus" propagate to summary, HWE.test, allele,
	  allele.count,
	  allele.ind, heterozygote, homozygote, and carrier. This should
	  make
	  it easier to keep track of what locus each of these correspond
	  to.
	  **This may create unanticipated side effects**

2001-05-22 18:21  warnes

	* R/locus.R: Created classes for "locus", "gene", and "marker"
	  along with basic
	  methods is.X, print.X, and generic utility function "location",
	  which
	  formats the locus infromation for printing.

2001-05-16 12:58  leisch

	* R/Genomics.R: cosmetics

2001-05-16 12:55  leisch

	* R/Genomics.R: genotype: bugfix for non-character allele vectors
	  (e.g., integers)
	  a2 is now ignored if a1 is a genotype
	  a1 can now also be a 2 column matrix of alleles

2001-05-10 16:15  leisch

	* DESCRIPTION: update

2001-05-10 16:07  leisch

	* R/Genomics.R: cosmetics

2001-05-07 13:22  warnes

	* examples, examples/Allele_Freq.R, examples/Allele_Freq.out,
	  examples/Examples.new, examples/Examples.out,
	  examples/Gene.examples, examples/Genomics.examples,
	  examples/HWE_Test.R, examples/HWE_Test.out,
	  examples/test.data.2.txt, examples/test.data.txt: Added example
	  files, code, and output.

2001-05-07 13:21  warnes

	* R, R/Gene.R, R/Genomics.R: Imported R code for
	  
	  - Genotype and Haplotype classes,
	  - corresponding summary function (gives allele and genotype
	  frequencies)
	  - Hardy-Weinburg Equilibrium testing.
	  
	  Also, a initial try at a Gene and Marker classes.

2001-05-03 13:07  leisch

	* ., DESCRIPTION: Initial revision