2005-06-30 Version 0.7
* hapassoc(): use initial weights in the glm to get initial parameter estimates.
* hapassoc(), pre.hapassoc(): replaced weights calcuation with a C function.
  Speed up computing time for large data sets.

2005-05-31 Version 0.6-2
* handleMissings(): fixed a bug for SNPs with a rare allele that is in no
  instance in a homozygous state.

2005-05-09 Version 0.6-1

* Added this ChangeLog file
* Added inst/CITATION file

2005-04-06 Version 0.6

* RecodeHaplos(): Allow input SNP data as alphabetic alleles (e.g.A,G,C,T),
  and for genotypes to be input either in a single two-character column
  ("genotypic format"), or as a pair of columns (the original "allelic
  format" from earlier versions of hapassoc)

* pre.hapassoc(): Added allelic argument to indicate whether SNP data are
  input in either genotypic fromat or allelic format

* RecodeHaplos(): Check for the number of alleles at each locus. If the
  check finds loci with >2 alleles, stop execution and print an error
  message that tells the user that only diallelic loci are allowed.

* RecodeHaplos(): Convert all missing data in "" format to NA.

* happasoc(): The convergence criteria for the EM algorithm has been
  tightened. We now require both absolute and relative changes in the
  parameter estimates from one iteration to the next to be below the
  user-specified tolerance.

* summary.hapassoc(): Added a check for converged FALSE, and now print a
  warning (used to just give a cryptic error).

* happasoc(): Changed the name of the variable 'gamma' to 'freq' and the
  name of the variable 'initGamma' to initFreq'
* pre.hapassoc(): Changed the name of the returned variable 'initGamma' to
  'initFreq'

pre.hapassoc man page 

* pre.hapassoc(): Added a new example of how to use pre.hapassoc with SNPs
  in the new genotypic format

* Added documentation to describe how single-locus genotypes may now be
  specified as a single two-character column ("genotypic format") in the
  input data frame

* Added a Note to alert users to ignore the possible warnings related to
  row.names being duplicated when there are missing genotypes on some of the
  loci for an individual

* Updated the reference to Burkett et al. to give journal volume and page
  numbers

hapassoc man page

* Added a Note to alert users to the warning they'll see when fitting
  logistic regression models (non-integer #successes...)

* Added more comments to the examples to make the coding of columns in
  haploDM more obvious, and added an example of a non-multiplicative
  logistic regression model

* Updated the reference to Burkett et al.

summary.hapassoc man page

* Updated the reference to Burkett et al.


2004-11-03 Version 0.5-1

* handleMissings() assignment to nonSNPdat changed to accomodate rbind of
  data frames which contain factors.

* hapassoc(): Assigned  response<-regr$y  
  We used to use model.response to extract the response variable, but this
  lead to problems in calculating the residuals in the pYgivenX function.
  It is better to fit the model with the glm function (see code) and then
  extract the response from the fitted model object


2004-09-29 Version 0.5

* Changed file name from PreEM.R to PreHap.R
* Changed function name from EM to hapassoc
* Changed function name from PreEM to pre.hapassoc
* changed function name from summary.EM to summary.hapassoc
