CHANGES IN bingat VERSION 1.3

CHANGES

* Tidied up every function's code, comments, and variable names

* Several function parameter names were changed.  The old names remain to support backwards compatibility.

* Added as.vector to the ga function -- update this later

* Changed pvalue calculations to include +1/+1 so it never is 0



CHANGES IN bingat VERSION 1.2

CHANGES

* Removed the cutoff parameter from all G Star calculations because it must be done at 50% for the math to be correct.

* Removed the PBMethod parameter from glrtPvalue 
 
* Change bootstraps to the number of permutations in the glrtPvalue function so it is consistant with the functionality.

* Added a function for paired data p-value test pairedPvalue

* Added numSims to testGoF for the chi squared test

* Added a function to plot the data on an MDS plot

* Added a function to plot the data as a heatmap

* Added a function to compute a p value using a LRT method

* Added a function that uses a genetic algorthim to find differences in groups



CHANGES IN bingat VERSION 1.1

CHANGES

* Made glrtReg and glmReg functions internal since they should only be called from the glrtPvalue function. 

* Change the initial clustering in the getGibbsMixture from pam to random sampling.


BUG FIXES

* Fixed a bug in getGibbsMixture and getLoglikeMixture where large graphs would cause errors or 0 to return.

* Fixed a bug in glrtPvalue where the tau and gstar weren't being computed correctly in some instances.