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.