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.