Changes in version 2.3.1: NEW FUNCTIONALITY o New output format is added: JSON format. In odred to get output in JSON format apply JSONOutput with the PhenTestResult object as an argument. COMPATIBILITY ISSUES o The Box-Cox transformation is switched off by default. In order to swithc in on the testDataset() function's argument “transformValues" has to be set to TRUE. Changes in version 2.1.3: NEW FUNCTIONALITY o Box-Cox transformation is applied when needed for the continues data. Transformation values are shown in output functions. Genotype effects are converted back into original scale if transformation was applied. o New statistical method is implemented for the categorical data - Logistic Regression. o New function is created boxplotSexGenotypeBatchAdjusted() that allows to evaluate Batch effect. o Major architectural changes: classes PhenList and PhenTestResult are S4 classes now. Different new methods are provided for the classes. o PhenTestResult object contains dataset analysedDataset() that was used for the analysis including original values, transformed values (if transformation has been applied) and values adjusted for batch effect. COMPATIBILITY ISSUES o The vectorOutput() has new element for transformation values which have increased its length. Changes in version 2.0.2: BUG FIXES o Column names in PhenList object. The check for the existing column names (Genotype, Batch, Sex, Weight) is added before the renaming of the columns. o 'generateGraphs' function is back to work o 'summaryOutput' function bug in FE framework is solved Changes in version 2.0.1: NEW FEATURES o Two new statistical methods implemented RR (Reference Range Plus) and TF (Time Fixed Effect) that can be called from testDataset() function with argument method set to RR and TF correspondingly. o Additional measure of biological effect added: Percentage Change to summaryOutput() and vectorOutput functions. o New function is added to suggest analysis paths for dataset: recommendMethod() o Function to implement the RR method: RRTest(). o Functions to implement the TF method: TFDataset() creates dataset suitanle for TF, startTFModel(), finalTFModel create model and fit it. o Changes in function summaryOutput() - additional information and clearer layout. COMPATIBILITY ISSUES o The vectorOutput() had additional elements which have increased its length. o The function boxplotSexGenotypeBatch() has been deprecated and replace with scatterplotSexGenotypeBatch(). o Additional argument (phenotypeThreshold) with default value 0.01 has been added to the summaryOutput() function BUG FIXES o Number of critical bugs fixed. These are detailed at