CHANGES IN VERSIO 1.33

NEW FEATURES (MPN, GBG)

    o aldex.clr: now takes a gamma parameter to incorporate scale modelling

    o aldex.makeScaleMatrix: new method to make an explicit scale model

    o all p-values calculated are now posterior p-values with consistent sign

CHANGES IN VERSION 1.11.0
-------------------------

NEW FEATURES (TPQ)

    o Iterative log-ratio transformation works with all aldex. methods
    
        o aldex.r: new "iterate = TRUE" works for any aldex. method

    o New aldex.corr function uses continuous outcome
    
        o aldex.corr.r: file with old aldex.corr function was removed
        
        o aldex.r: test = "cor" or test = "corr" calls aldex.corr
        
        o aldex.r: pass along ... correctly
        
    o Add verbose argument to aldex.kw, aldex.glm, aldex.corr
        
    o Remove conditions argument
    
        o Use clr@conds for aldex.ttest, aldex.kw, aldex.glm, aldex.corr, aldex.effect
        
        o aldex.clr: passes along any conditions argument (including matrix)
        
        o aldex.r: no longer pass along conditions
        
        o new test to verify multi-type clr@conds
        
        o old tests updated

CHANGES IN VERSION 1.10.3
-------------------------

NEW FEATURES (TPQ)

    o New aldex.glm function uses model matrix
    
        o aldex.r: test = "kw" calls old aldex.glm, test = "glm" calls new aldex.glm
        
        o AllClasses.R: change "conds" slot to accept "ANY" to expect model matrix
        
        o clr_function.r: tweak coerce.data to expect model matrix
        
            o Note: coerce.data function replaced with fewer lines of code
            
        o clr_ttest.r: Roxygenize documentation
        
        o clr_glm.r: old aldex.glm function renamed as aldex.kw + Roxygenize documentation
        
        o clr_glm-tpq.R: new aldex.glm uses model matrix + Roxygenize documentation
        
        o plot.aldex.r: no changes -- not compatible with new aldex.glm
        
        o test-aldex.kw.R: update test to reflect changes
        
        o ALDEx2_vignette.Rnw: use aldex.kw in vignette

CHANGES IN VERSION 1.10.2
-------------------------

NEW FEATURES (TPQ)

    o add README for the GitHub repository
    o let aldex.clr work even when 'conds' is missing

CHANGES IN VERSION 1.10.1
-------------------------

BUG FIXES

    o fixed a bug whereby the order of samples affected the centering of the data

CHANGES IN VERSION 1.9.2
-------------------------

NEW FEATURES (JRW, GBG)

    o added ability to auto-choose low variance high relative abundance features as
    the basis
    o added new class and generic definitions to get the features used as basis
    o the getDenom function can be exported
    o updated documentation for above
    o version bump

CHANGES IN VERSION 1.8.1
-------------------------

NEW FEATURES (TPQ)

    o rennovated aldex function

        o new 'test = iterative' uses results of one t-test as 'denom' input to a second

        o large improvements to function documentation

    o rennovated aldex.ttest function

        o "progress bar" tracks progress across Monte-Carlo instances

        o made aldex.ttest function faster (~300% for 10,000 features)

        o now uses Wilcox signed rank test when 'paired.test = TRUE'

    o added aldex.clr method for signature 'matrix'

CHANGES IN VERSION 1.5.2
-------------------------

NEW FEATURES

    o added ability to choose the basis for the clr: all, iqlr, zero or user-defined.
    useful when dealing with asymmetric datasets (selex, metagenomics, meta-RNA-seq)

    o updated vignette to show how the basis affects the analysis

    o made BiocParallel the only parallel package for multicore processing

    o made zero-replacement a prior probability rather than a pseudocount

CHANGES IN VERSION 0.99.2
-------------------------

NEW FEATURES

    o made aldex.clr into a class

    o allowed input of SummarizedExperiment object instead of a reads data frame

    o prioritized use of the BiocParallel package for multicore processing. If
    BiocParallel is not installed then the parallel package used, if neither
    packages are installed, then serial processing is used

CHANGES IN VERSION 0.99.1
-------------------------

NEW FEATURES

    o changed conditional tests for multiprocessor use, defaults to FALSE

CHANGES IN VERSION 0.99.0
-------------------------

NEW FEATURES

    o first submission to Bioc-devel