Changes in version 2.0 (2019-08-26)                   

CHANGES

    o   Added parallel computing to rpart cross validation

    o   The best rpart tree can now be the tree with the smallest error or plus/minus 1 standard error

    o   Changed rpart to run quicker by handling factors and numeric differently

    o   Data.filter now works with numtaxa and perTaxa as NULL by keeping all taxa

    o   Removed deprecated arguments

    o   Added vignette containing code to reproduce figures in the DM-Rpart paper

BUG FIXES

    o   Fixed labeling error in rpart

    o   Added error checking for rpart trees with 1 node and no surrogates

                  Changes in version 1.6 (2018-10-31)                   

CHANGES

    o   Added penalty for GA

    o   Changed rpart to use cross validation to find the best tree instead of permutations

    o   Changed KL to use MOM instead of MLE

BUG FIXES

    o   Fixed getBC so that it drops duplicates instead of crashing

    o   Fixed estPi to handle groups with 1 sample

                 Changes in version 1.5.1 (2017-12-20)                  

CHANGES

    o   Added ability to use custom covar distance matrix

    o   Added two new plotting functions

    o   Added text to indicate logging with the pi plot function

BUG FIXES

    o   Fixed labels in GA plots and results

    o   Fixed bug in Xmcupo.sevsample pvalue calculations

    o   Fixed bug with plot.pi not passing plot title

                  Changes in version 1.5 (2017-07-06)                   

CHANGES

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

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

    o   kullbackLieber was renamed to Kullback.Leibler.  kullbackLieber now just calls Kullback.Leibler.

    o   Added Plot.MDS to plot data

    o   Added Est.PI to estimate the pi vector and plot it with Plot.Pi 

    o   Changed data.filter to allow for percentage based filtering

    o   Added a function for testing paired data (Test.Paired)

    o   Added a function that uses rpart to find groups within the data (DM.Rpart and DM.Rpart.Perm)

    o   Added a function that use GA to find taxa that separate 2 groups (DM.GA and DM.GA.Consensus)

BUG FIXES

    o   DM.MoM can now take a single subject

    o   Added 1 to the numerator and denominators for permutation tests to prevent pvalues = 0

                 Changes in version 1.4.3 (2016-03-04)                  

BUG FIXES

    o   Fixed a bug in the DM.MoM function

                         Changes in version 1.4                         

CHANGES

    o   Changed several functions to improve performance

    o   MC.Xdc.statistic and MC.Xoc.statistics now calculates n.groups themselves

    o   Xmcupo.sevsample now calculates K itself

    o   Added a function to format and combine multiple data sets with different taxa

    o   Added a Kullback Leiber function

                 Changes in version 1.3.1 (2013-05-09)                  

CHANGES

    o   Changed the MC example files to use "DM.MoM" instead of "dirmult" for speed

BUG FIXES

    o   Fixed a bug in MC.Xmcupo.statistics that produced a incorrect result under type="ha"

                  Changes in version 1.3 (2013-04-13)                   

CHANGES

    o   Updated several of the MC functions to perform power calculations on unbalanced designs, 
	however it should be noted that this caused the Nrs parameter to change from a vector to a 
	list for several functions.

    o   Removed the initscalar parameter from the sevsample functions and replaced it with the value
	of gamma from the DM.MoM function.

    o   Change the names of some functions so they all follow the same formatting.  This change mainly 
	affected internal functions.

    o   Changed the wording of the return value in the MC functions from "effect size" to "size of the 
	test statistics" to correctly describe what is being returned.

    o   Changed the Barchart.data function to take a full title rather than just a taxa level.

    o   Changed Xdc.sevsample to select between 'mle' and 'mom' estimators.

    o   Added several warnings/notes clarifying that the value of MC should be >1000 in the MC.functions

    o   Added several warnings/notes clarifying the use of different number of reads in a sample

    o   Added two new functions: Xmcupo.effectsize and pioest

BUG FIXES

    o   Fixed a bug in MC.Xdc.statistics where k was not set to the right value under "ha".