CHANGES IN HMP VERSION 2.0

CHANGES

* Added parallel computing to rpart cross validation

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

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

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

* Removed deprecated arguments

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

BUG FIXES

* Fixed labeling error in rpart

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


CHANGES IN HMP VERSION 1.6

CHANGES

* Added penalty for GA

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

* Changed KL to use MOM instead of MLE

BUG FIXES

* Fixed getBC so that it drops duplicates instead of crashing

* Fixed estPi to handle groups with 1 sample


CHANGES IN HMP VERSION 1.5.1

CHANGES

* Added ability to use custom covar distance matrix

* Added two new plotting functions

* Added text to indicate logging with the pi plot function

BUG FIXES

* Fixed labels in GA plots and results

* Fixed bug in Xmcupo.sevsample pvalue calculations

* Fixed bug with plot.pi not passing plot title


CHANGES IN HMP VERSION 1.5

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.

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

* Added Plot.MDS to plot data

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

* Changed data.filter to allow for percentage based filtering

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

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

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

BUG FIXES

* DM.MoM can now take a single subject

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



CHANGES IN HMP VERSION 1.4.3

BUG FIXES

* Fixed a bug in the DM.MoM function



CHANGES IN HMP VERSION 1.4

CHANGES

* Changed several functions to improve performance

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

* Xmcupo.sevsample now calculates K itself

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

* Added a Kullback Leiber function



CHANGES IN HMP VERSION 1.3.1

CHANGES

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


BUG FIXES

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



CHANGES IN HMP VERSION 1.3

CHANGES

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

* Change the names of some functions so they all follow the same formatting.  This change mainly 
  affected internal functions.
  
* 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.
  
* Changed the Barchart.data function to take a full title rather than just a taxa level.

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

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

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

* Added two new functions: Xmcupo.effectsize and pioest

BUG FIXES

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