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".