NEWS
HMP 2.0 (2019-08-26)
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
HMP 1.6 (2018-10-31)
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
HMP 1.5.1 (2017-12-20)
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
HMP 1.5 (2017-07-06)
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
HMP 1.4.3 (2016-03-04)
BUG FIXES
- Fixed a bug in the DM.MoM function
HMP 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
HMP 1.3.1 (2013-05-09)
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"
HMP 1.3 (2013-04-13)
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".