News

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".

Reference manual