Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.


News

CHANGES IN HMP VERSION 1.6

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

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("HMP")

1.5.1 by Berkley Shands, 6 months ago


Browse source code at https://github.com/cran/HMP


Authors: Patricio S. La Rosa, Elena Deych, Sharina Carter, Berkley Shands, William D. Shannon


Documentation:   PDF Manual  


Apache License (== 2.0) license


Imports ggplot2, stats, foreach, doParallel, MASS, vegan, gplots, rpart, rpart.plot, parallel, graphics, lattice

Depends on dirmult


Imported by HMPTrees.


See at CRAN