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HMP (version 2.0.1)

Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

Description

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

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Version

Install

install.packages('HMP')

Monthly Downloads

381

Version

2.0.1

License

Apache License (== 2.0)

Maintainer

Berkley Shands

Last Published

August 31st, 2019

Functions in HMP (2.0.1)

DM.MoM

Method-of-Moments (MoM) Estimators of the Dirichlet-Multinomial Parameters
Gen.Alg

Find Taxa Separating Two Groups using Genetic Algorithm (GA)
C.alpha.multinomial

\(C(\alpha)\) - Optimal Test for Assessing Multinomial Goodness of Fit Versus Dirichlet-Multinomial Alternative
Barchart.data

A Graphical Representation of Taxa Proportions
Data.filter

A Data Filter
Est.PI

Estimate the Pi Vector
DM.Rpart

Dirichlet-Multinomial RPart
HMP-internal

Internal Functions
MC.Xdc.statistics

Size and Power for the Several-Sample DM Parameter Test Comparison
Gen.Alg.Consensus

Find Taxa Separating Two Groups using Multiple Genetic Algorithm's (GA) Consensus
HMP-package

Hypothesis Testing and Power Calculations for Comparing Metagenomics Samples
Multinomial

Generation of Multinomial Random Samples
Plot.MDS

Multidimensional Scaling Plot of Microbiome Data
Kullback.Leibler

Kullback Leibler
MC.Xmcupo.statistics

Size and Power of Several Sample RAD-Probability Mean Test Comparisons: Unknown Vector of Proportion
Dirichlet.multinomial

Generation of Dirichlet-Multinomial Random Samples
MC.Xoc.statistics

Size and Power of Several Sample-Overdispersion Test Comparisons
MC.Xsc.statistics

Size and Power for the One Sample RAD Probability-Mean Test Comparison
MC.Xmc.statistics

Size and Power of Several Sample RAD-Probability Mean Test Comparison
formatDataSets

Format Data
saliva

Saliva Data Set
MC.ZT.statistics

Size and Power of Goodness of Fit Test: Multinomial vs. Dirichlet-Multinomial
Plot.RM.Barchart

Plot the Pi Vector for Repeated Measures
Plot.PI

Plot the Pi Vector
Xmcupo.effectsize

Effect Size for Xmcupo Statistic
Xoc.sevsample

Likelihood-Ratio-Test Statistics: Several Sample Overdispersion Test Comparison
Xsc.onesample

Generalized Wald-Type Statistics: One Sample RAD Probability-Mean Test Comparison
Xmcupo.sevsample

Generalized Wald-type Statistics: Several Sample RAD Probability-Mean Test Comparison with an Unknown Common Vector
Plot.RM.Dotplot

Plot the Pi Vector for Repeated Measures
Xmc.sevsample

Generalized Wald-type Statistics: Several Sample RAD Probability-Mean Test Comparison with a Known Common Vector
Xdc.sevsample

Likelihood-Ratio-Test Statistics: Several Sample Dirichlet-Multinomial Test Comparison
dmrp_data

Paper Taxa Data Set
dmrp_covars

Paper Covariate Set
Test.Paired

Test Paired Data Sets
tonsils

Palatine Tonsil Data Set
tongue

Tongue Data Set
throat

Throat Data Set