Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

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Documentation for package ‘HMP’ version 2.0.1

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HMP-package Hypothesis Testing and Power Calculations for Comparing Metagenomics Samples
Barchart.data A Graphical Representation of Taxa Proportions
C.alpha.multinomial C(alpha) - Optimal Test for Assessing Multinomial Goodness of Fit Versus Dirichlet-Multinomial Alternative
Data.filter A Data Filter
Dirichlet.multinomial Generation of Dirichlet-Multinomial Random Samples
DM.MoM Method-of-Moments (MoM) Estimators of the Dirichlet-Multinomial Parameters
DM.Rpart Dirichlet-Multinomial RPart
DM.Rpart.Base Dirichlet-Multinomial RPart
DM.Rpart.CV Dirichlet-Multinomial RPart
DM.Rpart.CV.Consensus Dirichlet-Multinomial RPart
dmrp_covars Paper Covariate Set
dmrp_data Paper Taxa Data Set
Est.PI Estimate the Pi Vector
formatDataSets Format Data
Gen.Alg Find Taxa Separating Two Groups using Genetic Algorithm (GA)
Gen.Alg.Consensus Find Taxa Separating Two Groups using Multiple Genetic Algorithm's (GA) Consensus
HMP Hypothesis Testing and Power Calculations for Comparing Metagenomics Samples
Kullback.Leibler Kullback Leibler
kullbackLeiber Kullback Leibler
MC.Xdc.statistics Size and Power for the Several-Sample DM Parameter Test Comparison
MC.Xmc.statistics Size and Power of Several Sample RAD-Probability Mean Test Comparison
MC.Xmcupo.statistics Size and Power of Several Sample RAD-Probability Mean Test Comparisons: Unknown Vector of Proportion
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.ZT.statistics Size and Power of Goodness of Fit Test: Multinomial vs. Dirichlet-Multinomial
Multinomial Generation of Multinomial Random Samples
Plot.MDS Multidimensional Scaling Plot of Microbiome Data
Plot.PI Plot the Pi Vector
Plot.RM.Barchart Plot the Pi Vector for Repeated Measures
Plot.RM.Dotplot Plot the Pi Vector for Repeated Measures
saliva Saliva Data Set
Test.Paired Test Paired Data Sets
throat Throat Data Set
tongue Tongue Data Set
tonsils Palatine Tonsil Data Set
Xdc.sevsample Likelihood-Ratio-Test Statistics: Several Sample Dirichlet-Multinomial Test Comparison
Xmc.sevsample Generalized Wald-type Statistics: Several Sample RAD Probability-Mean Test Comparison with a Known Common Vector
Xmcupo.effectsize Effect Size for Xmcupo Statistic
Xmcupo.sevsample Generalized Wald-type Statistics: Several Sample RAD Probability-Mean Test Comparison with an Unknown Common Vector
Xoc.sevsample Likelihood-Ratio-Test Statistics: Several Sample Overdispersion Test Comparison
Xsc.onesample Generalized Wald-Type Statistics: One Sample RAD Probability-Mean Test Comparison