HMP: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

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

Author
Patricio S. La Rosa, Elena Deych, Berkley Shands, William D. Shannon
Date of publication
2016-03-04 22:42:08
Maintainer
Berkley Shands <rpackages@biorankings.com>
License
Apache License (== 2.0)
Version
1.4.3

View on CRAN

Man pages

Barchart.data
A Graphical Representation of Taxa Proportions
C.alpha.multinomial
C(alpha) - Optimal Test for Assessing Multinomial Goodness of...
Data.filter
A Data Filter
Dirichlet.multinomial
Generation of Dirichlet-Multinomial Random Samples
DM.MoM
Method-of-Moments (MoM) Estimators of the...
formatDataSets
Format Data
HMP-internal
Internal Functions
HMP-package
Hypothesis Testing and Power Calculations for Comparing...
kullbackLeiber
Kullback Leiber
MC.Xdc.statistics
Size and Power for the Several-Sample DM Parameter Test...
MC.Xmc.statistics
Size and Power of Several Sample RAD-Probability Mean Test...
MC.Xmcupo.statistics
Size and Power of Several Sample RAD-Probability Mean Test...
MC.Xoc.statistics
Size and Power of Several Sample-Overdispersion Test...
MC.Xsc.statistics
Size and Power for the One Sample RAD Probability-Mean Test...
MC.ZT.statistics
Size and Power of Goodness of Fit Test: Multinomial vs....
Multinomial
Generation of Multinomial Random Samples
pioest
Weighted Average of Taxa Frequency for Several Groups
saliva
Saliva Data Set
throat
Throat Data Set
tongue
Tongue Data Set
tonsils
Palatine Tonsil Data Set
Xdc.sevsample
Likelihood-Ratio-Test Statistics: Several Sample...
Xmc.sevsample
Generalized Wald-type Statistics: Several Sample RAD...
Xmcupo.effectsize
Effect Size for Xmcupo Statistic
Xmcupo.sevsample
Generalized Wald-type Statistics: Several Sample RAD...
Xoc.sevsample
Likelihood-Ratio-Test Statistics: Several Sample...
Xsc.onesample
Generalized Wald-Type Statistics: One Sample RAD...

Files in this package

HMP
HMP/NAMESPACE
HMP/NEWS
HMP/data
HMP/data/tongue.rda
HMP/data/tonsils.rda
HMP/data/saliva.rda
HMP/data/throat.rda
HMP/R
HMP/R/Xdc.sevsample.R
HMP/R/Data.filter.R
HMP/R/MC.Xmcupo.statistics.R
HMP/R/weirMoM.R
HMP/R/LLDM.R
HMP/R/MC.Xdc.statistics.R
HMP/R/MC.ZT.statistics.R
HMP/R/formatDataSets.R
HMP/R/DM.MoM.R
HMP/R/MC.Xmc.statistics.R
HMP/R/T.statistics.R
HMP/R/Xoc.sevsample.R
HMP/R/Z.statistics.R
HMP/R/MC.Xsc.statistics.R
HMP/R/ZT.statistics.Hnull.Ha.R
HMP/R/Dirichlet.multinomial.R
HMP/R/Xmcupo.effectsize.R
HMP/R/Xmcupo.statistics.Hnull.Ha.R
HMP/R/loglikDM.R
HMP/R/Multinomial.R
HMP/R/Xmc.statistics.R
HMP/R/Xmcupo.sevsample.R
HMP/R/Xdc.statistics.Hnull.Ha.R
HMP/R/kullbackLeiber.R
HMP/R/Xmc.statistics.Hnull.Ha.R
HMP/R/Xmcupo.statistics.R
HMP/R/pioest.R
HMP/R/Xdc.statistics.R
HMP/R/Barchart.data.R
HMP/R/Xdc.statistics.MoM.R
HMP/R/Xoc.statistics.Hnull.Ha.R
HMP/R/Xoc.statistics.R
HMP/R/Xsc.statistics.Hnull.Ha.R
HMP/R/C.alpha.multinomial.R
HMP/R/MC.Xoc.statistics.R
HMP/R/Xsc.onesample.R
HMP/R/Xsc.statistics.R
HMP/R/Xoc.statistics.MoM.R
HMP/R/Xmc.sevsample.R
HMP/MD5
HMP/DESCRIPTION
HMP/man
HMP/man/kullbackLeiber.Rd
HMP/man/Xmcupo.effectsize.Rd
HMP/man/Barchart.data.Rd
HMP/man/Data.filter.Rd
HMP/man/HMP-package.Rd
HMP/man/MC.Xsc.statistics.Rd
HMP/man/Xdc.sevsample.Rd
HMP/man/MC.Xoc.statistics.Rd
HMP/man/tongue.Rd
HMP/man/Xmcupo.sevsample.Rd
HMP/man/Dirichlet.multinomial.Rd
HMP/man/MC.Xmc.statistics.Rd
HMP/man/pioest.Rd
HMP/man/C.alpha.multinomial.Rd
HMP/man/throat.Rd
HMP/man/HMP-internal.Rd
HMP/man/Xoc.sevsample.Rd
HMP/man/MC.Xmcupo.statistics.Rd
HMP/man/MC.ZT.statistics.Rd
HMP/man/MC.Xdc.statistics.Rd
HMP/man/formatDataSets.Rd
HMP/man/tonsils.Rd
HMP/man/DM.MoM.Rd
HMP/man/saliva.Rd
HMP/man/Xsc.onesample.Rd
HMP/man/Multinomial.Rd
HMP/man/Xmc.sevsample.Rd