HMP: 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.

AuthorPatricio S. La Rosa, Elena Deych, Berkley Shands, William D. Shannon
Date of publication2016-03-04 22:42:08
MaintainerBerkley Shands <rpackages@biorankings.com>
LicenseApache License (== 2.0)
Version1.4.3

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...

Functions

Barchart.data Man page
C.alpha.multinomial Man page
Data.filter Man page
Dirichlet.multinomial Man page
DM.MoM Man page
formatDataSets Man page
HMP Man page
HMP-internal Man page
HMP-package Man page
kullbackLeiber Man page
LLDM Man page
loglikDM Man page
MC.Xdc.statistics Man page
MC.Xmc.statistics Man page
MC.Xmcupo.statistics Man page
MC.Xoc.statistics Man page
MC.Xsc.statistics Man page
MC.ZT.statistics Man page
Multinomial Man page
pioest Man page
saliva Man page
throat Man page
tongue Man page
tonsils Man page
T.statistics Man page
weirMoM Man page
Xdc.sevsample Man page
Xdc.statistics Man page
Xdc.statistics.Hnull.Ha Man page
Xdc.statistics.MoM Man page
Xmc.sevsample Man page
Xmc.statistics Man page
Xmc.statistics.Hnull.Ha Man page
Xmcupo.effectsize Man page
Xmcupo.sevsample Man page
Xmcupo.statistics Man page
Xmcupo.statistics.Hnull.Ha Man page
Xoc.sevsample Man page
Xoc.statistics Man page
Xoc.statistics.Hnull.Ha Man page
Xoc.statistics.MoM Man page
Xsc.onesample Man page
Xsc.statistics Man page
Xsc.statistics.Hnull.Ha Man page
Z.statistics Man page
ZT.statistics Man page
ZT.statistics.Hnull.Ha Man page

Files

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

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