Package: HMP 2.0.1

Berkley Shands

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.

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

HMP_2.0.1.tar.gz
HMP_2.0.1.tar.gz(r-4.5-noble)HMP_2.0.1.tar.gz(r-4.4-noble)
HMP_2.0.1.tgz(r-4.4-emscripten)HMP_2.0.1.tgz(r-4.3-emscripten)
HMP.pdf |HMP.html✨
HMP/json (API)
NEWS

# Install 'HMP' in R:
install.packages('HMP', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

63 exports 1 stars 3.60 score 43 dependencies 1 dependents 25 mentions 73 scripts 346 downloads

Last updated 5 years agofrom:30dadecea2. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 02 2024
R-4.5-linuxNOTESep 02 2024

Exports:Barchart.dataC.alpha.multinomialData.filterDirichlet.multinomialDM.MoMDM.RpartDM.Rpart.BaseDM.Rpart.Base.OldDM.Rpart.CVDM.Rpart.CV.ConsensusEst.PIformatDataSetsgaCreationgaPlotgaScoringGen.AlgGen.Alg.ConsensusgetBCKullback.LeiblerkullbackLeiberloglikDMMC.Xdc.statisticsMC.Xmc.statisticsMC.Xmcupo.statisticsMC.Xoc.statisticsMC.Xsc.statisticsMC.ZT.statisticsMultinomialpioestPlot.MDSPlot.PIPlot.RM.BarchartPlot.RM.DotplotrpartCIrpartCSrpartCVrpartCVSinglerpartEvalrpartInitrpartSplitrpartSplitOldT.statisticsTest.PairedweirMoMXdc.sevsampleXdc.statisticsXdc.statistics.Hnull.HaXdc.statistics.MoMXmc.sevsampleXmc.statisticsXmc.statistics.Hnull.HaXmcupo.effectsizeXmcupo.sevsampleXmcupo.statisticsXmcupo.statistics.Hnull.HaXoc.sevsampleXoc.statisticsXoc.statistics.Hnull.HaXsc.onesampleXsc.statisticsXsc.statistics.Hnull.HaZ.statisticsZT.statistics.Hnull.Ha

Dependencies:bitopscaToolscliclustercodetoolscolorspacedirmultdoParallelfansifarverforeachggplot2gluegplotsgtablegtoolsisobanditeratorsKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepermutepillarpkgconfigR6RColorBrewerrlangrpartrpart.plotscalestibbleutf8vctrsveganviridisLitewithr

Figures from Reference Paper

Rendered fromDMRP_Paper.Rnwusingutils::Sweaveon Sep 02 2024.

Last update: 2019-08-31
Started: 2019-08-26

Readme and manuals

Help Manual

Help pageTopics
Hypothesis Testing and Power Calculations for Comparing Metagenomics SamplesHMP-package HMP
A Graphical Representation of Taxa ProportionsBarchart.data
C(alpha) - Optimal Test for Assessing Multinomial Goodness of Fit Versus Dirichlet-Multinomial AlternativeC.alpha.multinomial
A Data FilterData.filter
Generation of Dirichlet-Multinomial Random SamplesDirichlet.multinomial
Method-of-Moments (MoM) Estimators of the Dirichlet-Multinomial ParametersDM.MoM
Dirichlet-Multinomial RPartDM.Rpart DM.Rpart.Base DM.Rpart.CV DM.Rpart.CV.Consensus
Paper Covariate Setdmrp_covars
Paper Taxa Data Setdmrp_data
Estimate the Pi VectorEst.PI
Format DataformatDataSets
Find Taxa Separating Two Groups using Genetic Algorithm (GA)Gen.Alg
Find Taxa Separating Two Groups using Multiple Genetic Algorithm's (GA) ConsensusGen.Alg.Consensus
Kullback LeiblerKullback.Leibler kullbackLeiber
Size and Power for the Several-Sample DM Parameter Test ComparisonMC.Xdc.statistics
Size and Power of Several Sample RAD-Probability Mean Test ComparisonMC.Xmc.statistics
Size and Power of Several Sample RAD-Probability Mean Test Comparisons: Unknown Vector of ProportionMC.Xmcupo.statistics
Size and Power of Several Sample-Overdispersion Test ComparisonsMC.Xoc.statistics
Size and Power for the One Sample RAD Probability-Mean Test ComparisonMC.Xsc.statistics
Size and Power of Goodness of Fit Test: Multinomial vs. Dirichlet-MultinomialMC.ZT.statistics
Generation of Multinomial Random SamplesMultinomial
Multidimensional Scaling Plot of Microbiome DataPlot.MDS
Plot the Pi VectorPlot.PI
Plot the Pi Vector for Repeated MeasuresPlot.RM.Barchart
Plot the Pi Vector for Repeated MeasuresPlot.RM.Dotplot
Saliva Data Setsaliva
Test Paired Data SetsTest.Paired
Throat Data Setthroat
Tongue Data Settongue
Palatine Tonsil Data Settonsils
Likelihood-Ratio-Test Statistics: Several Sample Dirichlet-Multinomial Test ComparisonXdc.sevsample
Generalized Wald-type Statistics: Several Sample RAD Probability-Mean Test Comparison with a Known Common VectorXmc.sevsample
Effect Size for Xmcupo StatisticXmcupo.effectsize
Generalized Wald-type Statistics: Several Sample RAD Probability-Mean Test Comparison with an Unknown Common VectorXmcupo.sevsample
Likelihood-Ratio-Test Statistics: Several Sample Overdispersion Test ComparisonXoc.sevsample
Generalized Wald-Type Statistics: One Sample RAD Probability-Mean Test ComparisonXsc.onesample