Introduction | Creating Weighted Graphs | The sequentially rejective MTP | Weighted parametric and Simes tests | Epsilon edges | Entangled graphs | Power Simulations | Options and Import/Export | Case Studies | Appendix - Example graphs | Appendix - Multiple Testing | Appendix - Graph Theory Basics
Package: gMCP 0.8-17
gMCP: Graph Based Multiple Comparison Procedures
Functions and a graphical user interface for graphical described multiple test procedures.
Authors:
gMCP_0.8-17.tar.gz
gMCP_0.8-17.zip(r-4.7)gMCP_0.8-17.zip(r-4.6)gMCP_0.8-17.zip(r-4.5)
gMCP_0.8-17.tgz(r-4.6-x86_64)gMCP_0.8-17.tgz(r-4.6-arm64)gMCP_0.8-17.tgz(r-4.5-x86_64)gMCP_0.8-17.tgz(r-4.5-arm64)
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gMCP_0.8-17.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gMCP/json (API)
| # Install 'gMCP' in R: |
| install.packages('gMCP', repos = c('https://kornl.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kornl/gmcp/issues
Datasets:
- hydroquinone - Hydroquinone Mutagenicity Assay
- simvastatin - Simvastatin and Colesevelam Treatment in Patients with Primary Hypercholesterolemia
Last updated from:6472ab8f6e. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 211 | ||
| linux-devel-x86_64 | OK | 174 | ||
| source / vignettes | OK | 246 | ||
| linux-release-arm64 | OK | 209 | ||
| linux-release-x86_64 | OK | 194 | ||
| macos-release-arm64 | OK | 134 | ||
| macos-release-x86_64 | OK | 333 | ||
| macos-oldrel-arm64 | OK | 161 | ||
| macos-oldrel-x86_64 | OK | 233 | ||
| windows-devel | OK | 149 | ||
| windows-release | OK | 123 | ||
| windows-oldrel | OK | 145 | ||
| wasm-release | OK | 112 |
Exports:BauerEtAl2001bdiagNAbonferroni.testbonferroni.trimmed.simes.testBonferroniHolmBretzEtAl2009aBretzEtAl2009bBretzEtAl2009cBretzEtAl2011calcPowercorMatWizardcycleGraphdoInterimedgeAttredgeAttr<-Entangled1Maurer2012Entangled2Maurer2012extractPowerfallbackFerber2011FerberTimeDose2011fixedSequencegeneralSuccessivegenerateBoundsgeneratePvalsgenerateTestgenerateWeightsgetJavaInfogetMatricesgetMatrixgetNodesgetRejectedgetWeightsgetXCoordinatesgetYCoordinatesgMCPgMCP.extendedgMCPReportgraph2latexgraph2matrixgraphAnalysisgraphGUIgraphTestHommelEtAl2007HommelEtAl2007SimpleHungEtWang2010HuqueAloshEtBhore2011improvedFallbackIimprovedFallbackIIimprovedParallelGatekeepingjoinGraphsmatrix2graphMaurerEtAl1995nodeAttrnodeAttr<-parallelGatekeepingparametric.testplaceNodesplotplotSimCIprintrejectNodereplaceVariablesrqmvnormsampSizesecondStageTestsetEdgesetRejected<-setWeightssimConfintsimes.on.subsets.testsimes.testsimpleSuccessiveIsimpleSuccessiveIIsubgraphsubstituteEpstruncatedHolmunitTestsGMCPWangTing2014
Dependencies:codetoolsCommonJavaJarsJavaGDlatticeMASSMatrixmultcompmvtnormPolynomFRcpprJavasandwichsurvivalTH.dataxlsxjarszoo
A Graphical Approach to Weighted Multiple Test Procedures
Last update: 2016-09-06
Started: 2013-07-12
Graphical approaches for multiple endpoint problems using weighted parametric tests
Introduction | Creating Graphs | Testing
Last update: 2014-03-10
Started: 2013-07-12
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Graphical described Multiple Comparison Procedures | gMCP-package |
| Create a Block Diagonal Matrix with NA outside the diagonal | bdiagNA |
| Weighted Bonferroni-test | bonferroni.test |
| Trimmed Simes test for intersections of two hypotheses and otherwise weighted Bonferroni-test | bonferroni.trimmed.simes.test |
| Calculate power values | calcPower |
| Graphical User Interface for the creation of correlation matrices | corMatWizard |
| EXPERIMENTAL: Evaluate conditional errors at interim for a pre-planned graphical procedure | doInterim |
| Class entangledMCP | entangledMCP entangledMCP-class getMatrices getMatrices,entangledMCP-method getNodes,entangledMCP-method getRejected,entangledMCP-method getWeights,entangledMCP-method getXCoordinates,entangledMCP-method getYCoordinates,entangledMCP-method print,entangledMCP-method |
| Functions that create different example graphs | BauerEtAl2001 BonferroniHolm BretzEtAl2009a BretzEtAl2009b BretzEtAl2009c BretzEtAl2011 cycleGraph Entangled1Maurer2012 Entangled2Maurer2012 exampleGraphs fallback Ferber2011 FerberTimeDose2011 fixedSequence generalSuccessive HommelEtAl2007 HommelEtAl2007Simple HungEtWang2010 HuqueAloshEtBhore2011 improvedFallbackI improvedFallbackII improvedParallelGatekeeping MaurerEtAl1995 parallelGatekeeping simpleSuccessiveI simpleSuccessiveII truncatedHolm WangTing2014 |
| Calculate power values | extractPower |
| generateBounds | generateBounds |
| generatePvals | generatePvals |
| generateTest | generateTest |
| generateWeights | generateWeights |
| Get Memory and Runtime Info from JVM | getJavaInfo |
| Graph based Multiple Comparison Procedures | gMCP |
| Graph based Multiple Comparison Procedures | gMCP.extended |
| Automatic Generation of gMCP Reports | gMCPReport |
| Class gMCPResult | getRejected,gMCPResult-method getWeights,gMCPResult-method gMCPResult gMCPResult-class plot,gMCPResult,ANY-method plot,gMCPResult-method print,gMCPResult-method |
| Class gPADInterim | getRejected,gPADInterim-method getWeights,gPADInterim-method gPADInterim gPADInterim-class plot,gPADInterim-method print,gPADInterim-method |
| Graph2LaTeX | graph2latex |
| Analysis of a gMCP-Graph | graphAnalysis |
| Graphical User Interface for graphical described multiple comparison procedures | graphGUI |
| Class graphMCP | edgeAttr edgeAttr,graphMCP,character,character,character-method edgeAttr<- edgeAttr<-,graphMCP,character,character,character-method getMatrix getMatrix,graphMCP-method getNodes getNodes,graphMCP-method getRejected getRejected,graphMCP-method getWeights getWeights,graphMCP-method getXCoordinates getXCoordinates,graphMCP-method getYCoordinates getYCoordinates,graphMCP-method graphMCP graphMCP-class nodeAttr nodeAttr,graphMCP,character,character-method nodeAttr<- nodeAttr<-,graphMCP,character,character-method plot,graphMCP,ANY-method plot,graphMCP-method print,graphMCP-method setEdge setEdge,character,character,graphMCP,character-method setEdge,character,character,graphMCP,numeric-method setRejected<- setRejected<-,graphMCP-method setWeights setWeights,graphMCP-method |
| Multiple testing using graphs | graphTest |
| Hydroquinone Mutagenicity Assay | hydroquinone |
| Joins two graphMCP objects | joinGraphs |
| Matrix2Graph and Graph2Matrix | graph2matrix matrix2graph |
| Weighted parametric test | parametric.test |
| Placement of graph nodes | placeNodes |
| Plot confidence intervals | plotSimCI |
| Rejects a node/hypothesis and updates the graph accordingly. | rejectNode |
| Replaces variables in a general graph with specified numeric values | replaceVariables |
| Random sample from the multivariate normal distribution | rqmvnorm |
| Sample size calculations | sampSize |
| Function for sample size calculation | sampSizeCore |
| EXPERIMENTAL: Construct a valid level alpha test for the second stage of an adaptive design that is based on a pre-planned graphical MCP | secondStageTest |
| Simultaneous confidence intervals for sequentially rejective multiple test procedures | simConfint simConfint,graphMCP-method |
| Simes on subsets, otherwise Bonferroni | simes.on.subsets.test |
| Weighted Simes test | simes.test |
| Simvastatin and Colesevelam Treatment in Patients with Primary Hypercholesterolemia | simvastatin |
| Get a subgraph | subgraph |
| Substitute Epsilon | substituteEps |
| Run the R unit (and optional the JUnit) test suite for gMCP | unitTestsGMCP |
| Weighted Test Functions for use with gMCP | weighted.test.functions |
