Package: gMCPLite 0.1.5
Nan Xiao
gMCPLite: Lightweight Graph Based Multiple Comparison Procedures
A lightweight fork of 'gMCP' with functions for graphical described multiple test procedures introduced in Bretz et al. (2009) <doi:10.1002/sim.3495> and Bretz et al. (2011) <doi:10.1002/bimj.201000239>. Implements a flexible function using 'ggplot2' to create multiplicity graph visualizations. Contains instructions of multiplicity graph and graphical testing for group sequential design, described in Maurer and Bretz (2013) <doi:10.1080/19466315.2013.807748>, with necessary unit testing using 'testthat'.
Authors:
gMCPLite_0.1.5.tar.gz
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gMCPLite.pdf |gMCPLite.html✨
gMCPLite/json (API)
NEWS
| # Install 'gMCPLite' in R: |
| install.packages('gMCPLite', repos = c('https://merck.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/merck/gmcplite/issues
Last updated 9 months agofrom:6e0bb8da16. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 13 2024 |
| R-4.5-win-x86_64 | OK | Nov 13 2024 |
| R-4.5-linux-x86_64 | OK | Nov 13 2024 |
| R-4.4-win-x86_64 | OK | Nov 13 2024 |
| R-4.4-mac-x86_64 | OK | Nov 13 2024 |
| R-4.4-mac-aarch64 | OK | Nov 13 2024 |
| R-4.3-win-x86_64 | OK | Nov 13 2024 |
| R-4.3-mac-x86_64 | OK | Nov 13 2024 |
| R-4.3-mac-aarch64 | OK | Nov 13 2024 |
Exports:BauerEtAl2001bdiagNAbonferroni.testbonferroni.trimmed.simes.testBonferroniHolmBretzEtAl2009aBretzEtAl2009bBretzEtAl2009cBretzEtAl2011checkCorrelationcycleGraphedgeAttredgeAttr<-Entangled1Maurer2012Entangled2Maurer2012fallbackFerber2011FerberTimeDose2011fixedSequencegeneralSuccessivegeneratePvalsgenerateWeightsgetMatricesgetMatrixgetNodesgetRejectedgetWeightsgetXCoordinatesgetYCoordinatesgMCPgMCP.extendedgraph2matrixgraphTesthGraphHommelEtAl2007HommelEtAl2007SimpleHungEtWang2010HuqueAloshEtBhore2011improvedFallbackIimprovedFallbackIIimprovedParallelGatekeepingjoinGraphsmatrix2graphMaurerEtAl1995nodeAttrnodeAttr<-parallelGatekeepingparametric.testpermutationsplaceNodesplotprintrejectNodereplaceVariablessetEdgesetRejected<-setWeightssimConfintsimes.on.subsets.testsimes.testsimpleSuccessiveIsimpleSuccessiveIIsubgraphsubstituteEpstruncatedHolmWangTing2014
Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 |
| Check correlation matrix | checkCorrelation |
| 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 |
| generatePvals | generatePvals |
| generateWeights | generateWeights |
| Graph based Multiple Comparison Procedures | gMCP |
| Graph based Multiple Comparison Procedures | gMCP.extended |
| 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 |
| 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 |
| Create multiplicity graphs using ggplot2 | hGraph |
| Joins two graphMCP objects | joinGraphs |
| Matrix2Graph and Graph2Matrix | graph2matrix matrix2graph |
| Weighted parametric test | parametric.test |
| Permutation for a design matrix | permutations |
| Placement of graph nodes | placeNodes |
| Rejects a node/hypothesis and updates the graph accordingly. | rejectNode |
| Replaces variables in a general graph with specified numeric values | replaceVariables |
| 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 |
| Get a subgraph | subgraph |
| Substitute Epsilon | substituteEps |
| Weighted Test Functions for use with gMCP | weighted.test.functions |
