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:Yalin Zhu [aut], Yilong Zhang [aut], Xuan Deng [aut], Keaven Anderson [aut], Nan Xiao [aut, cre], Kornelius Rohmeyer [ctb], Florian Klinglmueller [ctb], gMCP project contributors [cph], Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]

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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'))

Peer review:

Bug tracker:https://github.com/merck/gmcplite/issues

On CRAN:

66 exports 9 stars 1.87 score 29 dependencies 13 scripts 282 downloads

Last updated 7 months agofrom:6e0bb8da16. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 14 2024
R-4.5-win-x86_64OKSep 14 2024
R-4.5-linux-x86_64OKSep 14 2024
R-4.4-win-x86_64OKSep 14 2024
R-4.4-mac-x86_64OKSep 14 2024
R-4.4-mac-aarch64OKSep 14 2024
R-4.3-win-x86_64OKSep 14 2024
R-4.3-mac-x86_64OKSep 14 2024
R-4.3-mac-aarch64OKSep 14 2024

Exports:BauerEtAl2001bdiagNAbonferroni.testbonferroni.trimmed.simes.testBonferroniHolmBretzEtAl2009aBretzEtAl2009bBretzEtAl2009cBretzEtAl2011checkCorrelationcycleGraphedgeAttredgeAttr<-Entangled1Maurer2012Entangled2Maurer2012fallbackFerber2011FerberTimeDose2011fixedSequencegeneralSuccessivegeneratePvalsgenerateWeightsgetMatricesgetMatrixgetNodesgetRejectedgetWeightsgetXCoordinatesgetYCoordinatesgMCPgMCP.extendedgraph2matrixgraphTesthGraphHommelEtAl2007HommelEtAl2007SimpleHungEtWang2010HuqueAloshEtBhore2011improvedFallbackIimprovedFallbackIIimprovedParallelGatekeepingjoinGraphsmatrix2graphMaurerEtAl1995nodeAttrnodeAttr<-parallelGatekeepingparametric.testpermutationsplaceNodesplotprintrejectNodereplaceVariablessetEdgesetRejected<-setWeightssimConfintsimes.on.subsets.testsimes.testsimpleSuccessiveIsimpleSuccessiveIIsubgraphsubstituteEpstruncatedHolmWangTing2014

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Graphical testing for group sequential design

Rendered fromGraphicalMultiplicity.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2024-01-11
Started: 2022-08-02

Multiplicity graphs

Rendered fromhGraph.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2024-01-11
Started: 2022-08-02

Readme and manuals

Help Manual

Help pageTopics
Create a Block Diagonal Matrix with NA outside the diagonalbdiagNA
Weighted Bonferroni-testbonferroni.test
Trimmed Simes test for intersections of two hypotheses and otherwise weighted Bonferroni-testbonferroni.trimmed.simes.test
Check correlation matrixcheckCorrelation
Class entangledMCPentangledMCP 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 graphsBauerEtAl2001 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
generatePvalsgeneratePvals
generateWeightsgenerateWeights
Graph based Multiple Comparison ProceduresgMCP
Graph based Multiple Comparison ProceduresgMCP.extended
Class gMCPResultgetRejected,gMCPResult-method getWeights,gMCPResult-method gMCPResult gMCPResult-class plot,gMCPResult,ANY-method plot,gMCPResult-method print,gMCPResult-method
Class gPADInterimgetRejected,gPADInterim-method getWeights,gPADInterim-method gPADInterim gPADInterim-class plot,gPADInterim-method print,gPADInterim-method
Class graphMCPedgeAttr 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 graphsgraphTest
Create multiplicity graphs using ggplot2hGraph
Joins two graphMCP objectsjoinGraphs
Matrix2Graph and Graph2Matrixgraph2matrix matrix2graph
Weighted parametric testparametric.test
Permutation for a design matrixpermutations
Placement of graph nodesplaceNodes
Rejects a node/hypothesis and updates the graph accordingly.rejectNode
Replaces variables in a general graph with specified numeric valuesreplaceVariables
Simultaneous confidence intervals for sequentially rejective multiple test proceduressimConfint simConfint,graphMCP-method
Simes on subsets, otherwise Bonferronisimes.on.subsets.test
Weighted Simes testsimes.test
Get a subgraphsubgraph
Substitute EpsilonsubstituteEps
Weighted Test Functions for use with gMCPweighted.test.functions