Package index • gMCPLite

Graphical functions

Core graphical functions

gMCP(): Graph based Multiple Comparison Procedures

graphMCP-class graphMCP print,graphMCP-method plot,graphMCP,ANY-method plot,graphMCP-method getWeights getWeights,graphMCP-method getMatrix getMatrix,graphMCP-method setWeights setWeights,graphMCP-method setRejected<- setRejected<-,graphMCP-method getRejected getRejected,graphMCP-method getXCoordinates getXCoordinates,graphMCP-method getYCoordinates getYCoordinates,graphMCP-method setEdge setEdge,character,character,graphMCP,character-method setEdge,character,character,graphMCP,numeric-method getNodes getNodes,graphMCP-method edgeAttr edgeAttr<- edgeAttr,graphMCP,character,character,character-method edgeAttr<-,graphMCP,character,character,character-method nodeAttr nodeAttr<- nodeAttr,graphMCP,character,character-method nodeAttr<-,graphMCP,character,character-method: Class graphMCP

gMCPResult-class gMCPResult print,gMCPResult-method plot,gMCPResult,ANY-method plot,gMCPResult-method getWeights,gMCPResult-method getRejected,gMCPResult-method: Class gMCPResult

hGraph(): Create multiplicity graphs using ggplot2

matrix2graph() graph2matrix(): Matrix2Graph and Graph2Matrix

placeNodes(): Placement of graph nodes

rejectNode(): Rejects a node/hypothesis and updates the graph accordingly.

Advanced graphical functions

gMCP.extended(): Graph based Multiple Comparison Procedures

entangledMCP-class entangledMCP print,entangledMCP-method getWeights,entangledMCP-method getMatrices getMatrices,entangledMCP-method getRejected,entangledMCP-method getXCoordinates,entangledMCP-method getYCoordinates,entangledMCP-method getNodes,entangledMCP-method: Class entangledMCP

gPADInterim-class gPADInterim print,gPADInterim-method plot,gPADInterim-method getWeights,gPADInterim-method getRejected,gPADInterim-method: Class gPADInterim

joinGraphs(): Joins two graphMCP objects

subgraph(): Get a subgraph

Example graphs

BonferroniHolm() BretzEtAl2011() BauerEtAl2001() BretzEtAl2009a() BretzEtAl2009b() BretzEtAl2009c() HommelEtAl2007() HommelEtAl2007Simple() parallelGatekeeping() improvedParallelGatekeeping() fallback() fixedSequence() simpleSuccessiveI() simpleSuccessiveII() truncatedHolm() generalSuccessive() HuqueAloshEtBhore2011() HungEtWang2010() MaurerEtAl1995() cycleGraph() improvedFallbackI() improvedFallbackII() FerberTimeDose2011() Ferber2011() Entangled1Maurer2012() Entangled2Maurer2012() WangTing2014(): Functions that create different example graphs

Testing functions

Core testing functions

graphTest(): Multiple testing using graphs

generateWeights(): generateWeights

generatePvals(): generatePvals

Testing procedures

bonferroni.test(): Weighted Bonferroni-test

bonferroni.trimmed.simes.test(): Trimmed Simes test for intersections of two hypotheses and otherwise weighted Bonferroni-test

simes.test(): Weighted Simes test

simes.on.subsets.test(): Simes on subsets, otherwise Bonferroni

parametric.test(): Weighted parametric test

weighted.test.functions: Weighted Test Functions for use with gMCP

Confidence interval

simConfint(): Simultaneous confidence intervals for sequentially rejective multiple test procedures

Utility functions

substituteEps(): Substitute Epsilon

replaceVariables(): Replaces variables in a general graph with specified numeric values

bdiagNA(): Create a Block Diagonal Matrix with NA outside the diagonal

checkCorrelation(): Check correlation matrix

permutations(): Permutation for a design matrix