# Graph Based Multiple Comparison Procedures

## Documentation for package ‘gMCP’ version 0.8-15

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

B C D E F G H I J M N P R S T U W

gMCP-package | Graphical described Multiple Comparison Procedures

## -- B --

BauerEtAl2001 | Functions that create different example graphs
bdiagNA | Create a Block Diagonal Matrix with NA outside the diagonal
bonferroni.test | Weighted Bonferroni-test
bonferroni.trimmed.simes.test | Trimmed Simes test for intersections of two hypotheses and otherwise weighted Bonferroni-test
BonferroniHolm | Functions that create different example graphs
BretzEtAl2009a | Functions that create different example graphs
BretzEtAl2009b | Functions that create different example graphs
BretzEtAl2009c | Functions that create different example graphs
BretzEtAl2011 | Functions that create different example graphs

## -- C --

calcPower | Calculate power values
corMatWizard | Graphical User Interface for the creation of correlation matrices
cycleGraph | Functions that create different example graphs

## -- D --

doInterim | EXPERIMENTAL: Evaluate conditional errors at interim for a pre-planned graphical procedure

## -- E --

edgeAttr | Class graphMCP
edgeAttr-method | Class graphMCP
edgeAttr<- | Class graphMCP
edgeAttr<--method | Class graphMCP
Entangled1Maurer2012 | Functions that create different example graphs
Entangled2Maurer2012 | Functions that create different example graphs
entangledMCP | Class entangledMCP
entangledMCP-class | Class entangledMCP
exampleGraphs | Functions that create different example graphs
extractPower | Calculate power values

## -- F --

fallback | Functions that create different example graphs
Ferber2011 | Functions that create different example graphs
FerberTimeDose2011 | Functions that create different example graphs
fixedSequence | Functions that create different example graphs

## -- G --

generalSuccessive | Functions that create different example graphs
generateBounds | generateBounds
generatePvals | generatePvals
generateTest | generateTest
generateWeights | generateWeights
getJavaInfo | Get Memory and Runtime Info from JVM
getMatrices | Class entangledMCP
getMatrices-method | Class entangledMCP
getMatrix | Class graphMCP
getMatrix-method | Class graphMCP
getNodes | Class graphMCP
getNodes-method | Class entangledMCP
getNodes-method | Class graphMCP
getRejected | Class graphMCP
getRejected-method | Class entangledMCP
getRejected-method | Class gMCPResult
getRejected-method | Class gPADInterim
getRejected-method | Class graphMCP
getWeights | Class graphMCP
getWeights-method | Class entangledMCP
getWeights-method | Class gMCPResult
getWeights-method | Class gPADInterim
getWeights-method | Class graphMCP
getXCoordinates | Class graphMCP
getXCoordinates-method | Class entangledMCP
getXCoordinates-method | Class graphMCP
getYCoordinates | Class graphMCP
getYCoordinates-method | Class entangledMCP
getYCoordinates-method | Class graphMCP
gMCP | Graph based Multiple Comparison Procedures
gMCP.extended | Graph based Multiple Comparison Procedures
gMCPReport | Automatic Generation of gMCP Reports
gMCPResult | Class gMCPResult
gMCPResult-class | Class gMCPResult
gPADInterim | Class gPADInterim
gPADInterim-class | Class gPADInterim
graph2latex | Graph2LaTeX
graph2matrix | Matrix2Graph and Graph2Matrix
graphAnalysis | Analysis of a gMCP-Graph
graphGUI | Graphical User Interface for graphical described multiple comparison procedures
graphMCP | Class graphMCP
graphMCP-class | Class graphMCP
graphTest | Multiple testing using graphs

## -- H --

HommelEtAl2007 | Functions that create different example graphs
HommelEtAl2007Simple | Functions that create different example graphs
HungEtWang2010 | Functions that create different example graphs
HuqueAloshEtBhore2011 | Functions that create different example graphs
hydroquinone | Hydroquinone Mutagenicity Assay

## -- I --

improvedFallbackI | Functions that create different example graphs
improvedFallbackII | Functions that create different example graphs
improvedParallelGatekeeping | Functions that create different example graphs

## -- J --

joinGraphs | Joins two graphMCP objects

## -- M --

matrix2graph | Matrix2Graph and Graph2Matrix
MaurerEtAl1995 | Functions that create different example graphs

## -- N --

nodeAttr | Class graphMCP
nodeAttr-method | Class graphMCP
nodeAttr<- | Class graphMCP
nodeAttr<--method | Class graphMCP

## -- P --

parallelGatekeeping | Functions that create different example graphs
parametric.test | Weighted parametric test
placeNodes | Placement of graph nodes
plot-method | Class gMCPResult
plot-method | Class gPADInterim
plot-method | Class graphMCP
plotSimCI | Plot confidence intervals
print-method | Class entangledMCP
print-method | Class gMCPResult
print-method | Class gPADInterim
print-method | Class graphMCP

## -- R --

rejectNode | Rejects a node/hypothesis and updates the graph accordingly.
replaceVariables | Replaces variables in a general graph with specified numeric values
rqmvnorm | Random sample from the multivariate normal distribution

## -- S --

sampSize | Sample size calculations
sampSizeCore | Function for sample size calculation
secondStageTest | EXPERIMENTAL: Construct a valid level alpha test for the second stage of an adaptive design that is based on a pre-planned graphical MCP
setEdge | Class graphMCP
setEdge-method | Class graphMCP
setRejected<- | Class graphMCP
setRejected<--method | Class graphMCP
setWeights | Class graphMCP
setWeights-method | Class graphMCP
simConfint | Simultaneous confidence intervals for sequentially rejective multiple test procedures
simConfint-method | Simultaneous confidence intervals for sequentially rejective multiple test procedures
simes.on.subsets.test | Simes on subsets, otherwise Bonferroni
simes.test | Weighted Simes test
simpleSuccessiveI | Functions that create different example graphs
simpleSuccessiveII | Functions that create different example graphs
simvastatin | Simvastatin and Colesevelam Treatment in Patients with Primary Hypercholesterolemia
subgraph | Get a subgraph
substituteEps | Substitute Epsilon

## -- T --

truncatedHolm | Functions that create different example graphs

## -- U --

unitTestsGMCP | Run the R unit (and optional the JUnit) test suite for gMCP

## -- W --

WangTing2014 | Functions that create different example graphs
weighted.test.functions | Weighted Test Functions for use with gMCP