gMCP: Graph Based Multiple Comparison Procedures
Version 0.8-9

This package provides functions and a graphical user interface for graphical described multiple test procedures.

AuthorKornelius Rohmeyer [aut, cre], Florian Klinglmueller [aut]
Date of publication2014-10-03 15:46:41
MaintainerKornelius Rohmeyer <rohmeyer@small-projects.de>
LicenseGPL (>= 2)
Version0.8-9
URL http://gsrmtp.r-forge.r-project.org/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("gMCP", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

confint: Simultaneous confidence intervals for sequentially rejective...
extractPower: Calculate power values
getJavaInfo: Get Memory and Runtime Info from JVM
gMCP: Graph based Multiple Comparison Procedures
graph2latex: Graph2LaTeX
graphTest: Multiple testing using graphs
secondStageTest: EXPERIMENTAL: Construct a valid level alpha test for the...
See all...

All man pages Function index File listing

Man pages

bdiagNA: Create a Block Diagonal Matrix with NA outside the diagonal
calcPower: Calculate power values
confint: Simultaneous confidence intervals for sequentially rejective...
corMatWizard: Graphical User Interface for the creation of correlation...
doInterim: EXPERIMENTAL: Evaluate conditional errors at interim for a...
entangled: Class entangledMCP
exampleGraphs: Functions that create different example graphs
extractPower: Calculate power values
generateBounds: generateBounds
generatePvals: generatePvals
generateTest: generateTest
generateWeights: generateWeights
getJavaInfo: Get Memory and Runtime Info from JVM
gMCP: Graph based Multiple Comparison Procedures
gMCP-package: Graphical described Multiple Comparison Procedures
gMCPReport: Automatic Generation of gMCP Reports
gMCPResult: Class gMCPResult
gPADInterim: Class gPADInterim
graph2latex: Graph2LaTeX
graphAnalysis: Analysis of a gMCP-Graph
graphGUI: Graphical User Interface for graphical described multiple...
graphMCP: Class graphMCP
graphTest: Multiple testing using graphs
hydroquinone: Hydroquinone Mutagenicity Assay
joinGraphs: Joins two graphMCP objects
matrix2graph: Matrix2Graph and Graph2Matrix
placeNodes: Placement of graph nodes
plotSimCI: Plot confidence intervals
rejectNode: Rejects a node/hypothesis and updates the graph accordingly.
replaceVariables: Replaces variables in a general graph with specified numeric...
rqmvnorm: Random sample from the multivariate normal distribution
sampSize: Function for sample size calculation
secondStageTest: EXPERIMENTAL: Construct a valid level alpha test for the...
simvastatin: Simvastatin and Colesevelam Treatment in Patients with...
subgraph: Get a subgraph
substituteEps: Substitute Epsilon
unitTestsGMCP: Run the R unit (and optional the JUnit) test suite for gMCP

Functions

BauerEtAl2001 Man page Source code
BonferroniHolm Man page Source code
BretzEtAl2009a Man page Source code
BretzEtAl2009b Man page Source code
BretzEtAl2009c Man page Source code
BretzEtAl2011 Man page Source code
Entangled1Maurer2012 Man page Source code
Entangled2Maurer2012 Man page Source code
Ferber2011 Man page Source code
FerberTimeDose2011 Man page Source code
HommelEtAl2007 Man page Source code
HommelEtAl2007Simple Man page Source code
HungEtWang2010 Man page Source code
HuqueAloshEtBhore2011 Man page Source code
LaTeXHeader Source code
MaurerEtAl1995 Man page Source code
WangTing2014 Man page Source code
accessible Source code
ad.p Source code
adaptWeights Source code
adjPValues Source code
as.num Source code
b.dunnett Source code
bdiagNA Man page Source code
calcMultiPower Source code
calcPower Man page Source code
call2char Source code
canBeRejected Source code
checkArgs Source code
checkCorrelation Source code
checkOptimal Source code
checkPSD Source code
checkQuadraticMatrix Source code
checkValidWeights Source code
conn.comp Source code
convert Source code
corMatWizard Man page Source code
createGMCPCall Source code
createTable Source code
cycleGraph Man page Source code
decideTest Source code
doInterim Man page Source code
dput2 Source code
dputGraph Source code
dputMatrix Source code
edgeAttr Man page
edgeAttr,graphMCP,character,character,character-method Man page
edgeAttr<- Man page
edgeAttr<-,graphMCP,character,character,character-method Man page
entangledMCP Man page
entangledMCP-class Man page
equals Source code
exampleGraphs Man page
extractPower Man page Source code
fallback Man page Source code
fastgMCP Source code
fixedSequence Man page Source code
forceCorrelation Source code
gMCP Man page Source code
gMCP-package Man page
gMCPReport Man page Source code
gMCPResult Man page
gMCPResult-class Man page
gMCPVersion Source code
gPADInterim Man page
gPADInterim-class Man page
gatekeeping Source code
generalSuccessive Man page Source code
generateBounds Man page Source code
generatePvals Man page Source code
generateTest Man page Source code
generateWeights Man page Source code
getAllCorrelationMatrices Source code
getAllGraphs Source code
getAllQuadraticMatrices Source code
getAngle Source code
getArc Source code
getAvailableStandardDesigns Source code
getBalancedDesign Source code
getCenter Source code
getCorrMat Source code
getDebugInfo Source code
getEdges Source code
getFractionString Source code
getJavaInfo Man page Source code
getLaTeXFraction Source code
getLine Source code
getMatrices Man page
getMatrices,entangledMCP-method Man page
getMatrix Man page
getMatrix,graphMCP-method Man page
getNewestRVersion Source code
getNodes Man page
getNodes,entangledMCP-method Man page
getNodes,graphMCP-method Man page
getObjectInfo Source code
getRejectableNode Source code
getRejected Man page
getRejected,entangledMCP-method Man page
getRejected,gMCPResult-method Man page
getRejected,gPADInterim-method Man page
getRejected,graphMCP-method Man page
getUsableNames Source code
getWeightStr Source code
getWeights Man page
getWeights,entangledMCP-method Man page
getWeights,gMCPResult-method Man page
getWeights,gPADInterim-method Man page
getWeights,graphMCP-method Man page
getXCoordinates Man page
getXCoordinates,entangledMCP-method Man page
getXCoordinates,graphMCP-method Man page
getYCoordinates Man page
getYCoordinates,entangledMCP-method Man page
getYCoordinates,graphMCP-method Man page
graph2latex Man page Source code
graph2matrix Man page Source code
graphAnalysis Man page Source code
graphGUI Man page Source code
graphMCP Man page
graphMCP-class Man page
graphTest Man page Source code
hydroquinone Man page
improvedFallbackI Man page Source code
improvedFallbackII Man page Source code
improvedParallelGatekeeping Man page Source code
invertY Source code
isEpsilon Source code
joinGraphs Man page Source code
layers Source code
makeEpsilonString Source code
matchCE Source code
matrix2graph Man page Source code
mtp.edges Source code
mtp.weights Source code
myRowSums Source code
nextAvailableName Source code
nhyp Source code
nodeAttr Man page
nodeAttr,graphMCP,character,character-method Man page
nodeAttr<- Man page
nodeAttr<-,graphMCP,character,character-method Man page
onLoad Source code
onUnload Source code
p.dunnet Source code
parallelGatekeeping Man page Source code
parse.intersection Source code
parse2numeric Source code
parseEpsPolynom Source code
partialCE Source code
permutations Source code
placeNodes Man page Source code
plot,gMCPResult,ANY-method Man page
plot,gPADInterim-method Man page
plot,graphMCP,ANY-method Man page
plotSimCI Man page Source code
powerplot Source code
print,entangledMCP-method Man page
print,gMCPResult-method Man page
print,gPADInterim-method Man page
print,graphMCP-method Man page
pvals.dunnett Source code
rejectNode Man page Source code
removeSymbols Source code
replaceVariables Man page Source code
requireLibrary Source code
resultL2Text Source code
rlattice Source code
rqmvnorm Man page Source code
sampSize Man page Source code
secondStageTest Man page Source code
setEdge Man page
setEdge,character,character,graphMCP,character-method Man page
setEdge,character,character,graphMCP,numeric-method Man page
setRejected<- Man page
setRejected<-,graphMCP-method Man page
setWeights Man page
setWeights,graphMCP-method Man page
simConfint Man page
simConfint,graphMCP-method Man page
simpleSuccessiveI Man page Source code
simpleSuccessiveII Man page Source code
simvastatin Man page
stupidWorkAround Source code
subgraph Man page Source code
substituteEps Man page Source code
tests Source code
to.binom Source code
to.intersection Source code
triangle Source code
truncatedHolm Man page Source code
unitTestsGMCP Man page Source code
updateGraphToNewClassDefinition Source code
validEntangledGraph Source code
validPartialCEs Source code
validWeightedGraph Source code
w.dunnet Source code

Files

.Rinstignore
DESCRIPTION
INSTALL
NAMESPACE
NEWS
R
R/analysis.R
R/calcPower.R
R/closure.R
R/convertFromOldClassDefinition.R
R/doRUnitTests.R
R/exampleGraphs.R
R/gACT-internal.R
R/gMCP.R
R/gPAD.R
R/generateBounds.R
R/generatePvals.R
R/generateTest.R
R/generateWeights.R
R/graph2latex.R
R/graphMCP.R
R/graphTest.R
R/helperGUI.R
R/matrix2graph.R
R/misc.R
R/modifyGraphs.R
R/onLoad.R
R/plotCI.R
R/powerPlot.R
R/rqmvnorm.R
R/sampSize.R
R/startGUIs.R
R/subVariables.R
TODO
build
build/vignette.rds
data
data/hydroquinone.rda
data/simvastatin.rda
inst
inst/CITATION
inst/References.html
inst/doc
inst/doc/AQuickStart.Rnw
inst/doc/AQuickStart.pdf
inst/doc/gMCP.Rnw
inst/doc/gMCP.pdf
inst/doc/parametric.Rnw
inst/doc/parametric.pdf
inst/java
inst/java/gsrmtp.jar
inst/unitTests
inst/unitTests/runit.LaTeX.R
inst/unitTests/runit.adjPValues.R
inst/unitTests/runit.correlation.R
inst/unitTests/runit.cover.everything.R
inst/unitTests/runit.entangled.R
inst/unitTests/runit.fastgMCP.R
inst/unitTests/runit.gMCP.R
inst/unitTests/runit.graphGMCP.R
inst/unitTests/runit.misc.R
inst/unitTests/runit.power.R
inst/unitTests/runit.randomGraph.R
java
java/build.xml
java/org
java/org/af
java/org/af/gMCP
java/org/af/gMCP/config
java/org/af/gMCP/config/Configuration.java
java/org/af/gMCP/config/GeneralConfig.java
java/org/af/gMCP/config/JavaConfig.java
java/org/af/gMCP/config/PlotConfig.java
java/org/af/gMCP/config/SpecificConfig.java
java/org/af/gMCP/config/VersionComparator.java
java/org/af/gMCP/gui
java/org/af/gMCP/gui/AboutDialog.java
java/org/af/gMCP/gui/CreateGraphGUI.java
java/org/af/gMCP/gui/DebugTextConsole.java
java/org/af/gMCP/gui/ErrorDialogChooseLevel.java
java/org/af/gMCP/gui/ErrorDialogGMCP.java
java/org/af/gMCP/gui/JSplitPaneBugWorkAround.java
java/org/af/gMCP/gui/MenuBarMGraph.java
java/org/af/gMCP/gui/RCallServicesREngineWrapper.java
java/org/af/gMCP/gui/RControl.java
java/org/af/gMCP/gui/ReproducableLog.java
java/org/af/gMCP/gui/commons-logging-verbose.properties
java/org/af/gMCP/gui/commons-logging.properties
java/org/af/gMCP/gui/contrasts
java/org/af/gMCP/gui/contrasts/AnalysisDialogFactory.java
java/org/af/gMCP/gui/contrasts/AnalysisDialogListenerFactory.java
java/org/af/gMCP/gui/contrasts/ContrastColorRenderer.java
java/org/af/gMCP/gui/contrasts/ContrastDialog2.java
java/org/af/gMCP/gui/contrasts/ContrastTable.java
java/org/af/gMCP/gui/contrasts/ContrastTableModel.java
java/org/af/gMCP/gui/contrasts/GroupingBox.java
java/org/af/gMCP/gui/contrasts/GroupingListener.java
java/org/af/gMCP/gui/contrasts/LevelOrderListener.java
java/org/af/gMCP/gui/contrasts/LevelOrderSL.java
java/org/af/gMCP/gui/contrasts/LevelSelectBox.java
java/org/af/gMCP/gui/contrasts/ROptionBox.java
java/org/af/gMCP/gui/contrasts/StatMethodDialog.java
java/org/af/gMCP/gui/contrasts/VarSelectBox.java
java/org/af/gMCP/gui/datatable
java/org/af/gMCP/gui/datatable/CellEditorE.java
java/org/af/gMCP/gui/datatable/DataFramePanel.java
java/org/af/gMCP/gui/datatable/DataTable.java
java/org/af/gMCP/gui/datatable/DataTableModel.java
java/org/af/gMCP/gui/datatable/EpsilonTableCellRenderer.java
java/org/af/gMCP/gui/datatable/RDataFrameRef.java
java/org/af/gMCP/gui/datatable/RowModel.java
java/org/af/gMCP/gui/datatable/SingleDataFramePanel.java
java/org/af/gMCP/gui/dialogs
java/org/af/gMCP/gui/dialogs/AdjustedPValueDialog.java
java/org/af/gMCP/gui/dialogs/AlternativesDialog.java
java/org/af/gMCP/gui/dialogs/ColorChooseDialog.java
java/org/af/gMCP/gui/dialogs/DialogConfIntEstVar.java
java/org/af/gMCP/gui/dialogs/GraphSendToArchiveDialog.java
java/org/af/gMCP/gui/dialogs/GroupDialog.java
java/org/af/gMCP/gui/dialogs/ImagePanel.java
java/org/af/gMCP/gui/dialogs/InfoDialog.java
java/org/af/gMCP/gui/dialogs/LoadGraphFromArchiveDialog.java
java/org/af/gMCP/gui/dialogs/MatrixCreationDialog.java
java/org/af/gMCP/gui/dialogs/NewVersionDialog.java
java/org/af/gMCP/gui/dialogs/ParameterDialog.java
java/org/af/gMCP/gui/dialogs/PowerOptionsPanel.java
java/org/af/gMCP/gui/dialogs/PowerParameterPanel.java
java/org/af/gMCP/gui/dialogs/PowersettingsToXML.java
java/org/af/gMCP/gui/dialogs/RObjectLoadingDialog.java
java/org/af/gMCP/gui/dialogs/RearrangeNodesDialog.java
java/org/af/gMCP/gui/dialogs/RejectedDialog.java
java/org/af/gMCP/gui/dialogs/TellAboutOnlineUpate.java
java/org/af/gMCP/gui/dialogs/TextFileViewer.java
java/org/af/gMCP/gui/dialogs/VariableDialog.java
java/org/af/gMCP/gui/dialogs/VariableNameDialog.java
java/org/af/gMCP/gui/graph
java/org/af/gMCP/gui/graph/DView.java
java/org/af/gMCP/gui/graph/Edge.java
java/org/af/gMCP/gui/graph/EdgeWeight.java
java/org/af/gMCP/gui/graph/GraphMCP.java
java/org/af/gMCP/gui/graph/GraphPanel.java
java/org/af/gMCP/gui/graph/GraphView.java
java/org/af/gMCP/gui/graph/LaTeXTool.java
java/org/af/gMCP/gui/graph/NetList.java
java/org/af/gMCP/gui/graph/NetListPanel.java
java/org/af/gMCP/gui/graph/NetListPopUpMenu.java
java/org/af/gMCP/gui/graph/NetListSelectionPopUpMenu.java
java/org/af/gMCP/gui/graph/Node.java
java/org/af/gMCP/gui/graph/NodeListener.java
java/org/af/gMCP/gui/graph/PPanel.java
java/org/af/gMCP/gui/graph/PView.java
java/org/af/gMCP/gui/graph/Physics.java
java/org/af/gMCP/gui/graph/PrintableObject.java
java/org/af/gMCP/gui/graph/SubFamily.java
java/org/af/gMCP/gui/graph/UpdateEdge.java
java/org/af/gMCP/gui/graph/UpdateNode.java
java/org/af/gMCP/gui/graph/WrongInputException.java
java/org/af/gMCP/gui/graph/annotations
java/org/af/gMCP/gui/graph/annotations/Annotation.java
java/org/af/gMCP/gui/graph/annotations/AnnotationPanel.java
java/org/af/gMCP/gui/graph/annotations/Ellipse.java
java/org/af/gMCP/gui/graph/annotations/Legend.java
java/org/af/gMCP/gui/graph/annotations/Line.java
java/org/af/gMCP/gui/graph/annotations/Note.java
java/org/af/gMCP/gui/graph/annotations/Rectangle.java
java/org/af/gMCP/gui/graph/annotations/Text.java
java/org/af/gMCP/gui/graph/annotations/package-info.java
java/org/af/gMCP/gui/graph/images
java/org/af/gMCP/gui/graph/images/Reset.png
java/org/af/gMCP/gui/graph/images/StartTesting.png
java/org/af/gMCP/gui/graph/images/adjPval.png
java/org/af/gMCP/gui/graph/images/back.png
java/org/af/gMCP/gui/graph/images/confint2.png
java/org/af/gMCP/gui/graph/images/edge.png
java/org/af/gMCP/gui/graph/images/latex.png
java/org/af/gMCP/gui/graph/images/matrix.png
java/org/af/gMCP/gui/graph/images/rjavaicon64.png
java/org/af/gMCP/gui/graph/images/update.png
java/org/af/gMCP/gui/graph/images/update24.png
java/org/af/gMCP/gui/graph/images/vertex.png
java/org/af/gMCP/gui/graph/images/zoom_in.png
java/org/af/gMCP/gui/graph/images/zoom_out.png
java/org/af/gMCP/gui/options
java/org/af/gMCP/gui/options/GeneralPanel.java
java/org/af/gMCP/gui/options/MiscPanel.java
java/org/af/gMCP/gui/options/NumericPanel.java
java/org/af/gMCP/gui/options/OptionsDialog.java
java/org/af/gMCP/gui/options/OptionsPanel.java
java/org/af/gMCP/gui/options/SetLookAndFeelException.java
java/org/af/gMCP/gui/options/SetPropertiesException.java
java/org/af/gMCP/gui/pdf
java/org/af/gMCP/gui/pdf/PDFGenerator.java
java/org/af/gMCP/gui/pdf/PDFViewerStarter.java
java/org/af/gMCP/gui/pdf/Plot.java
java/org/af/gMCP/gui/pdf/Result.java
java/org/af/gMCP/gui/pdf/Step.java
java/org/af/gMCP/gui/power
java/org/af/gMCP/gui/power/CVPanel.java
java/org/af/gMCP/gui/power/Group.java
java/org/af/gMCP/gui/power/GroupPanel.java
java/org/af/gMCP/gui/power/MarginalPowerPanel.java
java/org/af/gMCP/gui/power/PDialog.java
java/org/af/gMCP/gui/power/PowerDialog.java
java/org/af/gMCP/gui/power/SampleSizeDialog.java
java/org/af/gMCP/gui/power/Scenario.java
java/org/af/gMCP/gui/power/ScenarioPanel.java
java/org/af/gMCP/gui/power/SettingsToXML.java
java/org/af/gMCP/gui/power/UserDefinedPanel.java
java/org/af/gMCP/poi
java/org/af/gMCP/poi/GraphDocXWriter.java
java/org/af/gMCP/tests
java/org/af/gMCP/tests/CircleTest.java
java/org/af/gMCP/tests/CircleTest3Points.java
java/org/af/gMCP/tests/FormatTest.java
java/org/af/gMCP/tests/TeXFormulaTest.java
java/org/af/gMCP/tests/TestImportExport.java
java/org/af/gMCP/tests/ThreadExceptionTest.java
java/org/apache
java/org/apache/poi
java/org/apache/poi/xwpf
java/org/apache/poi/xwpf/usermodel
java/org/apache/poi/xwpf/usermodel/XWPFRun.java
java/org/mutoss
java/org/mutoss/gui
java/org/mutoss/gui/JavaGD.java
java/org/mutoss/gui/JavaGDPanel.java
java/org/mutoss/gui/TransferableImage.java
java/tests
java/tests/DataTableTest.java
java/tests/EdgeTest.java
java/tests/InteractionTest.java
java/tests/LoadSaveTest.java
java/tests/NetListTest.java
java/tests/NodeTest.java
java/tests/OptionPaneTest.java
java/tests/PPanelTest.java
java/tests/PowerTest.java
java/tests/RControlTest.java
java/tests/RJavaUTF.java
java/tests/TestSuite.java
java/tests/TexFormulaTest.java
java/tests/ToolTest.java
man
man/bdiagNA.Rd
man/calcPower.Rd
man/confint.Rd
man/corMatWizard.Rd
man/doInterim.Rd
man/entangled.Rd
man/exampleGraphs.Rd
man/extractPower.Rd
man/gMCP-package.Rd
man/gMCP.Rd
man/gMCPReport.Rd
man/gMCPResult.Rd
man/gPADInterim.Rd
man/generateBounds.Rd
man/generatePvals.Rd
man/generateTest.Rd
man/generateWeights.Rd
man/getJavaInfo.Rd
man/graph2latex.Rd
man/graphAnalysis.Rd
man/graphGUI.Rd
man/graphMCP.Rd
man/graphTest.Rd
man/hydroquinone.Rd
man/joinGraphs.Rd
man/matrix2graph.Rd
man/placeNodes.Rd
man/plotSimCI.Rd
man/rejectNode.Rd
man/replaceVariables.Rd
man/rqmvnorm.Rd
man/sampSize.Rd
man/secondStageTest.Rd
man/simvastatin.Rd
man/subgraph.Rd
man/substituteEps.Rd
man/unitTestsGMCP.Rd
src
src/gMCP.c
src/mcp.c
tests
tests/doRUnit.R
vignettes
vignettes/AQuickStart.Rnw
vignettes/gMCP.Rnw
vignettes/literatur.bib
vignettes/myIndex.ist
vignettes/parametric.Rnw
vignettes/pictures
vignettes/pictures/CIDialog.png
vignettes/pictures/FullFeaturedGUI.png
vignettes/pictures/GeneratedRCode.png
vignettes/pictures/Reset.png
vignettes/pictures/StartTesting.png
vignettes/pictures/adjPval.png
vignettes/pictures/adjPval_b.png
vignettes/pictures/confint2.png
vignettes/pictures/confint2_b.png
vignettes/pictures/correlated.png
vignettes/pictures/createCM1.png
vignettes/pictures/createCM3.png
vignettes/pictures/docxExport.png
vignettes/pictures/edge.png
vignettes/pictures/entangled.png
vignettes/pictures/example.png
vignettes/pictures/filemenu.png
vignettes/pictures/power.png
vignettes/pictures/rjavaicon64.png
vignettes/pictures/variableEditor.png
vignettes/pictures/vertex.png
vignettes/pictures/zoom_in.png
vignettes/pictures/zoom_out.png
gMCP documentation built on May 21, 2017, 3:36 a.m.

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