gMCP: Graph Based Multiple Comparison Procedures

Functions and a graphical user interface for graphical described multiple test procedures.

Install the latest version of this package by entering the following in R:
install.packages("gMCP")
AuthorKornelius Rohmeyer [aut, cre], Florian Klinglmueller [aut]
Date of publication2015-08-31 14:30:03
MaintainerKornelius Rohmeyer <rohmeyer@small-projects.de>
LicenseGPL (>= 2)
Version0.8-10
http://gsrmtp.r-forge.r-project.org/

View on CRAN

Man pages

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...

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.extended: 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

parametric.test: Weighted parametric test

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: Sample size calculations

sampSizeCore: Function for sample size calculation

secondStageTest: EXPERIMENTAL: Construct a valid level alpha test for the...

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

simes.test: Weighted Simes test

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

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

Functions

BauerEtAl2001 Man page
bdiagNA Man page
BonferroniHolm Man page
bonferroni.test Man page
bonferroni.trimmed.simes.test Man page
BretzEtAl2009a Man page
BretzEtAl2009b Man page
BretzEtAl2009c Man page
BretzEtAl2011 Man page
calcPower Man page
corMatWizard Man page
cycleGraph Man page
doInterim Man page
edgeAttr Man page
edgeAttr<- Man page
edgeAttr<-,graphMCP,character,character,character-method Man page
edgeAttr,graphMCP,character,character,character-method Man page
Entangled1Maurer2012 Man page
Entangled2Maurer2012 Man page
entangledMCP Man page
entangledMCP-class Man page
exampleGraphs Man page
extractPower Man page
fallback Man page
Ferber2011 Man page
FerberTimeDose2011 Man page
fixedSequence Man page
generalSuccessive Man page
generateBounds Man page
generatePvals Man page
generateTest Man page
generateWeights Man page
getJavaInfo Man page
getMatrices Man page
getMatrices,entangledMCP-method Man page
getMatrix Man page
getMatrix,graphMCP-method Man page
getNodes Man page
getNodes,entangledMCP-method Man page
getNodes,graphMCP-method Man page
getRejected Man page
getRejected,entangledMCP-method Man page
getRejected,gMCPResult-method Man page
getRejected,gPADInterim-method Man page
getRejected,graphMCP-method Man page
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
gMCP Man page
gMCP.extended Man page
gMCP-package Man page
gMCPReport Man page
gMCPResult Man page
gMCPResult-class Man page
gPADInterim Man page
gPADInterim-class Man page
graph2latex Man page
graph2matrix Man page
graphAnalysis Man page
graphGUI Man page
graphMCP Man page
graphMCP-class Man page
graphTest Man page
HommelEtAl2007 Man page
HommelEtAl2007Simple Man page
HungEtWang2010 Man page
HuqueAloshEtBhore2011 Man page
hydroquinone Man page
improvedFallbackI Man page
improvedFallbackII Man page
improvedParallelGatekeeping Man page
joinGraphs Man page
matrix2graph Man page
MaurerEtAl1995 Man page
nodeAttr Man page
nodeAttr<- Man page
nodeAttr<-,graphMCP,character,character-method Man page
nodeAttr,graphMCP,character,character-method Man page
parallelGatekeeping Man page
parametric.test Man page
placeNodes Man page
plot,gMCPResult,ANY-method Man page
plot,gPADInterim-method Man page
plot,graphMCP,ANY-method Man page
plotSimCI Man page
print,entangledMCP-method Man page
print,gMCPResult-method Man page
print,gPADInterim-method Man page
print,graphMCP-method Man page
rejectNode Man page
replaceVariables Man page
rqmvnorm Man page
sampSize Man page
sampSizeCore Man page
secondStageTest Man page
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
simes.on.subsets.test Man page
simes.test Man page
simpleSuccessiveI Man page
simpleSuccessiveII Man page
simvastatin Man page
subgraph Man page
substituteEps Man page
truncatedHolm Man page
unitTestsGMCP Man page
WangTing2014 Man page
weighted.test.functions Man page

Files

TODO
inst
inst/References.html
inst/CITATION
inst/java
inst/java/gsrmtp.jar
inst/doc
inst/doc/AQuickStart.Rnw
inst/doc/parametric.Rnw
inst/doc/gMCP.R
inst/doc/gMCP.Rnw
inst/doc/gMCP.pdf
inst/doc/parametric.pdf
inst/doc/parametric.R
inst/doc/AQuickStart.pdf
inst/doc/AQuickStart.R
inst/unitTests
inst/unitTests/runit.entangled.R inst/unitTests/runit.randomGraph.R inst/unitTests/runit.LaTeX.R inst/unitTests/runit.misc.R inst/unitTests/runit.fastgMCP.R inst/unitTests/runit.adjPValues.R inst/unitTests/runit.gMCP.R inst/unitTests/runit.power.R inst/unitTests/runit.gMCP.extended.R inst/unitTests/runit.sampSize.R inst/unitTests/runit.correlation.R inst/unitTests/runit.graphGMCP.R inst/unitTests/runit.cover.everything.R
tests
tests/doRUnit.R
src
src/mcp.c
src/gMCP.c
NAMESPACE
INSTALL
NEWS
data
data/hydroquinone.rda
data/simvastatin.rda
R
R/subVariables.R R/onLoad.R R/gACT-internal.R R/gMCP.R R/generateBounds.R R/startGUIs.R R/closure.R R/exampleGraphs.R R/analysis.R R/graph2latex.R R/powerPlot.R R/generateTest.R R/gMCP.extended.R R/rqmvnorm.R R/modifyGraphs.R R/helperGUI.R R/graphMCP.R R/graphTest.R R/doRUnitTests.R R/sampSize.R R/misc.R R/plotCI.R R/generateWeights.R R/matrix2graph.R R/generatePvals.R R/convertFromOldClassDefinition.R R/gPAD.R R/calcPower.R
vignettes
vignettes/AQuickStart.Rnw
vignettes/parametric.Rnw
vignettes/pictures
vignettes/pictures/StartTesting.png
vignettes/pictures/edge.png
vignettes/pictures/createCM1.png
vignettes/pictures/zoom_in.png
vignettes/pictures/GeneratedRCode.png
vignettes/pictures/udpf.png
vignettes/pictures/rjavaicon64.png
vignettes/pictures/FullFeaturedGUI.png
vignettes/pictures/docxExport.png
vignettes/pictures/filemenu.png
vignettes/pictures/PowerResults.png
vignettes/pictures/confint2.png
vignettes/pictures/udpf2.png
vignettes/pictures/CIDialog.png
vignettes/pictures/vertex.png
vignettes/pictures/variableEditor.png
vignettes/pictures/entangled.png
vignettes/pictures/ImportTextLibreOffice.png
vignettes/pictures/exportPNG.png
vignettes/pictures/power_requirements.png
vignettes/pictures/adjPval_b.png
vignettes/pictures/correlated.png
vignettes/pictures/confint2_b.png
vignettes/pictures/example.png
vignettes/pictures/zoom_out.png
vignettes/pictures/arm.png
vignettes/pictures/corMat2.png
vignettes/pictures/Reset.png
vignettes/pictures/adjPval.png
vignettes/pictures/createCM3.png
vignettes/gMCP.Rnw
vignettes/pvals.RData
vignettes/literatur.bib
vignettes/myIndex.ist
MD5
java
java/tests
java/tests/DataTableTest.java
java/tests/ToolTest.java
java/tests/EdgeTest.java
java/tests/RControlTest.java
java/tests/LoadSaveTest.java
java/tests/NetListTest.java
java/tests/PowerTest.java
java/tests/RJavaUTF.java
java/tests/InteractionTest.java
java/tests/TestSuite.java
java/tests/TexFormulaTest.java
java/tests/NodeTest.java
java/tests/PPanelTest.java
java/tests/OptionPaneTest.java
java/org
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/TransferableImage.java
java/org/mutoss/gui/JavaGD.java
java/org/mutoss/gui/JavaGDPanel.java
java/org/af
java/org/af/gMCP
java/org/af/gMCP/tests
java/org/af/gMCP/tests/CircleTest.java
java/org/af/gMCP/tests/ThreadExceptionTest.java
java/org/af/gMCP/tests/CircleTest3Points.java
java/org/af/gMCP/tests/TestImportExport.java
java/org/af/gMCP/tests/FormatTest.java
java/org/af/gMCP/tests/TeXFormulaTest.java
java/org/af/gMCP/config
java/org/af/gMCP/config/JavaConfig.java
java/org/af/gMCP/config/Configuration.java
java/org/af/gMCP/config/PlotConfig.java
java/org/af/gMCP/config/GeneralConfig.java
java/org/af/gMCP/config/SpecificConfig.java
java/org/af/gMCP/config/VersionComparator.java
java/org/af/gMCP/poi
java/org/af/gMCP/poi/GraphDocXWriter.java
java/org/af/gMCP/gui
java/org/af/gMCP/gui/pdf
java/org/af/gMCP/gui/pdf/PDFViewerStarter.java
java/org/af/gMCP/gui/pdf/Step.java
java/org/af/gMCP/gui/pdf/PDFGenerator.java
java/org/af/gMCP/gui/pdf/Plot.java
java/org/af/gMCP/gui/pdf/Result.java
java/org/af/gMCP/gui/power
java/org/af/gMCP/gui/power/Arm.java
java/org/af/gMCP/gui/power/PowerResultDialog.java
java/org/af/gMCP/gui/power/PopulationDialog.java
java/org/af/gMCP/gui/power/SampleSizeDialog.java
java/org/af/gMCP/gui/power/SampSizeResultTableModel.java
java/org/af/gMCP/gui/power/KoutofNDialog.java
java/org/af/gMCP/gui/power/EndpointDialog.java
java/org/af/gMCP/gui/power/VariablePanel.java
java/org/af/gMCP/gui/power/NCPCalculatorDialog.java
java/org/af/gMCP/gui/power/XMLIO.java
java/org/af/gMCP/gui/power/CVPanel.java
java/org/af/gMCP/gui/power/ScenarioPanel2.java
java/org/af/gMCP/gui/power/PDialog.java
java/org/af/gMCP/gui/power/Scenario2.java
java/org/af/gMCP/gui/power/UserDefinedDialog.java
java/org/af/gMCP/gui/power/Scenario.java
java/org/af/gMCP/gui/power/RandomizationPanel.java
java/org/af/gMCP/gui/power/ScenarioPanel.java
java/org/af/gMCP/gui/power/PowerReq.java
java/org/af/gMCP/gui/power/PowerResultTableModel.java
java/org/af/gMCP/gui/power/MarginalPowerPanel.java
java/org/af/gMCP/gui/power/UserDefinedPanel.java
java/org/af/gMCP/gui/power/PowerDialog.java
java/org/af/gMCP/gui/power/SettingsToXML.java
java/org/af/gMCP/gui/power/PowerReqPanel.java
java/org/af/gMCP/gui/power/ScenarioPanelInterface.java
java/org/af/gMCP/gui/power/HorizontalButtonPane.java
java/org/af/gMCP/gui/power/NCPRequestor.java
java/org/af/gMCP/gui/ReproducableLog.java
java/org/af/gMCP/gui/AboutDialog.java
java/org/af/gMCP/gui/DebugTextConsole.java
java/org/af/gMCP/gui/ErrorDialogChooseLevel.java
java/org/af/gMCP/gui/graph
java/org/af/gMCP/gui/graph/PPanel.java
java/org/af/gMCP/gui/graph/NetListPanel.java
java/org/af/gMCP/gui/graph/PView.java
java/org/af/gMCP/gui/graph/DView.java
java/org/af/gMCP/gui/graph/annotations
java/org/af/gMCP/gui/graph/annotations/Legend.java
java/org/af/gMCP/gui/graph/annotations/Rectangle.java
java/org/af/gMCP/gui/graph/annotations/Note.java
java/org/af/gMCP/gui/graph/annotations/Annotation.java
java/org/af/gMCP/gui/graph/annotations/Ellipse.java
java/org/af/gMCP/gui/graph/annotations/Text.java
java/org/af/gMCP/gui/graph/annotations/AnnotationPanel.java
java/org/af/gMCP/gui/graph/annotations/Line.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/StartTesting.png
java/org/af/gMCP/gui/graph/images/edge.png
java/org/af/gMCP/gui/graph/images/zoom_in.png
java/org/af/gMCP/gui/graph/images/questionmark.png
java/org/af/gMCP/gui/graph/images/rjavaicon64.png
java/org/af/gMCP/gui/graph/images/matrix.png
java/org/af/gMCP/gui/graph/images/questionmark32.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/update24.png
java/org/af/gMCP/gui/graph/images/vertex.png
java/org/af/gMCP/gui/graph/images/update.png
java/org/af/gMCP/gui/graph/images/zoom_out.png
java/org/af/gMCP/gui/graph/images/questionmark64.png
java/org/af/gMCP/gui/graph/images/Reset.png
java/org/af/gMCP/gui/graph/images/adjPval.png
java/org/af/gMCP/gui/graph/images/latex.png
java/org/af/gMCP/gui/graph/EdgeWeight.java
java/org/af/gMCP/gui/graph/GraphView.java
java/org/af/gMCP/gui/graph/GraphMCP.java
java/org/af/gMCP/gui/graph/UpdateNode.java
java/org/af/gMCP/gui/graph/PrintableObject.java
java/org/af/gMCP/gui/graph/UpdateEdge.java
java/org/af/gMCP/gui/graph/Edge.java
java/org/af/gMCP/gui/graph/NetList.java
java/org/af/gMCP/gui/graph/NodeListener.java
java/org/af/gMCP/gui/graph/WrongInputException.java
java/org/af/gMCP/gui/graph/Physics.java
java/org/af/gMCP/gui/graph/NetListPopUpMenu.java
java/org/af/gMCP/gui/graph/GraphPanel.java
java/org/af/gMCP/gui/graph/SubFamily.java
java/org/af/gMCP/gui/graph/Node.java
java/org/af/gMCP/gui/graph/LaTeXTool.java
java/org/af/gMCP/gui/graph/NetListSelectionPopUpMenu.java
java/org/af/gMCP/gui/CreateGraphGUI.java
java/org/af/gMCP/gui/options
java/org/af/gMCP/gui/options/SetPropertiesException.java
java/org/af/gMCP/gui/options/SetLookAndFeelException.java
java/org/af/gMCP/gui/options/OptionsDialog.java
java/org/af/gMCP/gui/options/GeneralPanel.java
java/org/af/gMCP/gui/options/MiscPanel.java
java/org/af/gMCP/gui/options/OptionsPanel.java
java/org/af/gMCP/gui/options/NumericPanel.java
java/org/af/gMCP/gui/MenuBarMGraph.java
java/org/af/gMCP/gui/commons-logging-verbose.properties
java/org/af/gMCP/gui/commons-logging.properties
java/org/af/gMCP/gui/JSplitPaneBugWorkAround.java
java/org/af/gMCP/gui/ErrorDialogGMCP.java
java/org/af/gMCP/gui/datatable
java/org/af/gMCP/gui/datatable/DataFramePanel.java
java/org/af/gMCP/gui/datatable/DataTableModel.java
java/org/af/gMCP/gui/datatable/RowModel.java
java/org/af/gMCP/gui/datatable/EpsilonTableCellRenderer.java
java/org/af/gMCP/gui/datatable/CellEditorE.java
java/org/af/gMCP/gui/datatable/SingleDataFramePanel.java
java/org/af/gMCP/gui/datatable/DataTable.java
java/org/af/gMCP/gui/datatable/RDataFrameRef.java
java/org/af/gMCP/gui/ErrorDialogChooseLevelBase.java
java/org/af/gMCP/gui/contrasts
java/org/af/gMCP/gui/contrasts/ContrastTableModel.java
java/org/af/gMCP/gui/contrasts/VarSelectBox.java
java/org/af/gMCP/gui/contrasts/ROptionBox.java
java/org/af/gMCP/gui/contrasts/GroupingBox.java
java/org/af/gMCP/gui/contrasts/LevelOrderListener.java
java/org/af/gMCP/gui/contrasts/StatMethodDialog.java
java/org/af/gMCP/gui/contrasts/AnalysisDialogListenerFactory.java
java/org/af/gMCP/gui/contrasts/GroupingListener.java
java/org/af/gMCP/gui/contrasts/ContrastDialog2.java
java/org/af/gMCP/gui/contrasts/LevelOrderSL.java
java/org/af/gMCP/gui/contrasts/ContrastColorRenderer.java
java/org/af/gMCP/gui/contrasts/AnalysisDialogFactory.java
java/org/af/gMCP/gui/contrasts/ContrastTable.java
java/org/af/gMCP/gui/contrasts/LevelSelectBox.java
java/org/af/gMCP/gui/dialogs
java/org/af/gMCP/gui/dialogs/GroupDialog.java
java/org/af/gMCP/gui/dialogs/PowerOptionsPanel.java
java/org/af/gMCP/gui/dialogs/MatrixCreationDialog.java
java/org/af/gMCP/gui/dialogs/RejectedDialog.java
java/org/af/gMCP/gui/dialogs/RearrangeNodesDialog.java
java/org/af/gMCP/gui/dialogs/PowerParameterPanel.java
java/org/af/gMCP/gui/dialogs/VariableDialog.java
java/org/af/gMCP/gui/dialogs/InfoDialog.java
java/org/af/gMCP/gui/dialogs/VariableNameDialog.java
java/org/af/gMCP/gui/dialogs/GraphSendToArchiveDialog.java
java/org/af/gMCP/gui/dialogs/AlternativesDialog.java
java/org/af/gMCP/gui/dialogs/AdjustedPValueDialog.java
java/org/af/gMCP/gui/dialogs/TellAboutOnlineUpate.java
java/org/af/gMCP/gui/dialogs/ColorChooseDialog.java
java/org/af/gMCP/gui/dialogs/DialogConfIntEstVar.java
java/org/af/gMCP/gui/dialogs/PowersettingsToXML.java
java/org/af/gMCP/gui/dialogs/ParameterDialog.java
java/org/af/gMCP/gui/dialogs/NewVersionDialog.java
java/org/af/gMCP/gui/dialogs/TextFileViewer.java
java/org/af/gMCP/gui/dialogs/RObjectLoadingDialog.java
java/org/af/gMCP/gui/dialogs/ImageExportDialog.java
java/org/af/gMCP/gui/dialogs/LoadGraphFromArchiveDialog.java
java/org/af/gMCP/gui/dialogs/ImagePanel.java
java/org/af/gMCP/gui/dialogs/GraphSaveDialog.java
java/org/af/gMCP/gui/RCallServicesREngineWrapper.java
java/org/af/gMCP/gui/RControl.java
java/build.xml
build
build/vignette.rds
DESCRIPTION
man
man/plotSimCI.Rd man/substituteEps.Rd man/placeNodes.Rd man/gPADInterim.Rd man/gMCPResult.Rd man/graphGUI.Rd man/sampSize.Rd man/exampleGraphs.Rd man/subgraph.Rd man/gMCP-package.Rd man/entangled.Rd man/matrix2graph.Rd man/hydroquinone.Rd man/generateBounds.Rd man/gMCPReport.Rd man/bdiagNA.Rd man/rqmvnorm.Rd man/graphTest.Rd man/weighted.test.functions.Rd man/confint.Rd man/simvastatin.Rd man/generateTest.Rd man/graph2latex.Rd man/gMCP.Rd man/rejectNode.Rd man/gMCP.extended.Rd man/bonferroni.test.Rd man/secondStageTest.Rd man/extractPower.Rd man/joinGraphs.Rd man/graphAnalysis.Rd man/simes.on.subsets.test.Rd man/parametric.test.Rd man/bonferroni.trimmed.simes.test.Rd man/sampSizeCore.Rd man/generateWeights.Rd man/generatePvals.Rd man/unitTestsGMCP.Rd man/doInterim.Rd man/getJavaInfo.Rd man/graphMCP.Rd man/simes.test.Rd man/corMatWizard.Rd man/replaceVariables.Rd man/calcPower.Rd
.Rinstignore

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