gMCP: Graph Based Multiple Comparison Procedures

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

Author
Kornelius Rohmeyer [aut, cre], Florian Klinglmueller [aut]
Date of publication
2015-08-31 14:30:03
Maintainer
Kornelius Rohmeyer <rohmeyer@small-projects.de>
License
GPL (>= 2)
Version
0.8-10
URLs

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

Files in this package

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