MSToolkit: The MSToolkit library for clinical trial design

MSToolkit library for Clinical Trial Design

Author
Mike K Smith <mstoolkit@gmail.com>
Date of publication
2014-11-11 22:53:52
Maintainer
Mike K Smith <mstoolkit@gmail.com>
License
GPL
Version
3.2.3

View on R-Forge

Man pages

addResidualError
Add residual error to the response.
allocateTreatments
Allocate treatment to subjects
analyzeData
Analyze simulated data replicates
analyzeRep
Analyse a single replicate of data
applyPredCode
Parses and applys NONMEM statements
calculateDiffsFromBase
Calculate differences from baseline
calculateObsSummary
Calculate Observed Data Summary
calculateSimTrialMeans
Calculate Simulated Trial Means
checkColNames
Parse alpha value
checkDropOutFun
check the user supplied drop out function
checkMacroFormat
check the macro format dataset
checkMicroFormat
Check that an input data structure is a valid "Micro...
checkSimAlpha
Parse alpha value
checkSymmetricPDMatrix
Checks if a matrix is symmetric and positive definite
compileSummary
Compile all Micro or Macro evaluation data
convertSASIncludeRows
Create a SAS 'IF' statement
convertToSASCode
Convert R to SAS Statements
createContinuousCovariates
Create a set of continuous covariates
createCovariates
Create covariates
createDirectories
Create replicate data, micro evaluation, and macro evaluation...
createDiscreteCovariates
Create covariates from a discrete distribution
createDropout
Adds dropout to a simulated dataset
createEmptyMicro
Create an empty micro evaluation data frame
createExternalCovariates
Create covariates by sampling from an external file
createExternalParameters
Sample parameters from an external file
createInterims
create the interim flag
createMCAR
Missing Completely at Random
createNmMatrix
Creates a matrix based on a "NONMEM style" vector
createNmParSamples
Simulate parameter sets from a NONMEM run object
createNormalParameters
Create parameters based on a multivariate normal distribution
createParameters
Create parameter data for subjects in a simulated trial
createResponse
High-level function for the response component.
createResponseVariable
Create a response from a data set and an equation
createTimeVaryingCovariates
Create a set of time-varying covariates
createTreatments
Create Treatment Design Data
createTvDefinition
Create "Typical Value" Definition
ectdColNames
Control of default column names
ectdDataMethod
Current data storage method
ectdExternalPath
Controls paths to a set of external execution paths
ectdStop
Error handling functions for the ectd package.
generateData
Generate simulated data replicates
getReplicates
Trial replicates vector
initialChar
Convert the first letter that occurs in a string to lower...
interimAnalysis
interim Analysis
macroEvaluation
Macro Evaluation
MSToolkit-package
Generates and analyzes simulated trial data
mstoolkitUnitTests
Unit/System Tests suite for the MSToolkit package
parseCharInput
Parse a comma seperated string
parseCovMatrix
Parse a covariance matrix
parseHashString
Process a string seperated by hash symbols or a vector (or...
parseRangeCode
Parse a numerical range expression
parseRCode
Parse R Code
performAnalysis
Runs the analysis code against one dataset
readAllData
Read scenario data
readData
Read scenario data
removeDirectories
Remove directories
setEctdVerbose
MSToolkit package options
summarizeTrialMeans
Summarize Trial Mean Data
tvDefinition-class
tvDefinition class
validNames
Check if a character string is a valid R variable name
writeData
Write scenario data
writeLogFile
Write a job log file

Files in this package

MSToolkit/DESCRIPTION
MSToolkit/NAMESPACE
MSToolkit/R
MSToolkit/R/addResidualError.R
MSToolkit/R/allocateTreatments.R
MSToolkit/R/analyzeData.r
MSToolkit/R/analyzeRep.R
MSToolkit/R/applyPredCode.R
MSToolkit/R/calculateDiffsFromBase.R
MSToolkit/R/calculateObsSummary.R
MSToolkit/R/calculateSimTrialMeans.R
MSToolkit/R/checkDropOutFun.R
MSToolkit/R/checkMacroFormat.R
MSToolkit/R/checkMicroFormat.R
MSToolkit/R/checkSimAlpha.R
MSToolkit/R/checkSymmetricPDMatrix.R
MSToolkit/R/compileSummary.R
MSToolkit/R/convertSASIncludeRows.R
MSToolkit/R/convertToSASCode.R
MSToolkit/R/createContinuousCovariates.R
MSToolkit/R/createCovariates.R
MSToolkit/R/createDirectories.r
MSToolkit/R/createDiscreteCovariates.R
MSToolkit/R/createDropout.R
MSToolkit/R/createEmptyMicro.R
MSToolkit/R/createExternalCovariates.R
MSToolkit/R/createExternalParameters.R
MSToolkit/R/createInterims.R
MSToolkit/R/createMCAR.R
MSToolkit/R/createNmMatrix.R
MSToolkit/R/createNmParSamples.R
MSToolkit/R/createNormalParameters.R
MSToolkit/R/createParameters.R
MSToolkit/R/createResponse.R
MSToolkit/R/createResponseVariable.R
MSToolkit/R/createTimeVaryingCovariates.R
MSToolkit/R/createTreatments.R
MSToolkit/R/createTvDefinition.R
MSToolkit/R/ectdStop.R
MSToolkit/R/ectdWarning.R
MSToolkit/R/generateData.R
MSToolkit/R/getReplicates.R
MSToolkit/R/initialChar.R
MSToolkit/R/interimAnalysis.R
MSToolkit/R/internal.datastorage.R
MSToolkit/R/macroEvaluation.R
MSToolkit/R/metaManagement.R
MSToolkit/R/mstoolkitUnitTests.R
MSToolkit/R/operators.R
MSToolkit/R/parseCharInput.R
MSToolkit/R/parseCovMatrix.R
MSToolkit/R/parseHashString.R
MSToolkit/R/parsePredCode.R
MSToolkit/R/parseRCode.R
MSToolkit/R/parseRangeCode.R
MSToolkit/R/performAnalysis.R
MSToolkit/R/readAllData.R
MSToolkit/R/readData.R
MSToolkit/R/removeDirectories.r
MSToolkit/R/summarizeTrialMeans.R
MSToolkit/R/utils.R
MSToolkit/R/validNames.R
MSToolkit/R/writeData.r
MSToolkit/R/writeLogFile.R
MSToolkit/R/zzz.R
MSToolkit/TODO
MSToolkit/TODO.grep
MSToolkit/demo
MSToolkit/demo/00Index
MSToolkit/demo/emax.R
MSToolkit/demo/emaxfit.R
MSToolkit/exec
MSToolkit/exec/compile
MSToolkit/inst
MSToolkit/inst/COPYRIGHT
MSToolkit/inst/ECTD.ini
MSToolkit/inst/Runit
MSToolkit/inst/Runit/Makefile
MSToolkit/inst/Runit/data
MSToolkit/inst/Runit/data/NONMEM
MSToolkit/inst/Runit/data/NONMEM/waso.ctl
MSToolkit/inst/Runit/data/NONMEM/waso.out
MSToolkit/inst/Runit/data/NONMEM/waso.tab
MSToolkit/inst/Runit/data/NONMEM/wasodata.csv
MSToolkit/inst/Runit/data/analyseRep
MSToolkit/inst/Runit/data/analyseRep/ReplicateData
MSToolkit/inst/Runit/data/analyseRep/ReplicateData/replicate0001.csv
MSToolkit/inst/Runit/data/analyseRep/ReplicateData/replicate0002.csv
MSToolkit/inst/Runit/data/analyseRep/ReplicateData/replicate0003.csv
MSToolkit/inst/Runit/data/compileSummary
MSToolkit/inst/Runit/data/compileSummary/MacroEvaluation
MSToolkit/inst/Runit/data/compileSummary/MacroEvaluation/macro0001.csv
MSToolkit/inst/Runit/data/compileSummary/MacroEvaluation/macro0002.csv
MSToolkit/inst/Runit/data/compileSummary/MacroEvaluation/macro0003.csv
MSToolkit/inst/Runit/data/compileSummary/MacroEvaluation/macro0004.csv
MSToolkit/inst/Runit/data/compileSummary/MacroEvaluation/macro0005.csv
MSToolkit/inst/Runit/data/compileSummary/MicroEvaluation
MSToolkit/inst/Runit/data/compileSummary/MicroEvaluation/micro0001.csv
MSToolkit/inst/Runit/data/compileSummary/MicroEvaluation/micro0002.csv
MSToolkit/inst/Runit/data/compileSummary/MicroEvaluation/micro0003.csv
MSToolkit/inst/Runit/data/compileSummary/MicroEvaluation/micro0004.csv
MSToolkit/inst/Runit/data/compileSummary/MicroEvaluation/micro0005.csv
MSToolkit/inst/Runit/data/compileSummary/macroSummary.csv
MSToolkit/inst/Runit/data/compileSummary/microSummary.csv
MSToolkit/inst/Runit/data/compileSummary2
MSToolkit/inst/Runit/data/compileSummary2/MacroEvaluation
MSToolkit/inst/Runit/data/compileSummary2/MacroEvaluation/macro0001.csv
MSToolkit/inst/Runit/data/compileSummary2/MacroEvaluation/macro0002.csv
MSToolkit/inst/Runit/data/compileSummary2/MacroEvaluation/macro0003.csv
MSToolkit/inst/Runit/data/compileSummary2/MacroEvaluation/macro0004.csv
MSToolkit/inst/Runit/data/compileSummary2/MacroEvaluation/macro0005.csv
MSToolkit/inst/Runit/data/compileSummary2/MicroEvaluation
MSToolkit/inst/Runit/data/compileSummary2/MicroEvaluation/micro0001.csv
MSToolkit/inst/Runit/data/compileSummary2/MicroEvaluation/micro0002.csv
MSToolkit/inst/Runit/data/compileSummary2/MicroEvaluation/micro0003.csv
MSToolkit/inst/Runit/data/compileSummary2/MicroEvaluation/micro0004.csv
MSToolkit/inst/Runit/data/compileSummary2/MicroEvaluation/micro0005.csv
MSToolkit/inst/Runit/data/createCovariates
MSToolkit/inst/Runit/data/createCovariates/testCovariates.csv
MSToolkit/inst/Runit/data/createCovariates/testSameRow.csv
MSToolkit/inst/Runit/data/createCovariates/wrongTestCovariates.csv
MSToolkit/inst/Runit/data/createParameters
MSToolkit/inst/Runit/data/createParameters/testParam.csv
MSToolkit/inst/Runit/data/createParameters/testParam.nonmem
MSToolkit/inst/Runit/data/createParameters/testParam.spaceDelim
MSToolkit/inst/Runit/data/createParameters/testParam.tabDelim
MSToolkit/inst/Runit/data/createParameters/wrongTestParam.csv
MSToolkit/inst/Runit/data/macroEvaluation
MSToolkit/inst/Runit/data/macroEvaluation/micro0001.csv
MSToolkit/inst/Runit/micro0001.csv
MSToolkit/inst/Runit/report.html
MSToolkit/inst/Runit/runit.analyzeRep.R
MSToolkit/inst/Runit/runit.checkCsvFile.R
MSToolkit/inst/Runit/runit.checkmacroformat.R
MSToolkit/inst/Runit/runit.compileSummary.R
MSToolkit/inst/Runit/runit.data.allocate.R
MSToolkit/inst/Runit/runit.data.covariates.R
MSToolkit/inst/Runit/runit.data.interim.R
MSToolkit/inst/Runit/runit.data.missing.R
MSToolkit/inst/Runit/runit.data.parameter.R
MSToolkit/inst/Runit/runit.data.response.R
MSToolkit/inst/Runit/runit.data.treatment.R
MSToolkit/inst/Runit/runit.datastorage.R
MSToolkit/inst/Runit/runit.interimAnalysis.R
MSToolkit/inst/Runit/runit.logFile.R
MSToolkit/inst/Runit/runit.macroEvaluation.R
MSToolkit/inst/Runit/runit.meta.management.R
MSToolkit/inst/Runit/runit.nonmemSim.R
MSToolkit/inst/Runit/runit.performAnalysis.R
MSToolkit/inst/Runit/runit.reporting.core.R
MSToolkit/inst/Runit/runit.sf7.R
MSToolkit/inst/Runit/runit.supportfunctions.R
MSToolkit/inst/Runit/runit.typicalValue.R
MSToolkit/inst/Runit/testdata.datastorage
MSToolkit/inst/Runit/testdata.datastorage/MacroEvaluation
MSToolkit/inst/Runit/testdata.datastorage/MacroEvaluation/macro0001.csv
MSToolkit/inst/Runit/testdata.datastorage/MicroEvaluation
MSToolkit/inst/Runit/testdata.datastorage/MicroEvaluation/micro0001.csv
MSToolkit/inst/Runit/testdata.datastorage/NONMEMDataNoHeader.fit
MSToolkit/inst/Runit/testdata.datastorage/NONMEMDataWithHeader.fit
MSToolkit/inst/Runit/testdata.datastorage/NONMEMcsv.csv
MSToolkit/inst/Runit/testdata.datastorage/ReplicateData
MSToolkit/inst/Runit/testdata.datastorage/ReplicateData/replicate0010.csv
MSToolkit/inst/Runit/testdata.datastorage/ReplicateSample.csv
MSToolkit/inst/Runit/testdata.datastorage/macro0001.csv
MSToolkit/inst/Runit/testdata.datastorage/micro0001.csv
MSToolkit/inst/Runit/testdata.datastorage/microSummary.csv
MSToolkit/inst/Runit/testdata.datastorage/replicate0010.csv
MSToolkit/inst/Runit/testdata.supportfunctions
MSToolkit/inst/Runit/testdata.supportfunctions/micro0001.csv
MSToolkit/inst/Runit/testdata.supportfunctions/micro0002.csv
MSToolkit/inst/Runit/testdata.supportfunctions/micro0003.csv
MSToolkit/inst/Runit/testdata.supportfunctions/micro0004.csv
MSToolkit/inst/Runit/testdata.supportfunctions/micro0005.csv
MSToolkit/inst/Runit/testdata.supportfunctions/testdata.checkCsvFile.1.csv
MSToolkit/inst/Runit/testdata.supportfunctions/testdata.checkCsvFile.2.csv
MSToolkit/inst/Runit/testdata.supportfunctions/testdata.checkCsvFile.3.csv
MSToolkit/inst/Runit/testdata.supportfunctions/testdata.checkCsvFile.4.csv
MSToolkit/inst/Runit/testdata.supportfunctions/testdata.createEmptyMicro.1.csv
MSToolkit/inst/Runit/wrong1.csv
MSToolkit/inst/sasAnalysis.sas
MSToolkit/inst/systemTest
MSToolkit/inst/systemTest/data
MSToolkit/inst/systemTest/data/Interim
MSToolkit/inst/systemTest/data/Interim/ReplicateData
MSToolkit/inst/systemTest/data/Interim/ReplicateData/replicate0001.csv
MSToolkit/inst/systemTest/data/Interim/ReplicateData/replicate0002.csv
MSToolkit/inst/systemTest/data/Interim/ReplicateData/replicate0003.csv
MSToolkit/inst/systemTest/data/Interim/ReplicateData/replicate0004.csv
MSToolkit/inst/systemTest/data/Interim/ReplicateData/replicate0005.csv
MSToolkit/inst/systemTest/data/Interim/ReplicateData/replicate0006.csv
MSToolkit/inst/systemTest/data/Interim/ReplicateData/replicate0007.csv
MSToolkit/inst/systemTest/data/Interim/ReplicateData/replicate0008.csv
MSToolkit/inst/systemTest/data/Scripts
MSToolkit/inst/systemTest/data/Scripts/ReplicateData
MSToolkit/inst/systemTest/data/Scripts/ReplicateData/replicate0001.csv
MSToolkit/inst/systemTest/data/Scripts/ReplicateData/replicate0002.csv
MSToolkit/inst/systemTest/data/Scripts/ReplicateData/replicate0003.csv
MSToolkit/inst/systemTest/data/Scripts/analysisCode.sas
MSToolkit/inst/systemTest/data/Scripts/rAnalysisScript.R
MSToolkit/inst/systemTest/data/testCovariates.csv
MSToolkit/inst/systemTest/data/testParam.csv
MSToolkit/inst/systemTest/data/testParam.nonmem
MSToolkit/inst/systemTest/data/testParam.spaceDelim
MSToolkit/inst/systemTest/data/testParam.tabDelim
MSToolkit/inst/systemTest/runit.analyseData.R
MSToolkit/inst/systemTest/runit.generateData.R
MSToolkit/man
MSToolkit/man/MSToolkit-package.Rd
MSToolkit/man/addResidualError.Rd
MSToolkit/man/allocateTreatments.Rd
MSToolkit/man/analyzeData.Rd
MSToolkit/man/analyzeRep.Rd
MSToolkit/man/applyPredCode.Rd
MSToolkit/man/calculateDiffsFromBase.Rd
MSToolkit/man/calculateObsSummary.Rd
MSToolkit/man/calculateSimTrialMeans.Rd
MSToolkit/man/checkColNames.Rd
MSToolkit/man/checkDropOutFun.Rd
MSToolkit/man/checkMacroFormat.Rd
MSToolkit/man/checkMicroFormat.Rd
MSToolkit/man/checkSimAlpha.Rd
MSToolkit/man/checkSymmetricPDMatrix.Rd
MSToolkit/man/compileSummary.Rd
MSToolkit/man/convertSASIncludeRows.Rd
MSToolkit/man/convertToSASCode.Rd
MSToolkit/man/createContinuousCovariates.Rd
MSToolkit/man/createCovariates.Rd
MSToolkit/man/createDirectories.Rd
MSToolkit/man/createDiscreteCovariates.Rd
MSToolkit/man/createDropout.Rd
MSToolkit/man/createEmptyMicro.Rd
MSToolkit/man/createExternalCovariates.Rd
MSToolkit/man/createExternalParameters.Rd
MSToolkit/man/createInterims.Rd
MSToolkit/man/createMCAR.Rd
MSToolkit/man/createNmMatrix.Rd
MSToolkit/man/createNmParSamples.Rd
MSToolkit/man/createNormalParameters.Rd
MSToolkit/man/createParameters.Rd
MSToolkit/man/createResponse.Rd
MSToolkit/man/createResponseVariable.Rd
MSToolkit/man/createTimeVaryingCovariates.Rd
MSToolkit/man/createTreatments.Rd
MSToolkit/man/createTvDefinition.Rd
MSToolkit/man/ectdColNames.Rd
MSToolkit/man/ectdDataMethod.Rd
MSToolkit/man/ectdExternalPath.Rd
MSToolkit/man/ectdStop.Rd
MSToolkit/man/generateData.Rd
MSToolkit/man/getReplicates.Rd
MSToolkit/man/initialChar.Rd
MSToolkit/man/interimAnalysis.Rd
MSToolkit/man/macroEvaluation.Rd
MSToolkit/man/mstoolkitUnitTests.Rd
MSToolkit/man/parseCharInput.Rd
MSToolkit/man/parseCovMatrix.Rd
MSToolkit/man/parseHashString.Rd
MSToolkit/man/parseRCode.Rd
MSToolkit/man/parseRangeCode.Rd
MSToolkit/man/performAnalysis.Rd
MSToolkit/man/readAllData.Rd
MSToolkit/man/readData.Rd
MSToolkit/man/removeDirectories.Rd
MSToolkit/man/setEctdVerbose.Rd
MSToolkit/man/summarizeTrialMeans.Rd
MSToolkit/man/tvDefinition-class.Rd
MSToolkit/man/validNames.Rd
MSToolkit/man/writeData.Rd
MSToolkit/man/writeLogFile.Rd
MSToolkit/tests
MSToolkit/tests/doRUnit.R
MSToolkit/tests/ectd.log