MSToolkit: The MSToolkit library for clinical trial design

MSToolkit library for Clinical Trial Design

AuthorMike K Smith <mstoolkit@gmail.com>
Date of publication2014-11-11 22:53:52
MaintainerMike K Smith <mstoolkit@gmail.com>
LicenseGPL
Version3.2.3

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

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