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

Functions

addResidualError Man page
allocateTreatments Man page
analyzeData Man page
analyzeRep Man page
applyPredCode Man page
calculateDiffsFromBase Man page
calculateObsSummary Man page
calculateSimTrialMeans Man page
checkColNames Man page
checkDropOutFun Man page
checkMacroFormat Man page
checkMicroFormat Man page
checkSimAlpha Man page
checkSymmetricPDMatrix Man page
compileSummary Man page
convertSASIncludeRows Man page
convertToSASCode Man page
createContinuousCovariates Man page
createCovariates Man page
createDirectories Man page
createDiscreteCovariates Man page
createDropout Man page
createEmptyMicro Man page
createExternalCovariates Man page
createExternalParameters Man page
createInterims Man page
createMCAR Man page
createNmMatrix Man page
createNmParSamples Man page
createNormalParameters Man page
createParameters Man page
createResponse Man page
createResponseVariable Man page
createTimeVaryingCovariates Man page
createTreatments Man page
createTvDefinition Man page
ectdStop Man page
ectdWarning Man page
generateData Man page
getEctdColName Man page
getEctdDataMethod Man page
getEctdDateFormat Man page
getEctdExternalPath Man page
getEctdLogFile Man page
getEctdPossibleColNames Man page
getEctdVerbose Man page
getReplicates Man page
initialChar Man page
interimAnalysis Man page
macroEvaluation Man page
matchEctdColNames Man page
MSToolkit Man page
MSToolkit-package Man page
mstoolkitUnitTests Man page
parseCharInput Man page
parseCovMatrix Man page
parseHashString Man page
parsePredCode Man page
parseRangeCode Man page
parseRCode Man page
performAnalysis Man page
readAllData Man page
readData Man page
removeDirectories Man page
resetEctdColNames Man page
setEctdColName Man page
setEctdDataMethod Man page
setEctdDateFormat Man page
setEctdExternalPath Man page
setEctdLogFile Man page
setEctdPossibleColNames Man page
setEctdVerbose Man page
summarizeTrialMeans Man page
tvDefinition-class Man page
validNames Man page
writeData Man page
writeLogFile Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.