RNMImport: Tools for importing and manipulating NONMEM data.
Version 4.0-27

Imports NONMEM data, and provides utilities for manipulation reporting on it.

AuthorMango Solutions <support@mango-solutions.com>
Date of publication2014-08-15 07:48:35
MaintainerMango Solutions <support@mango-solutions.com>
LicenseClear BSD + file LICENSE
Version4.0-27
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RNMImport", repos="http://R-Forge.R-project.org")

Popular man pages

defaultDataSubset: Configure the global data subset attached to NONMEM problems...
getOmegas: Retrieve OMEGA estimates, initial values of
getSimInfo: Get Simulation Information.
importNm: Import a NONMEM run
importNmMod: Parse a NONMEM control file
nmRunReport-class: Auxilliary classes for representing report file statements
readNmData: Read NONMEM dataset removing any "IGNORE" rows and dealing...
See all...

All man pages Function index File listing

Man pages

addDerivedCategorical: Add binned variable to NONMEM object
addedData: Get added data
addVarDescription: Adds a variable description
applyDataSubset: Modify and apply data subsets
defaultDataSubset: Configure the global data subset attached to NONMEM problems...
getEstimateCov: Returns variance-covariance matrix, if available, from a...
getFileinfo: Various miscellaneous "getter"/extractor functions
getIterations: Extract parameter estimate iteration information from a given...
getMethodNames: Get method names
getNmFileExtensions: Gets allowed NONMEM file extensions
getNmPath: Gets a user defined path
getObjective: Retrieve objective function value
getOmegas: Retrieve OMEGA estimates, initial values of
getProblem: Extract an individual NONMEM problem
getSigmas: A generic function that extracts sigma estimates (and initial...
getSimInfo: Get Simulation Information.
getThetas: A generic function that extracts theta estimates (and initial...
getVarDescription: Gets a variable description
importNm: Import a NONMEM run
importNm7Tables: Import new NONMEM 7 table files
importNmInter: Import NONMEM "inter" file
importNmMod: Parse a NONMEM control file
importNmReport: Import the information in an output report file
imposeCategoryFormat: Forces the data in a NONMEM object to conform to the variable...
logging: Logging utilities
NMBasicModel-class: Standard/"basic" NONMEM individual problem
NMBasicModelNM7-class: Standard/"basic" NONMEM 7 individual problem
nmData: Extract input and / or output data tables from a NONMEM...
nmDatabyVarType: Get NONMEM data by variable type
nmModel-class: Auxilliary class for representing control file statements
NMProblem-class: Class "NMProblem"
NMRun-class: NONMEM run container class
nmRunReport-class: Auxilliary classes for representing report file statements
NMSimDataGen-class: Class for holding simulation problems that don't fit models
NMSimModel-class: Class "NMSimModel"
NMSimModelNM7-class: Class "NMSimModelNM7"
readNmData: Read NONMEM dataset removing any "IGNORE" rows and dealing...
removeNmPath: Removes a user specified path
runRNMImportTests: run package regression tests
setNmFileExtensions: file allowed file extensions
setNmPath: Stores a user specified path
setVarDescription: Sets new variable characteristics

Functions

CSLtoVector Source code
NMBasicModel Source code
NMBasicModel-class Man page
NMBasicModelNM7 Source code
NMBasicModelNM7-class Man page
NMProblem-class Man page
NMRun-class Man page
NMSimDataGen Source code
NMSimDataGen-class Man page
NMSimModel Source code
NMSimModel-class Man page
NMSimModelNM7 Source code
NMSimModelNM7-class Man page
RNMImportStop Source code
RNMImportStopifnot Source code
RNMImportWarning Source code
addDerivedCategorical Man page Source code
addDerivedCategorical,NMBasicModel-method Man page
addDerivedCategorical,NMBasicModelNM7-method Man page
addDerivedCategorical,NMRun-method Man page
addDerivedCategorical,NMSimDataGen-method Man page
addDerivedCategorical,NMSimModel-method Man page
addDerivedCategorical,NMSimModelNM7-method Man page
addDerivedCategorical.NMBasicModel Source code
addDerivedCategorical.NMRun Source code
addDerivedCategorical.NMSimDataGen Source code
addDerivedCategorical.NMSimModel Source code
addDerivedCategorical.data.frame Source code
addVarDescription Man page Source code
addedData Man page Source code
addedData,NMProblem-method Man page
addedData,NMRun-method Man page
addedData.NMProblem Source code
addedData.NMRun Source code
applyDataSubset Man page Source code
applySubsetOnLoad Source code
arrayFromMatrixList Source code
assertClass Source code
augmentDataSubset<- Man page
augmentDefaultDataSubset Man page Source code
availableLogs Man page Source code
block.parser Source code
blockBind Source code
bracketPop Source code
buildSymMatrix Source code
canOpen Source code
cleanReportContents Source code
closeLogConnection Man page Source code
colonPop Source code
commentPop Source code
commentSplit Source code
convertFortran95Ops Source code
convertNm Source code
convertNmFunctions Source code
convertNmOperators Source code
convertNmVariables Source code
dataSubset Man page Source code
dataSubset<- Man page
defaultDataSubset Man page Source code
deriveNmColumns Source code
dirname.abs Source code
equalExpressionPop Source code
extractBalanced Source code
extractInformation Source code
fortranPop Source code
getControlStatements Man page Source code
getControlStatements,NMProblem-method Man page
getControlStatements,NMRun-method Man page
getControlStatements.NMProblem Source code
getControlStatements.NMRun Source code
getControltext Man page Source code
getEstimateCov Man page Source code
getEstimateCov,NMBasicModel-method Man page
getEstimateCov,NMBasicModelNM7-method Man page
getEstimateCov,NMRun-method Man page
getEstimateCov.NMBasicModel Source code
getEstimateCov.NMBasicModelNM7 Source code
getEstimateCov.NMRun Source code
getFile Source code
getFileinfo Man page Source code
getIterations Man page Source code
getIterations,NMBasicModel-method Man page
getIterations,NMBasicModelNM7-method Man page
getIterations,NMRun-method Man page
getIterations.NMProb Source code
getIterations.NMRun Source code
getLogConfig Source code
getMethodNames Man page Source code
getMethodNames,NMBasicModelNM7-method Man page
getMethodNames,NMRun-method Man page
getMethodNames,NMSimModelNM7-method Man page
getMethodNames.NMProblemNM7 Source code
getMethodNames.NMRun Source code
getNmFileExtensions Man page Source code
getNmPath Man page Source code
getNmVersion Man page Source code
getNmVersion,NMProblem-method Man page
getNmVersion,NMRun-method Man page
getNmVersion.NMRunProb Source code
getObjective Man page Source code
getObjective,NMBasicModel-method Man page
getObjective,NMBasicModelNM7-method Man page
getObjective,NMRun-method Man page
getObjective,NMSimModel-method Man page
getObjective,NMSimModelNM7-method Man page
getObjective.NMBasicModel Source code
getObjective.NMBasicModelNM7 Source code
getObjective.NMRun Source code
getObjective.NMSimModel Source code
getObjective.NMSimModelNM7 Source code
getOmegas Man page Source code
getOmegas,NMBasicModel-method Man page
getOmegas,NMBasicModelNM7-method Man page
getOmegas,NMRun-method Man page
getOmegas,NMSimDataGen-method Man page
getOmegas,NMSimModel-method Man page Man page
getOmegas,NMSimModelNM7-method Man page
getOmegas,nmModel-method Man page
getOmegas.NMBasicModel Source code
getOmegas.NMBasicModelNM7 Source code
getOmegas.NMRun Source code
getOmegas.NMSimDataGen Source code
getOmegas.NMSimModel Source code
getOmegas.NMSimModelNM7 Source code
getOmegas.nmModel Source code
getProblem Man page Source code
getReporttext Man page Source code
getSigmas Man page Source code
getSigmas,NMBasicModel-method Man page
getSigmas,NMBasicModelNM7-method Man page
getSigmas,NMRun-method Man page
getSigmas,NMSimDataGen-method Man page
getSigmas,NMSimModel-method Man page Man page
getSigmas,NMSimModelNM7-method Man page
getSigmas,nmModel-method Man page
getSigmas.NMBasicModel Source code
getSigmas.NMBasicModelNM7 Source code
getSigmas.NMRun Source code
getSigmas.NMSimDataGen Source code
getSigmas.NMSimModel Source code
getSigmas.NMSimModelNM7 Source code
getSigmas.nmModel Source code
getSigmasOrOmegas.NM7 Source code
getSimInfo Man page Man page Source code
getSimInfo,NMRun-method Man page
getSimInfo,NMSimDataGen-method Man page
getSimInfo,NMSimModel-method Man page
getSimInfo,NMSimModelNM7-method Man page
getSimInfo.NMRun Source code
getSimInfo.NMSim Source code
getSubset Source code
getThetas Man page Source code
getThetas,NMBasicModel-method Man page Man page
getThetas,NMBasicModelNM7-method Man page
getThetas,NMRun-method Man page Man page
getThetas,NMSimDataGen-method Man page
getThetas,NMSimModel-method Man page Man page
getThetas,NMSimModelNM7-method Man page
getThetas,nmModel-method Man page
getThetas.NMBasicModel Source code
getThetas.NMBasicModelNM7 Source code
getThetas.NMRun Source code
getThetas.NMSimDataGen Source code
getThetas.NMSimModel Source code
getThetas.NMSimModelNM7 Source code
getThetas.nmModel Source code
getVarDescription Man page Source code
hasExtension Source code
importModelData Source code
importModelOutputTables Source code
importNm Man page Source code
importNm7Iterations Source code
importNm7Tables Man page Source code
importNmInter Man page Source code
importNmLstSimDataGen Source code
importNmLstSimModel Source code
importNmLstSimModel.NM7 Source code
importNmLstSimOnly.NM7 Source code
importNmMod Man page Source code
importNmReport Man page Source code
importNmReport.NM7 Source code
imposeCategoryFormat Man page Source code
imposeCategoryFormat,NMBasicModel-method Man page
imposeCategoryFormat,NMBasicModelNM7-method Man page
imposeCategoryFormat,NMRun-method Man page
imposeCategoryFormat,NMSimDataGen-method Man page
imposeCategoryFormat,NMSimModel-method Man page
imposeCategoryFormat,NMSimModelNM7-method Man page
imposeCategoryFormat.NMBasicModel Source code
imposeCategoryFormat.NMRun Source code
imposeCategoryFormat.NMSimDataGen Source code
imposeCategoryFormat.NMSimModel Source code
imposeCategoryFormat.data.frame Source code
initializeDataPath Source code
initializeFileNameExtensions Source code
initializeLogs Source code
initializeMiscOptions Source code
initializeSubsets Source code
initializeVariables Source code
insertSubscript Source code
killRegex Source code
logConnection Man page Source code
logMessage Man page Source code
logicalPop Source code
lookFor Source code
lseq Source code
makeMixNumColumn Source code
makeNewindColumn Source code
mergeMissing Source code
mportDataNumeric Source code
mportMethodBlock Source code
mportNmLstBasicProb Source code
mportNmLstBasicProb.NM7 Source code
mportNmLstEstimates Source code
mportNmLstIter Source code
mportNmLstMatrix Source code
mportNmLstVector Source code
mportNmLstWithCtl Source code
mportNmModData Source code
mportNmModEst Source code
mportNmModInput Source code
mportNmModOmega Source code
mportNmModPrior Source code
mportNmModSim Source code
mportNmModSingleProblem Source code
mportNmModSingleProblemNM7 Source code Source code
mportNmModSub Source code
mportNmModTables Source code
mportNmModTheta Source code
mportSubProb Source code
mportSubProbNM7 Source code
mportTablesSafely Source code
na.omit.NMProblem Source code
na.replace.NMProblem Source code
negGrep Source code
nmData Man page Source code
nmData,NMBasicModel-method Man page
nmData,NMBasicModelNM7-method Man page
nmData,NMRun-method Man page
nmData,NMSimDataGen-method Man page
nmData,NMSimModel-method Man page
nmData,NMSimModelNM7-method Man page
nmData.NMBasicModel Source code
nmData.NMRun Source code
nmData.NMSim Source code
nmDatabyVarType Man page Source code
nmDatabyVarType,NMProblem-method Man page
nmDatabyVarType,NMRun-method Man page
nmDatabyVarType.NMProblem Source code
nmDatabyVarType.NMRun Source code
nmMVOF Source code
nmModel-class Man page
nmRunReport-class Man page
nmTitle Source code
nmVariableNames Source code
nmVersion Source code
nonames Source code
nonames.default Source code
normalize.table.statements Source code
nullIfBlank Source code
ogrep Source code
onLoad Source code
partitionByProblem Source code
partitionLstSubproblems Source code
partitionMethods Source code
pop Source code
processPath Source code
readIterSection Source code
readNmData Man page Source code
readNmData.nmRecords Source code
readNmData.nmSubset Source code
readNmData.nmTranslate Source code
readValues Source code
rearrangeEstimates Source code
regexMatches Source code
regexSplit Source code
removeMethName Source code
removeNmPath Man page Source code
reportPartitionedByProblems Source code
rmSpaceInBrackets Source code
runRNMImportTests Man page Source code
scanFile Source code
section Source code
sectionLst Source code
sectionMethodBlock Source code
sectionStart Source code
sectionTitles Source code
selectMethod Source code
setDefaultDataSubset Man page Source code
setLogConnection Man page Source code
setLogFile Man page Source code
setNmFileExtensions Man page Source code
setNmPath Man page Source code
setVarDescription Man page Source code
sfullpath Source code
show,NMBasicModel-method Man page
show,NMBasicModelNM7-method Man page
show,NMRun-method Man page
show,NMSimDataGen-method Man page
show,NMSimModel-method Man page
show,NMSimModelNM7-method Man page
show.NMBasicModel Source code
show.NMBasicModelNM7 Source code
show.NMRun Source code
show.NMSimDataGen Source code
show.NMSimModel Source code
show.NMSimModelNM7 Source code
showOutput Source code
sinpath Source code
split.file.into Source code
splitVector Source code
stripBlanks Source code
validity.NMBasicModel Source code
validity.NMBasicModelNM7 Source code
validity.NMProblem Source code
validity.NMRun Source code Source code
validity.NMSimDataGen Source code
validity.NMSimModel Source code
validity.NMSimModelNM7 Source code
windowsToLower Source code
ynPop Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/CSLtoVector.R
R/NMBasicModelNM7_factory.R
R/NMBasicModel_factory.R
R/NMRun_class.R
R/NMSimDataGen_factory.R
R/NMSimModelNM7_factory.R
R/NMSimModel_factory.R
R/a_NMClasses.R
R/addedData.R
R/block.parser.R
R/blockBind.R
R/buildSymMatrix.R
R/convertFortran.R
R/covertNmCode.R
R/createCategorical.R
R/datamaniputils.R
R/deriveNmColumns.R
R/errorhandling.R
R/getIterations.R
R/getMethodNames.R
R/getOmegaSigma.R
R/getOmegas.R
R/getProblem.R
R/getSigmas.R
R/getThetas.R
R/importDataNumeric.R
R/importModelData.R
R/importModelOutputTables.R
R/importNM7Iterations.R
R/importNm.R
R/importNm7Table.R
R/importNmInter.R
R/importNmLst.R
R/importNmLstEstimates.R
R/importNmLstIter.R
R/importNmLstMatrix.R
R/importNmLstNM7.R
R/importNmLstVector.R
R/importNmMod.R
R/importNmModData.R
R/importNmModEst.R
R/importNmModInput.R
R/importNmModNM7.R
R/importNmModOmega.R
R/importNmModPrior.R
R/importNmModSim.R
R/importNmModSingleProblem.R
R/importNmModSingleProblemNM7.R
R/importNmModSub.R
R/importNmModTables.R
R/importNmModTheta.R
R/importutils.R
R/imposeCategoryFormat.R
R/logutils.R
R/lstparseutiles.R
R/nmData.R
R/nmDatabyVarType.R
R/nmfileextensions.R
R/nmmissing.R
R/nonames.R
R/normalize.table.statements.R
R/operators.R
R/packagemeta.R
R/parseutils.R
R/readNmData.R
R/retrieveMisc.R
R/runRNMImportTests.R
R/section.R
R/show_methods.R
R/subsetting.R
R/testutils.R
R/zzz.R
demo
demo/00Index
demo/ImportBasicRun.R
inst
inst/configdata
inst/configdata/NONMEM2_Variables.csv
inst/configdata/searchPatterns.R
inst/doc
inst/doc/Notes_on_RNMImport.R
inst/doc/Notes_on_RNMImport.Rnw
inst/doc/Notes_on_RNMImport.pdf
inst/doc/index.html
inst/examples
inst/examples/theoph
inst/examples/theoph/data.csv
inst/examples/theoph/theoph.con
inst/examples/theoph/theoph.lst
inst/examples/theoph/theoph.out
inst/unittests
inst/unittests/runit.blockBind.R
inst/unittests/runit.commentsplit.R
inst/unittests/runit.convertFortran.R
inst/unittests/runit.convertNm.R
inst/unittests/runit.createCategorical.R
inst/unittests/runit.errorfunctions.R
inst/unittests/runit.importMethodBlock.R
inst/unittests/runit.importModelData.R
inst/unittests/runit.importModelOutputTables.R
inst/unittests/runit.importNM7Iterations.R
inst/unittests/runit.importNm.R
inst/unittests/runit.importNm7Tables.R
inst/unittests/runit.importNmLstIter.R
inst/unittests/runit.importNmLstMatrix.R
inst/unittests/runit.importNmLstVector.R
inst/unittests/runit.importNmMod.R
inst/unittests/runit.importNmModData.R
inst/unittests/runit.importNmModEst.R
inst/unittests/runit.importNmModInput.R
inst/unittests/runit.importNmModOmega.R
inst/unittests/runit.importNmModPrior.R
inst/unittests/runit.importNmModSim.R
inst/unittests/runit.importNmModSub.R
inst/unittests/runit.importNmModTables.R
inst/unittests/runit.importNmModTheta.R
inst/unittests/runit.importNmReport.R
inst/unittests/runit.importutils.R
inst/unittests/runit.imposeCategoryFormat.R
inst/unittests/runit.logging.R
inst/unittests/runit.lstparseutils.R
inst/unittests/runit.nmData.R
inst/unittests/runit.normalize.table.statements.R
inst/unittests/runit.packagemeta.R
inst/unittests/runit.pop.R
inst/unittests/runit.readNmData.R
inst/unittests/runit.retrieveParameters.R
inst/unittests/runit.retrievemisc.R
inst/unittests/runit.section.R
inst/unittests/runit.show.R
inst/unittests/runit.subsetting.R
inst/unittests/testdata
inst/unittests/testdata/TestData1_stoptimefooter.lst
inst/unittests/testdata/TestDataNM7
inst/unittests/testdata/TestDataNM7/Data1
inst/unittests/testdata/TestDataNM7/TestData1.EXT
inst/unittests/testdata/TestDataNM7/TestData1.coi
inst/unittests/testdata/TestDataNM7/TestData1.cor
inst/unittests/testdata/TestDataNM7/TestData1.cov
inst/unittests/testdata/TestDataNM7/TestData1.ctl
inst/unittests/testdata/TestDataNM7/TestData1.lst
inst/unittests/testdata/TestDataNM7/TestData1.phi
inst/unittests/testdata/TestDataNM7/TestData1_2.EXT
inst/unittests/testdata/TestDataNM7/TestData1_missingtab.ctl
inst/unittests/testdata/TestDataNM7/extfile2_2.EXT
inst/unittests/testdata/TestDataNM7/tab1
inst/unittests/testdata/TestDataNM7/testdata1.MSF
inst/unittests/testdata/TestDataNM7/testdata1_ETAS.MSF
inst/unittests/testdata/TestNoSigMaxeval0
inst/unittests/testdata/TestNoSigMaxeval0/Test.ctl
inst/unittests/testdata/TestNoSigMaxeval0/Test.lst
inst/unittests/testdata/TestNoSigMaxeval0/input.tab
inst/unittests/testdata/TestRun
inst/unittests/testdata/TestRun/Data1
inst/unittests/testdata/TestRun/TestData1.ctl
inst/unittests/testdata/TestRun/TestData1.lst
inst/unittests/testdata/TestRun/TestData1_missingtab.ctl
inst/unittests/testdata/TestRun/catab1
inst/unittests/testdata/TestRun/cotab1
inst/unittests/testdata/TestRun/mutab1
inst/unittests/testdata/TestRun/mytab1
inst/unittests/testdata/TestRun/patab1
inst/unittests/testdata/TestRun/sdtab1
inst/unittests/testdata/TestRunNoTab
inst/unittests/testdata/TestRunNoTab/Data1
inst/unittests/testdata/TestRunNoTab/TestData1notab.ctl
inst/unittests/testdata/TestRunNoTab/TestData1notab.lst
inst/unittests/testdata/TestSimRun
inst/unittests/testdata/TestSimRun/Data1
inst/unittests/testdata/TestSimRun/TestData1SIM.con
inst/unittests/testdata/TestSimRun/TestData1SIM.lst
inst/unittests/testdata/TestSimRun/TestData1SIM_missingtab.con
inst/unittests/testdata/TestSimRun/catab1
inst/unittests/testdata/TestSimRun/cotab1
inst/unittests/testdata/TestSimRun/mutab1
inst/unittests/testdata/TestSimRun/mytab1
inst/unittests/testdata/TestSimRun/patab1
inst/unittests/testdata/TestSimRun/sdtab1
inst/unittests/testdata/control3.con
inst/unittests/testdata/control4.con
inst/unittests/testdata/data3
inst/unittests/testdata/data3.dat
inst/unittests/testdata/data4
inst/unittests/testdata/data4.dat
inst/unittests/testdata/data5.csv
inst/unittests/testdata/multiprob1.mod
inst/unittests/testdata/phenobarb.con
inst/unittests/testdata/simexampl.ctl
inst/unittests/testdata/subprob1.mod
inst/unittests/testdata/subsettest.csv
inst/unittests/testdata/tabletest2_1.TAB
inst/unittests/testdata/tabletest2_2.tab
inst/unittests/testdata/test.lst
inst/unittests/testdata/test_stoptimefooter.lst
inst/unittests/testdata/testtab.tab
man
man/NMBasicModel-class.Rd
man/NMBasicModelNM7-class.Rd
man/NMProblem-class.Rd
man/NMRun-class.Rd
man/NMSimDataGen-class.Rd
man/NMSimModel-class.Rd
man/NMSimModelNM7-class.Rd
man/addDerivedCategorical.Rd
man/addVarDescription.Rd
man/addedData.Rd
man/applyDataSubset.Rd
man/defaultDataSubset.Rd
man/getEstimateCov.Rd
man/getFileinfo.Rd
man/getIterations.Rd
man/getMethodNames.Rd
man/getNmFileExtensions.Rd
man/getNmPath.Rd
man/getObjective.Rd
man/getOmegas.Rd
man/getProblem.Rd
man/getSigmas.Rd
man/getSimInfo.Rd
man/getThetas.Rd
man/getVarDescription.Rd
man/importNm.Rd
man/importNm7Tables.Rd
man/importNmInter.Rd
man/importNmMod.Rd
man/importNmReport.Rd
man/imposeCategoryFormat.Rd
man/logging.Rd
man/nmData.Rd
man/nmDatabyVarType.Rd
man/nmModel-class.Rd
man/nmRunReport-class.Rd
man/readNmData.Rd
man/removeNmPath.Rd
man/runRNMImportTests.Rd
man/setNmFileExtensions.Rd
man/setNmPath.Rd
man/setVarDescription.Rd
RNMImport documentation built on May 21, 2017, 1:15 a.m.

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

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

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