RNMImport: Tools for importing and manipulating NONMEM data.

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

View on R-Forge

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

addDerivedCategorical Man page
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
addedData Man page
addedData,NMProblem-method Man page
addedData,NMRun-method Man page
addVarDescription Man page
applyDataSubset Man page
augmentDataSubset<- Man page
augmentDefaultDataSubset Man page
availableLogs Man page
closeLogConnection Man page
dataSubset Man page
dataSubset<- Man page
defaultDataSubset Man page
getControlStatements Man page
getControlStatements,NMProblem-method Man page
getControlStatements,NMRun-method Man page
getControltext Man page
getEstimateCov Man page
getEstimateCov,NMBasicModel-method Man page
getEstimateCov,NMBasicModelNM7-method Man page
getEstimateCov,NMRun-method Man page
getFileinfo Man page
getIterations Man page
getIterations,NMBasicModel-method Man page
getIterations,NMBasicModelNM7-method Man page
getIterations,NMRun-method Man page
getMethodNames Man page
getMethodNames,NMBasicModelNM7-method Man page
getMethodNames,NMRun-method Man page
getMethodNames,NMSimModelNM7-method Man page
getNmFileExtensions Man page
getNmPath Man page
getNmVersion Man page
getNmVersion,NMProblem-method Man page
getNmVersion,NMRun-method Man page
getObjective Man page
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
getOmegas Man page
getOmegas,NMBasicModel-method Man page
getOmegas,NMBasicModelNM7-method Man page
getOmegas,nmModel-method Man page
getOmegas,NMRun-method Man page
getOmegas,NMSimDataGen-method Man page
getOmegas,NMSimModel-method Man page
getOmegas,NMSimModel-method Man page
getOmegas,NMSimModelNM7-method Man page
getProblem Man page
getReporttext Man page
getSigmas Man page
getSigmas,NMBasicModel-method Man page
getSigmas,NMBasicModelNM7-method Man page
getSigmas,nmModel-method Man page
getSigmas,NMRun-method Man page
getSigmas,NMSimDataGen-method Man page
getSigmas,NMSimModel-method Man page
getSigmas,NMSimModel-method Man page
getSigmas,NMSimModelNM7-method Man page
getSimInfo Man page
getSimInfo Man page
getSimInfo,NMRun-method Man page
getSimInfo,NMSimDataGen-method Man page
getSimInfo,NMSimModel-method Man page
getSimInfo,NMSimModelNM7-method Man page
getThetas Man page
getThetas,NMBasicModel-method Man page
getThetas,NMBasicModel-method Man page
getThetas,NMBasicModelNM7-method Man page
getThetas,nmModel-method Man page
getThetas,NMRun-method Man page
getThetas,NMRun-method Man page
getThetas,NMSimDataGen-method Man page
getThetas,NMSimModel-method Man page
getThetas,NMSimModel-method Man page
getThetas,NMSimModelNM7-method Man page
getVarDescription Man page
importNm Man page
importNm7Tables Man page
importNmInter Man page
importNmMod Man page
importNmReport Man page
imposeCategoryFormat Man page
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
logConnection Man page
logMessage Man page
NMBasicModel-class Man page
NMBasicModelNM7-class Man page
nmData Man page
nmDatabyVarType Man page
nmDatabyVarType,NMProblem-method Man page
nmDatabyVarType,NMRun-method Man page
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
nmModel-class Man page
NMProblem-class Man page
NMRun-class Man page
nmRunReport-class Man page
NMSimDataGen-class Man page
NMSimModel-class Man page
NMSimModelNM7-class Man page
readNmData Man page
removeNmPath Man page
runRNMImportTests Man page
setDefaultDataSubset Man page
setLogConnection Man page
setLogFile Man page
setNmFileExtensions Man page
setNmPath Man page
setVarDescription Man page
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

Files

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

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.