RNMImport: Tools for importing and manipulating NONMEM data.

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

Author
Mango Solutions <support@mango-solutions.com>
Date of publication
2014-08-15 07:48:35
Maintainer
Mango Solutions <support@mango-solutions.com>
License
Clear BSD + file LICENSE
Version
4.0-27

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

Files in this package

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