Package: babelmixr2 0.1.12.9000

Matthew Fidler

babelmixr2: Use 'nlmixr2' to Interact with Open Source and Commercial Software

Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>) interface including 'PKNCA', 'NONMEM' and 'Monolix'. It also converts 'nlmixr2'/'rxode2' models to 'PopED' optimal design databases (Fidler et al (2024) <doi:10.70534/XUMG6226>). While not required, you can get/install the 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When 'lixoftConnectors' is available, 'Monolix' can be run directly instead of setting up command line usage.

Authors:Matthew Fidler [aut, cre], Bill Denney [aut], Theodoros Papathanasiou [ctb], Nook Fulloption [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
babelmixr2/json (API)

# Install 'babelmixr2' in R:
install.packages('babelmixr2', repos = c('https://nlmixr2.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nlmixr2/babelmixr2/issues

Pkgdown/docs site:https://nlmixr2.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

monolixnonmempharmacometricscpp

6.70 score 16 stars 125 scripts 752 downloads 157 exports 150 dependencies

Last updated from:e85ab2858b. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK443
linux-devel-x86_64OK531
source / vignettesOK291
linux-release-arm64OK456
linux-release-x86_64OK515
macos-release-arm64OK508
macos-release-x86_64OK671
macos-oldrel-arm64OK531
macos-oldrel-x86_64OK776
windows-devel-arm64OK571
windows-devel-x86_64OK660
windows-release-arm64OK618
windows-release-x86_64OK663
windows-oldrel-x86_64OK661
wasm-releaseOK247

Exports:.fmeMcmcF.minfo.nlmerCurrentFormula.nlmerNlmerFun.nlmixrNlmeFun.popedCluster.popedF.popedFree.popedRxRunSetup.popedSolveIdME.popedSolveIdME2.popedW.pseudoOptimF%>%ACFadd.dosingadd.samplingaddCwresaddNpdeaddTableas.monolixas.nlmixras.nlmixr2as.nonmemas.nonmem2rxaugPredbabel.poped.databasebabelBpopIdxbblDatToMonolixbblDatToMrgsolvebblDatToNonmembblDatToPkncabblDatToRxodebobyqaControlbootplotbootstrapFitetetExpandeventTableexpitfixed.effectsfixeffmeMcmcControlfoceiControlgeom_amtgeom_censgetDatagetStandardColNamesgetValidNlmixrCtlgetVarCovgroupedDatainiini<-iterPrintControllbfgsb3cControllogitlotrimlxtranmodelmodel<-modelUnitConversionmonolix2rxmonolixControln1qn1ControlnewuoaControlnlmControlnlmenlmeControlnlmerControlnlminbControlnlmixrnlmixr2nlmixr2AllEstnlmixr2Estnlmixr2NlmeControlnlmixr2NlmerControlnlsControlnmcovnmextnmGetDistributionMonolixLinesnmGetDistributionNonmemLinesnminfonmObjGetControlnmObjGetFoceiControlnmObjHandleControlObjectnmtabnmxmlnonmem2rxnonmemControloptimControlpdBlockedpdCompSymmpdConstructpdDiagpdFactorpdIdentpdLogCholpdMatpdMatrixpdNaturalpdSymmpkncaControlpopedControlpopedGetMultipleEndpointModelingTimespopedMultipleEndpointIndexDataFramepopedMultipleEndpointParampopedMultipleEndpointResetTimeIndexpreconditionFitprobitprobitInvprofileFixedprofileFixedSingleprofileLlppseudoOptimControlrandom.effectsranefreStructrxCatrxCleanrxControlrxDerivedrxFunrxModelVarsrxodeRxODErxode2rxParamrxParamsrxSetPipingAutorxSetSeedrxSolverxToMonolixrxToNonmemrxUiGetsaemControlsaemixControlsetOfvsimplifyUnitstat_amtstat_censtableControltraceplotuobyqaControlvarCombvarConstPowerVarCorrvarExpvarFixedvarFuncvarIdentvarPowervarWeightsvpcCensvpcCensTadvpcPlotvpcPlotTadvpcSim

Dependencies:armadillo4raskpassassertthatbackportsbase64encBHbinombitbit64bitopsbootbslibcachemcellrangercheckmateclassclicliprclustercolorspacecpp11cpp4rcrayoncurldata.tableDerivDescToolsdigestdparserdplyre1071evaluateExactexpmfarverfastmapfontawesomeforcatsforeignFormulafsgenericsggforceggplot2ggtibblegldgluegridExtragtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrinlineisobandjquerylibjsonliteknitrL0Learnlabelinglatticelbfgsb3clifecyclelmomlotrimagrittrMASSMatrixmemoisemimeminpack.lmminqamiraimonolix2rxmvtnormn1qn1nanonextnlmenlmixr2datanlmixr2estnlmixr2extranlmixr2plotnnetnonmem2rxnumDerivopensslpanderpillarpkgconfigplyrpngpolyclipPreciseSumsprettyunitsprogressproxypurrrqs2R6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRcppTrustRCurlreadrreadxlrematchreshape2rexrlangrmarkdownrootSolverpartrstudioapirxode2rxode2lincmtrxode2llS7sassscalessitmoStanHeadersstringfishstringistringrsymenginesyssystemfontstibbletidyrtidyselecttinytextweenrtzdbutf8vctrsviridisLitevroomwithrxfunxgxrxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Surrogate gradient function for lme4::nlmer.nlmerNlmerFun
Setup the poped database.setupPopEDdatabase
Convert an object to a nlmixr2 fit objectas.nlmixr as.nlmixr2
Convert an nlmixr2 model to a NONMEM control stream or Monolix projectas.monolix as.nonmem
Expand a babelmixr2 PopED databasebabel.poped.database
Get the bpop_idx by variable name for a poped database created by 'babelmixr2'babelBpopIdx
Convert nlmixr2-compatible data to other formats (if possible)bblDatToMonolix bblDatToMrgsolve bblDatToNonmem bblDatToPknca bblDatToRxode
Control for fmeMcmc estimation method in nlmixr2fmeMcmcControl
Determine standardized rxode2 column names from datagetStandardColNames
Unit conversion for pharmacokinetic modelsmodelUnitConversion
Monolix Controller for nlmixr2monolixControl
nlmixr2 estimation using lme4::nlmernlmixr2Est.nlmer
Estimate starting parameters using PKNCAnlmixr2Est.pknca
Control for nlmer estimation method in nlmixr2nlmerControl nlmixr2NlmerControl
NONMEM estimation controlnonmemControl
PKNCA estimation controlpkncaControl
Control for a PopED design taskpopedControl
Get Multiple Endpoint Modeling TimespopedGetMultipleEndpointModelingTimes popedMultipleEndpointIndexDataFrame
Reset the Global Time Indexer for Multiple Endpoint ModelingpopedMultipleEndpointResetTimeIndex
Control for fmeMcmc estimation method in nlmixr2pseudoOptimControl
Convert RxODE syntax to monolix syntaxrxToMonolix
Convert RxODE syntax to NONMEM syntaxrxToNonmem
Load pruned nlmer model into symengine (no sensitivity promotion)rxUiGet.loadPruneNlmer
Load pruned nlmer model into symengine (with sensitivity promotion)rxUiGet.loadPruneNlmerSens
Full nlmer symengine environment with sensitivitiesrxUiGet.nlmerEnv
Build the full 3-part nlmer formularxUiGet.nlmerFormula
Compute d(f)/d('THETA[i]') for all nlmer parametersrxUiGet.nlmerHdTheta
nlmer base model (saem-dropped etas, 'THETA[i]' prefix, nlme error lines)rxUiGet.nlmerModel0
params() string for the nlmer 'THETA[i]'-indexed modelrxUiGet.nlmerParams
Build the random-effects part (part 3) of the nlmer 3-part formularxUiGet.nlmerRandomFormula
Compiled nlmer sensitivity model (prediction + gradients)rxUiGet.nlmerSensModel
Starting values for nlmer fixed effectsrxUiGet.nlmerStart
Get the structural params to estimate for nlmer (= saemParamsToEstimate)rxUiGet.nlmerThetas
Compute d(state)/d('THETA[i]') sensitivities for nlmerrxUiGet.nlmerThetaS
Control for saemix estimation method in nlmixr2saemixControl
Simplify units by removing repeated units from the numerator and denominatorsimplifyUnit