_pkgdown.yml

url: https://nlmixr2.github.io/rxode2/
template:
  bootstrap: 5
  params:
    bootswatch: flatly
  includes:
    in_header: |
      <meta name="google-site-verification" content="fp9A3qPrCar1DKeVQg4Mfrf6-An5keP9OwhIxUkntbU" />
reference:
- title: Creating/Deleting/Loading rxode2 compiled objects
  contents:
  - rxClean
  - rxCompile
  - rxCreateCache
  - rxDelete
  - rxUnloadAll
  - rxode2
- title: Creating rxode2 event tables/data frames
  contents:
  - et
  - toTrialDuration
  - etRbind
  - etRep
  - etSeq
  - etExpand
  - as.et
  - eventTable
  - add.dosing
  - add.sampling
- title: Solving, Simulating and Solving options
  contents:
  - rxSolve
  - rxCbindStudyIndividual
- title: Functions for working with nlmixr2/rxode2 functions
  contents:
  - as.ini
  - as.model
  - as.rxUi
  - assertCompartmentExists
  - assertCompartmentName
  - assertCompartmentNew
  - assertRxUi
  - assertVariableExists
  - assertVariableNew
  - ini
  - ini<-
  - model
  - model<-
  - modelExtract
  - rxAppendModel
  - rxFixPop
  - rxRename
  - rxSetCovariateNamesForPiping
  - rxSetPipingAuto
  - rxUiCompress
  - rxUiDecompress
  - rxode2<-
  - testIniDf
  - testRxLinCmt
  - testRxUnbounded
  - update.rxUi
  - zeroRe
- title: ggplot2/plot support functions
  contents:
  - stat_cens
  - stat_amt
  - plot.rxSolve
- title: Exploring rxode2 and creating models with Shiny
  contents:
  - rxShiny
  - genShinyApp.template
- title: Using rxode2 in Packages
  contents:
  - rxUse
  - rxPkg
- title: Specialized Simulation functions
  contents:
  - binomProbs
  - cvPost
  - dfWishart
  - meanProbs
  - rinvchisq
  - rxGetSeed
  - rxPp
  - rxSetSeed
  - rxSimThetaOmega
  - rxWithSeed
  - rxbeta
  - rxbinom
  - rxcauchy
  - rxchisq
  - rxexp
  - rxf
  - rxgamma
  - rxgeom
  - rxnbinom
  - rxnorm
  - rxord
  - rxpois
  - rxt
  - rxunif
  - rxweibull
- title: Optimizing models and/or adding precision
  contents:
  - rxOptExpr
  - rxSumProdModel
  - rxSetProd
  - rxSetSum
- title: Adding/Modifying rxode2 C-based functions and derivatives
  contents:
  - rxD
- title: Running unit tests in rxode2
  contents:
  - rxValidate
- title: Special Functions for rxode2
  contents:
    - boxCox
    - erf
    - forderForceBase
    - gammap
    - gammapDer
    - gammapInv
    - gammaq
    - gammaqInv
    - logit
    - lowergamma
    - phi
    - probit
    - rxRmvn
- title: log likelihood functions supporting generalized likelihoods for focei methods
  contents:
    - llikBeta
    - llikBinom
    - llikCauchy
    - llikChisq
    - llikExp
    - llikF
    - llikGamma
    - llikGeom
    - llikNbinom
    - llikNbinomMu
    - llikNorm
    - llikPois
    - llikT
    - llikUnif
    - llikWeibull
- title: Parallel processing support commands
  contents:
  -  getRxThreads
- title: rxode2 utility functions
  contents:
  - rxDerived
  - rxInv
  - rxIsCurrent
  - rxLhs
  - rxLock
  - rxNorm
  - rxParams
  - rxProgress
  - rxState
  - rxSymInvChol
  - swapMatListWithCube
  - uppergamma
- title: User functions
  contents:
  - linMod
  - rxIntToBase
  - rxIntToLetter
  - rxUdfUiControl
  - rxUdfUiData
  - rxUdfUiEst
  - rxUdfUiIniDf
  - rxUdfUiIniLhs
  - rxUdfUiMv
  - rxUdfUiNum
  - rxUdfUiParsing
- title: Internal Functions
  contents:
  - .cbindOme
  - .collectWarnings
  - .copyUi
  - .handleSingleErrTypeNormOrTFoceiBase
  - .matchesLangTemplate
  - .modelHandleModelLines
  - .quoteCallInfoLines
  - .rxLinCmtGen
  - .rxWithOptions
  - .rxWithWd
  - .rxode2ptrs
  - .toClassicEvid
  - .vecDf
  - invWR1d
  - is.rxStackData
  - odeMethodToInt
  - print.rxModelVars
  - rLKJ1
  - rxAllowUnload
  - rxAssignControlValue
  - rxAssignPtr
  - rxChain
  - rxControlUpdateSens
  - rxDfdy
  - rxEtDispatchSolve
  - rxEvid
  - rxFun
  - rxGetControl
  - rxGetLin
  - rxGetrxode2
  - rxHtml
  - rxIndLinState
  - rxIndLinStrategy
  - rxParseSuppressMsg
  - rxPreferredDistributionName
  - rxRateDur
  - rxRemoveControl
  - rxReservedKeywords
  - rxS
  - rxSetControl
  - rxSetIni0
  - rxSetProgressBar
  - rxStack
  - rxSupportedFuns
  - rxSuppressMsg
  - rxSyncOptions
  - rxSyntaxFunctions
  - rxTempDir
  - rxTheme
  - rxToSE
  - rxTrans
  - rxUiGet
  - rxode2parse
  - rxode2parseAssignTranslation
  - rxode2parseD
  - rxode2parseGetPackagesToLoad
  - rxode2parseGetPointerAssignment
  - rxode2parseGetTranslation
  - summary.rxode2
  - rxUiDeparse
- title: Neural Network Activation functions
  contents:
  - ELU
  - GELU
  - PReLU
  - ReLU
  - SELU
  - Swish
  - dELU
  - dGELU
  - dPReLU
  - dReLU
  - dSELU
  - dSwish
  - dlReLU
  - dsoftplus
  - lReLU
  - softplus
- title: Rxode2 data sets
  contents:
  - rxResidualError
navbar:
  left:
  - text: Articles
    icon: fas fa-book
    menu:
        - text: "--------------------------"
        - text: "Getting started"
        - text: "rxode2 mini language syntax"
          href: articles/rxode2-syntax.html
        - text: "rxode2 model modification %>%"
          href: articles/Modifying-Models.html
        - text: "rxode2 pipeline ie %>%"
          href: articles/rxode2-pipeline.html
        - text: "Speeding up rxode2 ODE solving"
          href: articles/rxode2-speed.html
        - text: "Adaptive Data Frames with rxode2"
          href: articles/rxode2-data-frame.html
        - text: "Plotting with rxode2"
          href: articles/rxode2-plot.html
        - text: "--------------------------"
        - text: "Advanced Features, Model Types, Technical Details"
        - text: "rxode2 model types"
          href: articles/rxode2-model-types.html
        - text: "Chainging rxode2 compartment numbers"
          href: articles/rxode2-cmt.html
        - text: "rxode2 transit compartment models"
          href: articles/rxode2-transit-compartments.html
        - text: "Using Shiny with rxode2"
          href: articles/rxode2-shiny.html
        - text: "rxode2 covariates"
          href: articles/rxode2-covariates.html
        - text: "Stiff Systems and Jacobian specification"
          href: articles/rxode2-stiff.html
        - text: "Adding compiled rxode2 models to your package"
          href: articles/rxode2-rxUse.html
  - text: "Dosing/Events"
    icon: fas fa-stethoscope
    menu:
        - text: "nlmixr/rxode2 dataset overview"
          href: articles/rxode2-datasets.html
        - text: "Supported Event Types"
          href: articles/rxode2-event-types.html
        - text: "Easy rxode2 Event Tables"
          href: articles/rxode2-event-table.html
        - text: "Classic rxode2 events explained"
          href: articles/rxode2-events-classic.html
  - text: "Simulations"
    icon: fas fa-desktop
    menu:
        - text: "Single Subject ODE solving"
          href: articles/rxode2-single-subject.html
        - text: "Multiple Subject rxode2 Simulation"
          href: articles/rxode2-sim-var.html
        - text: "Using Prior Data for ODE solving"
          href: articles/rxode2-prior-data.html
  - text: "Help"
    icon: fas fa-life-ring
    menu:
       - text: Running the interactive tutorials
         href: articles/rxode2-tutorials.html
       - text: 2015 CPT tutorial
         href: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728294/pdf/PSP4-5-03.pdf
       - text: "--------------------------"
       - text: Adding Circadian Rythmn (time-varying covariates)
         href: articles/rxode2-covariates.html
       - text: Weight Based Dosing
         href: articles/rxode2-wt.html
       - text: Simulating Multiple levels of nesting (iov, between study etc)
         href: articles/rxode2-nesting.html
       - text: "--------------------------"
       - text: Changes/News
         href: news/index.html
  - text: "Functions"
    icon: fa-file-code-o
    href: https://nlmixr2.github.io/rxode2/reference/index.html
  right:
  - icon: fas fa-archive
    menu:
      - text: rxode2 User Guide
        href: https://nlmixr2.github.io/rxode2-manual/
      - text: nlmixr2
        href: https://nlmixr2.org/
  - icon: fa-github
    href: https://github.com/nlmixr2/rxode2
  - icon: fa-download
    href: https://github.com/nlmixr2/rxode2/releases