_pkgdown.yml

template:
  params:
    bootswatch: flatly
reference:
- title: Interfacing nlmixr models
  contents:
  - '`nlmixr`'
- title: Adding residuals & covariance to fit object
  contents:
  - '`addCwres`'
  - '`addNpde`'
  - '`getVarCov`'
- title: Model diagnostics
  contents: 
  - '`vpc`'
  - '`traceplot`'
- title: Datasets
  contents:
  - '`Bolus_1CPTMM`'
  - '`Bolus_1CPT`'
  - '`Bolus_2CPTMM`'
  - '`Bolus_2CPT`'
  - '`Infusion_1CPT`'
  - '`Oral_1CPT`'
  - '`Wang2007`'
  - '`pump`'
  - '`rats`'
  - '`warfarin`'
- title: Options for fitting and output
  contents:
  - '`foceiControl`'
  - '`nlmeControl`'
  - '`nmDocx`'
  - '`nmSave`'
  - '`saemControl`'
  - '`tableControl`'
- title: Low level estimation routines
  contents:
  - '`as.dynmodel`'
  - '`as.focei.dynmodel`'
  - '`dynmodel.mcmc`'
  - '`dynmodelControl`'
  - '`dynmodel`'
  - '`foceiFit`'
  - '`gnlmm`'
  - '`nlme_lin_cmpt`'
  - '`nlme_ode`'
  - '`saem.fit`'
- title: Unit tests and validation functions
  contents:
  - '`nlmixrValidate`'
- title: Utilities
  contents:
  - '`bootplot`'
  - '`bootstrapFit`'
  - '`preCondInv`'
  - '`preconditionFit`'
- title: Covariate Search Functions
  contents:
  - '`addCovMultiple`'
  - '`addCovVar`'
  - '`addCovariate`'
  - '`backwardSearch`'
  - '`covarSearchAuto`'
  - '`forwardSearch`'
  - '`initializeCovars`'
  - '`makeDummies`'
  - '`makeHockeyStick`'
  - '`performNorm`'
  - '`removeCovMultiple`'
  - '`removeCovVar`'
  - '`removeCovariate`'
- title: ggplot2 functions
  contents:
  - '`stat_amt`'
  - '`stat_cens`'
- title: Internal functions
  contents:
  - '`VarCorr.nlmixrNlme`'
  - '`as.focei`'
  - '`bootdata`'
  - '`calc.2LL`'
  - '`calc.COV`'
  - '`calcCov`'
  - '`cholSE`'
  - '`configsaem`'
  - '`coxBox`'
  - '`focei.eta`'
  - '`focei.theta`'
  - '`frwd_selection`'
  - '`gauss.quad`'
  - '`gen_saem_user_fn`'
  - '`getOMEGA`'
  - '`ini`'
  - '`instant.stan.extension`'
  - '`invgaussian`'
  - '`lin_cmt`'
  - '`lincmt`'
  - '`metabolite`'
  - '`model`'
  - '`nlme_gof`'
  - '`nlmixrAugPred`'
  - '`nlmixrBounds.eta.names`'
  - '`nlmixrBounds.focei.upper.lower`'
  - '`nlmixrBoundsParser`'
  - '`nlmixrBounds`'
  - '`nlmixrDynmodelConvert`'
  - '`nlmixrEst`'
  - '`nlmixrEval_`'
  - '`nlmixrGill83`'
  - '`nlmixrHess`'
  - '`nlmixrLogo`'
  - '`nlmixrPred`'
  - '`nlmixrSim`'
  - '`nlmixrTest`'
  - '`nlmixrUI.dynmodelfun2`'
  - '`nlmixrUI.dynmodelfun`'
  - '`nlmixrUI.focei.fixed`'
  - '`nlmixrUI.focei.inits`'
  - '`nlmixrUI.nlme.specs`'
  - '`nlmixrUI.rxode.pred`'
  - '`nlmixrUI.saem.ares`'
  - '`nlmixrUI.saem.bres`'
  - '`nlmixrUI.saem.cres`'
  - '`nlmixrUI.saem.distribution`'
  - '`nlmixrUI.saem.eta.trans`'
  - '`nlmixrUI.saem.fit`'
  - '`nlmixrUI.saem.fixed`'
  - '`nlmixrUI.saem.init.omega`'
  - '`nlmixrUI.saem.init.theta`'
  - '`nlmixrUI.saem.init`'
  - '`nlmixrUI.saem.log.eta`'
  - '`nlmixrUI.saem.model.omega`'
  - '`nlmixrUI.saem.model`'
  - '`nlmixrUI.saem.res.mod`'
  - '`nlmixrUI.saem.res.name`'
  - '`nlmixrUI.saem.rx1`'
  - '`nlmixrUI.saem.theta.name`'
  - '`nlmixrUI.theta.pars`'
  - '`nlmixrVersion`'
  - '`nlmixr_fit`'
  - '`nlmixr`'
  - '`nmLst`'
  - '`nmsimplex`'
  - '`ofv`'
  - '`pheno_sd`'
  - '`plot.dyn.ID`'
  - '`plot.dyn.mcmc`'
  - '`plot.nlmixrFitData`'
  - '`plot.saemFit`'
  - '`prediction`'
  - '`print.dyn.ID`'
  - '`print.dyn.mcmc`'
  - '`print.gnlmm.fit`'
  - '`print.nlmixrUI`'
  - '`print.saemFit`'
  - '`residuals.nlmixrFitData`'
  - '`saem.cleanup`'
  - '`setCov`'
  - '`setOfv`'
  - '`sqrtm`'
  - '`summary.dyn.ID`'
  - '`summary.dyn.mcmc`'
  - '`summary.saemFit`'
  - '`theo_md`'
  - '`theo_sd`'
  - '`vpc_nlmixr_nlme`'
  - '`vpc_saemFit`'
  - '`vpc_ui`'
  - '`yeoJohnson`'
navbar:
  left:
  - text: Articles
    icon: fas fa-book
    menu:
        - text: "--------------------------"
        - text: "Getting started"
        - text: "Introduction to Running Nlmixr"
          href: articles/running_nlmixr.html
        - text: "Using Multiple Endpoints in Nlmixr"
          href: articles/multiple-endpoints.html
        - text: "--------------------------"
        - text: "Going further"
        - text: "Model Piping"
          href: articles/modelPiping.html
        - text: "Sweeping models to tidy datasets (broom)"
          href: articles/broom.html
        - text: "--------------------------"
        - text: "Integrated development with xgxr/nlmixr/ggPMX"
          href: articles/xgxr-nlmixr-ggpmx.html
  - text: Example models
    icon: fas fa-chalkboard-teacher
    menu:
        - text: "Phenobarbatol with correlations"
          href: articles/addingCovariances.html
        - text: "--------------------------"
        - text: "Nonlinear PK/PD -- Nimotuzumab"
          href: articles/nimo.html
        - text: "PBPK -- Mavoglurant"
          href: articles/mavoglurant.html
        - text: "PKPD -- Myelosuppression model"
          href: articles/wbc.html
  - text: "Cheat Sheet"
    icon: fa-scroll fa-lg
    href: https://github.com/nlmixrdevelopment/nlmixr/raw/master/CheatSheet_nlmixr.pdf
  - text: "Tutorial"
    icon: fas fa-life-ring
    href: https://doi.org/10.1002/psp4.12445
  - text: "Functions"
    icon: fa-file-code-o fa-lg
    href: reference/index.html
  right:
  - icon: fa-github fa-lg
    href: https://github.com/nlmixrdevelopment/nlmixr
  - icon: fa-download
    href: https://github.com/nlmixrdevelopment/nlmixr/releases