Man pages for nlmixrdevelopment/nlmixr
Nonlinear Mixed Effects Models in Population PK/PD
| addCovariate | Add covariate expression to a function string |
| addCovMultiple | Add multiple covariates to a given model, sequentially or all... |
| addCovVar | Adding covariate to a given variable in an nlmixr model... |
| addCwres | Add CWRES |
| addNpde | NPDE calculation for nlmixr |
| addTable | Add table information to nlmixr fit object without tables |
| as.dynmodel | Convert fit to classic dynmodel object |
| as.focei | Convert fit to FOCEi style fit |
| as.focei.dynmodel | Output nlmixr format for dynmodel |
| as.nlme | Return composite nlme/focei to nlme |
| as.saem | Return composite saem/focei to saem |
| backwardSearch | Backward covariate search |
| Bolus_1CPT | Bolus_1CPT - 1 Compartment Model Simulated Data from ACOP... |
| Bolus_1CPTMM | 1 Compartment Model w/ Michaelis-Menten Elimination |
| Bolus_2CPT | 2 Compartment Model |
| Bolus_2CPTMM | 2 Compartment Model with Michaelis-Menten Clearance |
| bootdata | Bootstrap data |
| bootplot | Produce trace-plot for fit if applicable |
| bootstrapFit | Bootstrap nlmixr fit |
| boxCox | Cox Box, Yeo Johnson and inverse transformation |
| calc.2LL | Log-likelihood using Gaussian Quadrature |
| calcCov | Calculate gnlmm variance-covariance matrix of fixed effects |
| calc.COV | Covariance matrix by Fisher Information Matrix via... |
| cholSE | Generalized Cholesky Matrix Decomposition |
| configsaem | Configure an SAEM model |
| covarSearchAuto | Stepwise Covariate Model-selection (SCM) method |
| dot-nmGetData | This gets the parsed data in the lower-level manner that... |
| dynmodel | Fit a non-population dynamic model |
| dynmodelControl | Control Options for dynmodel |
| dynmodel.mcmc | Fit a non-population dynamic model using mcmc |
| foceiControl | Control Options for FOCEi |
| focei.eta | Get the FOCEi theta or eta specification for model. |
| foceiFit | FOCEi fit |
| foceiFitCpp_ | Fit/Evaulate FOCEi |
| focei.theta | Get the FOCEi theta specification for the model |
| forwardSearch | Forward covariate search |
| frwd_selection | Forward covariate selection for nlme-base non-linear mixed... |
| gauss.quad | Sets nodes and weights of Gauss-Hermite quadrature |
| gen_saem_user_fn | Generate an SAEM model |
| getOMEGA | Calculate gnlmm variance-covariance matrix of random effects |
| gnlmm | Fit a generalized nonlinear mixed-effect model |
| gof | Plot of a non-population dynamic model fit |
| Infusion_1CPT | Infusion_1CPT - 1 Compartment Model Simulated Data from ACOP... |
| ini | nlmixr ini block handling |
| initializeCovars | Initializing covariates before estimation |
| instant.stan.extension | instant.stan.extension. |
| invgaussian | Inverse Guassian absorption model |
| lin_cmt | concentrations from a linear compartment model |
| makeDummies | Create categorical covariates |
| makeHockeyStick | Creating Hockey-stick covariates |
| metabolite | Parent/Metabolite dataset |
| model | nlmixr model block |
| nlme_gof | GOF plots for nlme-based mixed-effect models |
| nlme_lin_cmpt | Fit nlme-based linear compartment mixed-effect model using... |
| nlmeModList | Access the model list information for nlmixr's nlme user... |
| nlme_ode | Fit nlme-based mixed-effect model using ODE implementation |
| nlmixr | nlmixr fits population PK and PKPD non-linear mixed effects... |
| nlmixrAugPred | Augmented Prediction for nlmixr fit |
| nlmixrBounds | Extract the nlmixr bound information from a function. |
| nlmixrBounds.eta.names | Get ETA names |
| nlmixrBounds.focei.upper.lower | Get upper/lower/names for THETAs |
| nlmixrBoundsParser | Functions to assist with setting initial conditions and... |
| nlmixrData | Convert/Format the data appropriately for nlmixr |
| nlmixrDynmodelConvert | Converting nlmixr objects to dynmodel objects |
| nlmixrEst | Generic for nlmixr estimation methods |
| nlmixrfindLhs | Find the assignments in R expression |
| nlmixr_fit | Fit a nlmixr model |
| nlmixrGill83 | Get the optimal forward difference interval by Gill83 method |
| nlmixrGradFun | Create a gradient function based on gill numerical... |
| nlmixrHess | Calculate Hessian |
| nlmixrLogo | Messages the nlmixr logo... |
| nlmixrPosthoc | Get a posthoc estimate of x |
| nlmixrPred | Predict a nlmixr solved system |
| nlmixrPrint | Print x using the message facility |
| nlmixrSim | Simulate a nlmixr solved system |
| nlmixrTest | nlmixTest function for testing |
| nlmixrUI | Prepares the UI function and returns a list. |
| nlmixrUI.dynmodelfun | Return dynmodel variable translation function |
| nlmixrUI.dynmodelfun2 | Return dynmodel variable translation function |
| nlmixrUI.focei.fixed | Get parameters that are fixed |
| nlmixrUI.focei.inits | Get the FOCEi initializations |
| nlmixrUI.nlmefun | Create the nlme parameter transform function from the UI... |
| nlmixrUI.nlme.specs | Create the nlme specs list for nlmixr nlme solving |
| nlmixrUI.nlme.var | Get the variance for the nlme fit process based on UI |
| nlmixrUI.rxode.pred | Return RxODE model with predictions appended |
| nlmixrUI.saem.ares | Get initial estimate for ares SAEM. |
| nlmixrUI.saem.bres | Get initial estimate for bres SAEM. |
| nlmixrUI.saem.cres | Get initial estimate for bres SAEM. |
| nlmixrUI.saem.distribution | Get SAEM distribution |
| nlmixrUI.saem.eta.trans | Get the eta->eta.trans for SAEM |
| nlmixrUI.saem.fit | Generate saem.fit user function. |
| nlmixrUI.saem.fixed | Get parameters that are fixed for SAEM |
| nlmixrUI.saem.init | Get saem initilization list |
| nlmixrUI.saem.init.omega | SAEM's init$omega |
| nlmixrUI.saem.init.theta | Generate SAEM initial estimates for THETA. |
| nlmixrUI.saem.log.eta | Get model$log.eta for SAEM |
| nlmixrUI.saem.model | Generate SAEM model list |
| nlmixrUI.saem.model.omega | Get the SAEM model Omega |
| nlmixrUI.saem.res.mod | Get the SAEM model$res.mod code |
| nlmixrUI.saem.res.name | Get error names for SAEM |
| nlmixrUI.saem.rx1 | Return RxODE model with predictions appended |
| nlmixrUI.saem.theta.name | Get THETA names for nlmixr's SAEM |
| nlmixrUI.theta.pars | Get the Parameter function with THETA/ETAs defined |
| nlmixrValidate | Validate nlmixr |
| nlmixrVersion | Display nlmixr's version |
| nmDataConvert | Convert data to RxODE format (depreciated) |
| nmDocx | Create a run summary word document |
| nmLst | Create a large output based on a nlmixr fit |
| nmsimplex | Nelder-Mead simplex search |
| ofv | Return the objective function |
| Oral_1CPT | Oral_1CPT - 1 Compartment Model with Oral Absorption... |
| performNorm | Perform normalization of the covariate |
| pheno_sd | Single Dose Phenobarbitol PK/PD |
| plot.dyn.mcmc | Plot of a non-population dynamic model fit using mcmc |
| plot.nlmixrFitData | Plot a nlmixr data object |
| plot.saemFit | Plot an SAEM model fit |
| preCondInv | Calculate the inverse preconditioning matrix |
| preconditionFit | Linearly re-parameterize the model to be less sensitive to... |
| prediction | Prediction after a gnlmm fit |
| print.dyn.ID | Print a non-population dynamic model fit object |
| print.dyn.mcmc | Print summary of a non-population dynamic model fit using... |
| print.gnlmm.fit | Print a gnlmm fit |
| print.nlmixrUI | Print UI function |
| print.saemFit | Print an SAEM model fit summary |
| pump | Pump failure example dataset |
| rats | Pregnant Rat Diet Experiment |
| reexports | Objects exported from other packages |
| removeCovariate | Remove covariate expression from a function string |
| removeCovMultiple | Removing multiple covariates |
| removeCovVar | Remove covariate from function string |
| residuals.nlmixrFitData | Extract residuals from the FOCEI fit |
| saemControl | Control Options for SAEM |
| saem.fit | Fit an SAEM model |
| setCov | Set the covariance type based on prior calculated covariances |
| setOfv | Set/get Objective function type for a nlmixr object |
| sqrtm | Return the square root of general square matrix A |
| summary.dyn.ID | Summary of a non-population dynamic model fit |
| summary.saemFit | Print an SAEM model fit summary |
| tableControl | Output table/data.frame options |
| theo_md | Multiple dose theophylline PK data |
| theo_sd | Multiple dose theophylline PK data |
| traceplot | Produce trace-plot for fit if applicable |
| VarCorr.nlmixrNlme | Return VarCorr for nlmixr nlme |
| vpc | Vpc function for nlmixr |
| vpc_nlmixr_nlme | Visual predictive check (VPC) for nlmixr nlme objects |
| vpc_saemFit | VPC for nlmixr saemFit objects |
| vpc_ui | VPC based on ui model |
| Wang2007 | Simulated Data Set for comparing objective functions |
| warfarin | Warfarin PK/PD data |
