Numeric or logical (no character expressions are currently supported). Specifies the change of that variable with respect to timeĮxpressions in assignment and ‘ if’ statements can be Special “time-derivative” assignments, where the left hand Assignment statements can be either “simple”Īssignments, where the left hand is an identifier (i.e., variable), or Statements can be either assignments or conditional if NB: Comments are not allowedĪ block of statements is a set of statements delimited by Optional comments (comments are delimited by # and anĮnd-of-line marker). Statements terminated by semi-colons, ‘ ’, and Structure (closure) with various member functions (see SectionĪn RxODE model specification consists of one or more Produces an object of class RxODE which consists of a list-like Translates the ODE system into C, compiles it, and dynamically loads the An internal RxODE compilation manager object String or in a text file, see Section RxODE Syntax below forĬoding details. The ODE-based model specification may be coded inside a character Number of cores used in fitting (only for Linux) The maximum order to be allowed for the stiff (BDF) The maximum order to be allowed for the nonstiff Theĭefault value is determined by the solver (when hini = 0) The step size to be attempted on the first step. Hmax=NULL RxODE uses the maximum difference in times in Specified parameter and which defaults to zero. Hmax=NA (default), uses the average difference + Maximum number of (internally defined) steps allowedĭuring one call to the solver. This is also used in the solved linear model to check If prior doses do not add anything to the solution.Ī numeric relative tolerance ( 1e-6 by default) usedĪchieved. default is NULLĪ numeric absolute tolerance (1e-8 by default) usedīy the ODE solver to determine if a good solution has beenĪchieved This is also used in the solved linear model to check List: model for fixed effects, randoms effects and initial values. For details, see the sections “Details” and “ RxODE Syntax” below. Specification of fixed effects, random effects and initial values followsĪ string containing the set of ordinary differential equations (ODE) and other expressions defining the changes in the dynamic system. 'nlme_ode' fits a mixed-effect model described using ordinary differentialĮquation (ODEs). makeHockeyStick: Creating Hockey-stick covariatesįit nlme-based mixed-effect model using ODE implementation Description.makeDummies: Create categorical covariates.lin_cmt: concentrations from a linear compartment model.invgaussian: Inverse Guassian absorption model.initializeCovars: Initializing covariates before estimation.Infusion_1CPT: Infusion_1CPT - 1 Compartment Model Simulated Data from ACOP.gof: Plot of a non-population dynamic model fit.gnlmm: Fit a generalized nonlinear mixed-effect model.getOMEGA: Calculate gnlmm variance-covariance matrix of random effects.gen_saem_user_fn: Generate an SAEM model.gauss.quad: Sets nodes and weights of Gauss-Hermite quadrature.frwd_selection: Forward covariate selection for nlme-base non-linear mixed.forwardSearch: Forward covariate search.focei.theta: Get the FOCEi theta specification for the model.focei.eta: Get the FOCEi theta or eta specification for model.foceiControl: Control Options for FOCEi.dynmodel.mcmc: Fit a non-population dynamic model using mcmc.dynmodelControl: Control Options for dynmodel.dynmodel: Fit a non-population dynamic model.dot-nmGetData: This gets the parsed data in the lower-level manner that.covarSearchAuto: Stepwise Covariate Model-selection (SCM) method.cholSE: Generalized Cholesky Matrix Decomposition.calc.COV: Covariance matrix by Fisher Information Matrix via.calcCov: Calculate gnlmm variance-covariance matrix of fixed effects.calc.2LL: Log-likelihood using Gaussian Quadrature.boxCox: Cox Box, Yeo Johnson and inverse transformation.bootplot: Produce trace-plot for fit if applicable.Bolus_2CPTMM: 2 Compartment Model with Michaelis-Menten Clearance.Bolus_1CPTMM: 1 Compartment Model w/ Michaelis-Menten Elimination.Bolus_1CPT: Bolus_1CPT - 1 Compartment Model Simulated Data from ACOP.backwardSearch: Backward covariate search.as.saem: Return composite saem/focei to saem.as.nlme: Return composite nlme/focei to nlme.as.focei.dynmodel: Output nlmixr format for dynmodel.as.focei: Convert fit to FOCEi style fit.as.dynmodel: Convert fit to classic dynmodel object.addTable: Add table information to nlmixr fit object without tables.addCovVar: Adding covariate to a given variable in an nlmixr model.addCovMultiple: Add multiple covariates to a given model, sequentially or all.addCovariate: Add covariate expression to a function string.
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