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A B C D E F G I K L M N O P R S T V Y misc
| saemix-package | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| advanced.gof | Wrapper functions to produce certain sets of default plots |
| AIC.SaemixObject | Extract likelihood from a saemixObject resulting from a call to saemix |
| basic.gof | Wrapper functions to produce certain sets of default plots |
| BIC.SaemixObject | Extract likelihood from a saemixObject resulting from a call to saemix |
| coef | Extract coefficients from a saemix fit |
| coef.saemix | Extract coefficients from a saemix fit |
| coef.SaemixObject | Extract coefficients from a saemix fit |
| compute.eta.map | Functions implementing each type of plot in SAEM |
| compute.sres | Functions implementing each type of plot in SAEM |
| compute.Uy | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| conddist.saemix | Estimate conditional mean and variance of individual parameters using the MCMC algorithm |
| conditional.distribution | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| covariate.fits | Wrapper functions to produce certain sets of default plots |
| cow.saemix | Evolution of the weight of 560 cows, in SAEM format |
| cutoff | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| cutoff.eps | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| cutoff.max | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| cutoff.res | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| default.saemix.plots | Wrapper functions to produce certain sets of default plots |
| derivphi | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| dtransphi | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| error | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| estep | Stochastic Approximation Expectation Maximization (SAEM) algorithm |
| eta | Functions to extract the individual estimates of the parameters and random effects |
| eta-method | Functions to extract the individual estimates of the parameters and random effects |
| eta-methods | Functions to extract the individual estimates of the parameters and random effects |
| fim.saemix | Computes the Fisher Information Matrix by linearisation |
| fitted | Extract Model Predictions |
| fitted.saemix | Extract Model Predictions |
| fitted.SaemixObject | Extract Model Predictions |
| fitted.SaemixRes | Extract Model Predictions |
| gammarnd.mlx | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| ggq.mlx | Log-likelihood using Gaussian Quadrature |
| gqg.mlx | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| individual.fits | Wrapper functions to produce certain sets of default plots |
| initialiseMainAlgo | Stochastic Approximation Expectation Maximization (SAEM) algorithm |
| initialize-method | Methods for Function initialize |
| initialize-methods | Methods for Function initialize |
| kurtosis | Tests for normalised prediction distribution errors |
| llgq.saemix | Log-likelihood using Gaussian Quadrature |
| llis.saemix | Log-likelihood using Importance Sampling |
| llqg.saemix | Log-likelihood using Gaussian Quadrature |
| logLik | Extract likelihood from a saemixObject resulting from a call to saemix |
| logLik.SaemixObject | Extract likelihood from a saemixObject resulting from a call to saemix |
| map.saemix | Estimates of the individual parameters (conditional mode) |
| mstep | Stochastic Approximation Expectation Maximization (SAEM) algorithm |
| mydiag | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| normcdf | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| norminv | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| oxboys.saemix | Heights of Boys in Oxford |
| PD1.saemix | Data simulated according to an Emax response model, in SAEM format |
| PD2.saemix | Data simulated according to an Emax response model, in SAEM format |
| phi | Functions to extract the individual estimates of the parameters and random effects |
| phi-method | Functions to extract the individual estimates of the parameters and random effects |
| phi-methods | Functions to extract the individual estimates of the parameters and random effects |
| plot | General plot function from SAEM |
| plot,SaemixData-methods | Plot of longitudinal data |
| plot,SaemixModel-methods | Plot model predictions using an SaemixModel object |
| plot,SaemixObject | General plot function from SAEM |
| plot,SaemixSimData | Plot of longitudinal data |
| plot-method | Plot of longitudinal data |
| plot-method | General plot function from SAEM |
| plot-method | Methods for Function plot |
| plot-methods | Methods for Function plot |
| plot-SaemixData | Plot of longitudinal data |
| plot-SaemixModel | Plot model predictions using an SaemixModel object |
| plot.saemix | General plot function from SAEM |
| predict,SaemixObject | Class "SaemixObject" |
| predict-method | Methods for Function predict |
| predict-methods | Methods for Function predict |
| print,SaemixObject | Class "SaemixObject" |
| print-method | Methods for Function print |
| print-methods | Methods for Function print |
| print.saemix | Methods for Function print |
| psi | Functions to extract the individual estimates of the parameters and random effects |
| psi-method | Functions to extract the individual estimates of the parameters and random effects |
| psi-methods | Functions to extract the individual estimates of the parameters and random effects |
| replace.data.options | Function setting the default options for the plots in SAEM |
| replace.plot.options | Function setting the default options for the plots in SAEM |
| resid.saemix | Extract Model Residuals |
| resid.SaemixObject | Extract Model Residuals |
| resid.SaemixRes | Extract Model Residuals |
| residuals.SaemixRes | Extract Model Residuals |
| saemix | Stochastic Approximation Expectation Maximization (SAEM) algorithm |
| saemix.data.setoptions | Function setting the default options for the plots in SAEM |
| saemix.plot.convergence | Functions implementing each type of plot in SAEM |
| saemix.plot.correlations | Functions implementing each type of plot in SAEM |
| saemix.plot.data | Functions implementing each type of plot in SAEM |
| saemix.plot.distpsi | Functions implementing each type of plot in SAEM |
| saemix.plot.distribresiduals | Functions implementing each type of plot in SAEM |
| saemix.plot.fits | Functions implementing each type of plot in SAEM |
| saemix.plot.llis | Functions implementing each type of plot in SAEM |
| saemix.plot.npde | Functions implementing each type of plot in SAEM |
| saemix.plot.obsvspred | Functions implementing each type of plot in SAEM |
| saemix.plot.parcov | Functions implementing each type of plot in SAEM |
| saemix.plot.parcov.aux | Functions implementing each type of plot in SAEM |
| saemix.plot.randeff | Functions implementing each type of plot in SAEM |
| saemix.plot.randeffcov | Functions implementing each type of plot in SAEM |
| saemix.plot.scatterresiduals | Functions implementing each type of plot in SAEM |
| saemix.plot.select | Plots of the results obtained by SAEM |
| saemix.plot.setoptions | Function setting the default options for the plots in SAEM |
| saemix.plot.vpc | Functions implementing each type of plot in SAEM |
| saemix.predict | Compute model predictions after an saemix fit |
| saemixControl | List of options for running the algorithm SAEM |
| SaemixData | Class "SaemixData" |
| saemixData | Function to create a SaemixData object |
| SaemixData-class | Class "SaemixData" |
| SaemixModel | Class "SaemixModel" |
| saemixModel | Function to create a SaemixModel object |
| SaemixModel-class | Class "SaemixModel" |
| SaemixObject | Class "SaemixObject" |
| SaemixObject-class | Class "SaemixObject" |
| SaemixRepData-class | Class "SaemixData" |
| SaemixRes | Class "SaemixRes" |
| SaemixRes-class | Class "SaemixRes" |
| SaemixSimData-class | Class "SaemixData" |
| show,SaemixObject | Class "SaemixObject" |
| show-method | Methods for Function show |
| show-methods | Methods for Function show |
| showall | Methods for Function showall |
| showall,SaemixObject | Class "SaemixObject" |
| showall-method | Methods for Function showall |
| showall-methods | Methods for Function showall |
| simul.saemix | Perform simulations under the model |
| skewness | Tests for normalised prediction distribution errors |
| subset | Data subsetting |
| subset-methods | Data subsetting |
| subset.SaemixData | Data subsetting |
| summary | Methods for Function summary |
| summary,SaemixData | Methods for Function summary |
| summary,SaemixObject | Class "SaemixObject" |
| summary-method | Methods for Function summary |
| summary-methods | Methods for Function summary |
| testnpde | Tests for normalised prediction distribution errors |
| theo.saemix | Pharmacokinetics of theophylline, in SAEM format |
| tpdf.mlx | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| transform.SaemixData | Transform covariates |
| transformCatCov | Transform covariates |
| transformContCov | Transform covariates |
| transphi | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| transpsi | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| trnd.mlx | Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models |
| validate.names | Name validation (## )Helper function not intended to be called by the user) |
| vcov | Extracts the Variance-Covariance Matrix for a Fitted Model Object |
| vcov,SaemixObject | Extracts the Variance-Covariance Matrix for a Fitted Model Object |
| vcov.SaemixObject | Extracts the Variance-Covariance Matrix for a Fitted Model Object |
| vcov.SaemixRes | Extracts the Variance-Covariance Matrix for a Fitted Model Object |
| yield.saemix | Wheat yield in crops treated with fertiliser, in SAEM format |
| ##vcov,SaemixRes | Extracts the Variance-Covariance Matrix for a Fitted Model Object |
| [ | Get/set methods for SaemixData object |
| [-method | Get/set methods for SaemixData object |
| [-method | Get/set methods for SaemixModel object |
| [-method | Get/set methods for SaemixObject object |
| [-method | Get/set methods for SaemixRes object |
| [-methods | Methods for "get" Function [ |
| [<--method | Class "SaemixModel" |
| [<--method | Class "SaemixObject" |
| [<--method | Get/set methods for SaemixData object |
| [<--methods | Methods for "set" Function [<- |