# Stochastic Approximation Expectation Maximization (SAEM) Algorithm

## Documentation for package ‘saemix’ version 2.3

- DESCRIPTION file.

## Help Pages

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

## -- A --

advanced.gof | Wrapper functions to produce certain sets of default plots
AIC.SaemixObject | Extract likelihood from a saemixObject resulting from a call to saemix

## -- B --

basic.gof | Wrapper functions to produce certain sets of default plots
BIC.SaemixObject | Extract likelihood from a saemixObject resulting from a call to saemix

## -- C --

coef | Extract coefficients from a saemix fit
coef,SaemixObject | Extract coefficients from a saemix fit
coef-method | 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

## -- D --

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

## -- E --

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
eta.saemix | Functions to extract the individual estimates of the parameters and random effects
eta.SaemixObject | Functions to extract the individual estimates of the parameters and random effects

## -- F --

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

## -- G --

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

## -- I --

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

## -- K --

kurtosis | Tests for normalised prediction distribution errors

## -- L --

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

## -- M --

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

## -- N --

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

## -- O --

oxboys.saemix | Heights of Boys in Oxford

## -- P --

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
phi.saemix | Functions to extract the individual estimates of the parameters and random effects
phi.SaemixObject | Functions to extract the individual estimates of the parameters and random effects
plot | General plot function from SAEM
plot,SaemixData | Plot of longitudinal data
plot,SaemixData-methods | Plot of longitudinal data
plot,SaemixModel | Plot model predictions using an SaemixModel object
plot,SaemixModel-methods | Plot model predictions using an SaemixModel object
plot,SaemixObject | General plot function from SAEM
plot,SaemixRes | Class "SaemixRes"
plot,SaemixSimData | Plot of longitudinal data
plot-method | Plot of longitudinal data
plot-method | Plot model predictions using an SaemixModel object
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.saemix | General plot function from SAEM
plotnpde | General plot function from SAEM
predict,SaemixObject | Class "SaemixObject"
predict-method | Methods for Function predict
predict-methods | Methods for Function predict
print,SaemixData | Class "SaemixData"
print,SaemixModel | Class "SaemixModel"
print,SaemixObject | Class "SaemixObject"
print,SaemixRes | Class "SaemixRes"
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
psi.saemix | Functions to extract the individual estimates of the parameters and random effects
psi.SaemixObject | Functions to extract the individual estimates of the parameters and random effects

## -- R --

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 | Extract Model Residuals
resid.saemix | Extract Model Residuals
resid.SaemixObject | Extract Model Residuals
resid.SaemixRes | Extract Model Residuals
residuals | Extract Model Residuals
residuals.saemix | Extract Model Residuals
residuals.SaemixObject | Extract Model Residuals
residuals.SaemixRes | Extract Model Residuals

## -- S --

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 "SaemixData"
SaemixRepData-class | Class "SaemixData"
SaemixRes | Class "SaemixRes"
SaemixRes-class | Class "SaemixRes"
SaemixSimData | Class "SaemixData"
SaemixSimData-class | Class "SaemixData"
show,SaemixData | Class "SaemixData"
show,SaemixModel | Class "SaemixModel"
show,SaemixObject | Class "SaemixObject"
show,SaemixRes | Class "SaemixRes"
show-method | Methods for Function show
show-methods | Methods for Function show
showall | Methods for Function showall
showall,SaemixData | Class "SaemixData"
showall,SaemixModel | Class "SaemixModel"
showall,SaemixObject | Class "SaemixObject"
showall,SaemixRes | Class "SaemixRes"
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,SaemixModel | Class "SaemixModel"
summary,SaemixObject | Class "SaemixObject"
summary-method | Methods for Function summary
summary-methods | Methods for Function summary

## -- T --

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

## -- V --

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

## -- Y --

yield.saemix | Wheat yield in crops treated with fertiliser, in SAEM format

## -- misc --

##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 [<-