PD1.saemix              Data simulated according to an Emax response
                        model, in SAEM format
SaemixData-class        Class "SaemixData"
SaemixModel-class       Class "SaemixModel"
SaemixObject-class      Class "SaemixObject"
SaemixRes-class         Class "SaemixRes"
[                       Get/set methods for SaemixData object
[,SaemixModel-method    Get/set methods for SaemixModel object
[,SaemixObject-method   Get/set methods for SaemixObject object
[,SaemixRes-method      Get/set methods for SaemixRes object
backward.procedure      Backward procedure for joint selection of
                        covariates and random effects
checkInitialFixedEffects
                        Check initial fixed effects for an SaemixModel
                        object applied to an SaemixData object
coef.saemix             Extract coefficients from an saemix fit
compare.saemix          Model comparison with information criteria
                        (AIC, BIC).
conddist.saemix         Estimate conditional mean and variance of
                        individual parameters using the MCMC algorithm
cow.saemix              Evolution of the weight of 560 cows, in SAEM
                        format
createSaemixObject      Create saemix objects with only data filled in
dataGen.case            Bootstrap datasets
default.saemix.plots    Wrapper functions to produce certain sets of
                        default plots
discreteVPC             VPC for non Gaussian data models
discreteVPCTTE          VPC for time-to-event models
epilepsy.saemix         Epilepsy count data
fim.saemix              Computes the Fisher Information Matrix by
                        linearisation
fitted.saemix           Extract Model Predictions
forward.procedure       Backward procedure for joint selection of
                        covariates and random effects
initialize-methods      Methods for Function initialize
knee.saemix             Knee pain data
llgq.saemix             Log-likelihood using Gaussian Quadrature
llis.saemix             Log-likelihood using Importance Sampling
logLik                  Extract likelihood from an SaemixObject
                        resulting from a call to saemix
lung.saemix             NCCTG Lung Cancer Data, in SAEM format
map.saemix              Estimates of the individual parameters
                        (conditional mode)
mydiag                  Matrix diagonal
npdeSaemix              Create an npdeObject from an saemixObject
oxboys.saemix           Heights of Boys in Oxford
plot,SaemixModel,ANY-method
                        Plot model predictions using an SaemixModel
                        object
plot,SaemixModel,SaemixData-method
                        Plot model predictions for a new dataset. If
                        the dataset is large, only the first 20
                        subjects (id's) will be shown.
plot,SaemixObject,ANY-method
                        General plot function from SAEM
plot-methods            Methods for Function plot
plot.SaemixData         Plot of longitudinal data
plotDiscreteData        Plot non Gaussian data
predict-methods         Methods for Function predict
predict.SaemixModel     Predictions for a new dataset
print-methods           Methods for Function print
psi-methods             Functions to extract the individual estimates
                        of the parameters and random effects
rapi.saemix             Rutgers Alcohol Problem Index
readSaemix,SaemixData-method
                        Create a longitudinal data structure from a
                        file or a dataframe Helper function not
                        intended to be called by the user
replaceData             Replace the data element in an SaemixObject
                        object
resid.saemix            Extract Model Residuals
saemix                  Stochastic Approximation Expectation
                        Maximization (SAEM) algorithm
saemix.bootstrap        Bootstrap for saemix fits
saemix.plot.data        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.predict          Compute model predictions after an saemix fit
saemixControl           List of options for running the algorithm SAEM
saemixData              Function to create an SaemixData object
saemixModel             Function to create an SaemixModel object
saemixPredictNewdata    Predictions for a new dataset
show-methods            Methods for Function show
showall-methods         Methods for Function showall
simulate.SaemixObject   Perform simulations under the model for an
                        saemixObject object
simulateDiscreteSaemix
                        Perform simulations under the model for an
                        saemixObject object defined by its
                        log-likelihood
step.saemix             Stepwise procedure for joint selection of
                        covariates and random effects
stepwise.procedure      Stepwise procedure for joint selection of
                        covariates and random effects
subset                  Data subsetting
summary-methods         Methods for Function summary
testnpde                Tests for normalised prediction distribution
                        errors
theo.saemix             Pharmacokinetics of theophylline
toenail.saemix          Toenail data
transform               Transform covariates
transformCatCov         Transform covariates
transformContCov        Transform covariates
validate.covariance.model
                        Validate the structure of the covariance model
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
xbinning                Internal functions used to produce prediction
                        intervals (from the npde package)
yield.saemix            Wheat yield in crops treated with fertiliser,
                        in SAEM format
