Stochastic Approximation Expectation Maximization (SAEM) Algorithm

Documentation for package ‘saemix’ version 2.3

DESCRIPTION file.

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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

-- 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 [<-