Stochastic Approximation Expectation Maximization (SAEM) algorithm

Documentation for package ‘saemix’ version 1.2

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A B C D E F G I K L M N O P R S T 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

-- B --

basic.gof

Wrapper functions to produce certain sets of default plots

-- C --

coef,SaemixObject	Class "SaemixObject"
coef-method	Class "SaemixObject"
coef-method	Methods for Function coef
coef-methods	Methods for Function coef
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
eta	Functions to extract the individual estimates of the parameters and random effects
eta-method	Methods for Functions psi, phi and eta
eta-methods	Methods for Functions psi, phi and eta

-- F --

fim.saemix

Computes the Fisher Information Matrix by linearisation

-- G --

gammarnd.mlx	Stochastic Approximation Expectation Maximization (SAEM) algorithm for non-linear mixed effects models
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
initialize-method	Class "SaemixData"
initialize-method	Class "SaemixModel"
initialize-method	Class "SaemixObject"
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
logLik-method	~~ Methods for Function 'logLik' ~~
logLik-methods	~~ Methods for Function 'logLik' ~~

-- M --

map.saemix	Estimates of the individual parameters (conditional mode)
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	Methods for Functions psi, phi and eta
phi-methods	Methods for Functions psi, phi and eta
plot	General plot function from SAEM
plot,SaemixData	Class "SaemixData"
plot,SaemixModel	Class "SaemixModel"
plot,SaemixObject	General plot function from SAEM
plot-method	Class "SaemixData"
plot-method	Class "SaemixModel"
plot-method	Class "SaemixObject"
plot-method	Methods for Function plot
plot-methods	Methods for Function plot
plot.saemix	General plot function from SAEM
predict,SaemixObject	Class "SaemixObject"
predict-method	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 "SaemixObject"
print-method	Class "SaemixData"
print-method	Class "SaemixModel"
print-method	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	Methods for Functions psi, phi and eta
psi-methods	Methods for Functions psi, phi and eta

-- R --

read.saemixData	Class "SaemixData"
read.saemixData-method	Class "SaemixData"
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

-- 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
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 "SaemixObject"
SaemixRes-class	Class "SaemixObject"
SaemixSimData	Class "SaemixData"
SaemixSimData-class	Class "SaemixData"
show,SaemixData	Class "SaemixData"
show,SaemixModel	Class "SaemixModel"
show,SaemixObject	Class "SaemixObject"
show,SaemixRes	Class "SaemixObject"
show-method	Class "SaemixData"
show-method	Class "SaemixModel"
show-method	Class "SaemixObject"
show-methods	Methods for Function show
showall	Prints out an extensive summary of an object
showall,SaemixData	Class "SaemixData"
showall,SaemixModel	Class "SaemixModel"
showall,SaemixObject	Class "SaemixObject"
showall,SaemixRes	Class "SaemixObject"
showall-method	Class "SaemixData"
showall-method	Class "SaemixModel"
showall-method	Class "SaemixObject"
showall-methods	Methods for Function showall
simul.saemix	Perform simulations under the model
skewness	Tests for normalised prediction distribution errors
subset-method	Methods for subset
subset-methods	Methods for subset
subset.SaemixData	Methods for subset
summary,SaemixData	Class "SaemixData"
summary,SaemixModel	Class "SaemixModel"
summary,SaemixObject	Class "SaemixObject"
summary-method	Class "SaemixData"
summary-method	Class "SaemixModel"
summary-method	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
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

-- Y --

yield.saemix

Wheat yield in crops treated with fertiliser, in SAEM format

-- misc --

[-method	Class "SaemixData"
[-method	Class "SaemixModel"
[-method	Class "SaemixObject"
[-methods	Methods for "get" Function [
[<--method	Class "SaemixData"
[<--method	Class "SaemixModel"
[<--method	Class "SaemixObject"
[<--methods	Methods for "set" Function [<-