Stochastic Approximation Expectation Maximization (SAEM) algorithm


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Documentation for package ‘saemix’ version 0.96.1

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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

-- M --

map.saemix Estimates of the individual parameters (conditional mode)

-- 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-method Class "SaemixData"

-- S --

saemix Stochastic Approximation Expectation Maximization (SAEM) algorithm
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
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 [<-