# Linear mixed-effects models using S4 classes

A B C D E F G H I L M N O P Q R S T U V W misc

$,groupedData-method | Class "groupedData"
$<-,groupedData-method | Class "groupedData"

## -- A --

Alfalfa | Split-Plot Experiment on Varieties of Alfalfa
anova,lme-method | Class "lme"
Assay | Bioassay on Cell Culture Plate

## -- B --

bdf | Language scores
BIC | Bayesian Information Criterion
BIC,logLik-method | Bayesian Information Criterion
BodyWeight | Rat weight over time for different diets

## -- C --

Cefamandole | Pharmacokinetics of Cefamandole
coef,lme-method | Class "lme"
coef,lmeLevel-method | Class "lmeLevel"
coef,lmList-method | Class "lmList"
coef,pdMat-method | Class pdMat, positive-definite matrices
coef,reStruct-method | Class "reStruct"
coef<-,lmeLevel,numeric-method | Assign parameters
coef<-,pdCompSymm,numeric-method | Assign parameters
coef<-,pdDiag,numeric-method | Assign parameters
coef<-,pdIdent,numeric-method | Assign parameters
coef<-,pdLogChol,numeric-method | Assign parameters
coef<-,pdNatural,numeric-method | Assign parameters
coef<-,reStruct,numeric-method | Assign parameters
coef<--methods | Assign parameters
coerce,groupedData,data.frame | Coercion methods and assignments
coerce,groupedData,data.frame-method | Class "groupedData"
coerce,lme,reStruct-method | Coercion methods and assignments
coerce,matrix,pdmatrix-method | Coercion methods and assignments
coerce,pdCompSymm,pdmatrix-method | Coercion methods and assignments
coerce,pdDiag,pdmatrix-method | Coercion methods and assignments
coerce,pdfactor,pdmatrix-method | Coercion methods and assignments
coerce,pdIdent,corrmatrix-method | Coercion methods and assignments
coerce,pdIdent,pdmatrix-method | Coercion methods and assignments
coerce,pdLogChol,pdmatrix-method | Coercion methods and assignments
coerce,pdMat,corrmatrix-method | Coercion methods and assignments
coerce,pdMat,matrix-method | Coercion methods and assignments
coerce,pdMat,pdfactor-method | Class pdMat, positive-definite matrices
coerce,pdmatrix,corrmatrix-method | Coercion methods and assignments
coerce,pdmatrix,pdfactor-method | Coercion methods and assignments
coerce,pdNatural,corrmatrix-method | Coercion methods and assignments
coerce,pdNatural,pdmatrix-method | Coercion methods and assignments
coerce-methods | Coercion methods and assignments
coerce<-,lme,reStruct-method | Coercion methods and assignments
coerce<-,pdDiag,pdmatrix-method | Coercion methods and assignments
coerce<-,pdIdent,pdmatrix-method | Coercion methods and assignments
coerce<-,pdLogChol,pdmatrix-method | Coercion methods and assignments
coerce<-,pdMat,matrix-method | Coercion methods and assignments
coerce<-,pdMat,pdfactor-method | Coercion methods and assignments
coerce<-,pdmatrix,pdfactor-method | Coercion methods and assignments
coerce<-,pdNatural,corrmatrix-method | Coercion methods and assignments
coerce<-,pdNatural,pdmatrix-method | Coercion methods and assignments
convertFromS3groupedData | Creation of groupedData objects
corFactor | Extract the correlation factor
corMatrix | Generate the correlation matrix
corMatrix,pdMat-method | Generate the correlation matrix
corrmatrix-class | Class "corrmatrix"

## -- D --

Dialyzer | High-Flux Hemodialyzer
dim,pdMat-method | Class pdMat, positive-definite matrices

## -- E --

Earthquake | Earthquake Intensity
EMsteps<-,reStruct,list-method | Perform EM iterations
EMupdate<-,lmeLevel,missing,matrix-method | Update an object in the EM algorithm
EMupdate<-,pdDiag,numeric,matrix-method | Update an object in the EM algorithm
EMupdate<-,pdIdent,numeric,matrix-method | Update an object in the EM algorithm
EMupdate<-,pdLogChol,numeric,matrix-method | Update an object in the EM algorithm
EMupdate<--methods | Update an object in the EM algorithm
ergoStool | Ergometrics experiment with stool types

## -- F --

family-class | Class "family"
Fatigue | Cracks caused by metal fatigue
fitted,lme-method | Class "lme"
fitted,reStruct-method | Class "reStruct"
fixed.effects | Extract Fixed Effects
fixef | Extract Fixed Effects
fixef,ANY-method | Extract Fixed Effects
fixef,lme-method | Class "lme"
fixef,reStruct-method | Extract Fixed Effects
fixef<-,glmm,numeric-method | Class "glmm"
fixef<-,reStruct,numeric-method | Class "reStruct"
formula,groupedData-method | Class "groupedData"
formula,lme-method | Class "lme"
formula,lmList-method | Class "lmList"
formula,pdMat-method | Class pdMat, positive-definite matrices

## -- G --

Gasoline | Refinery yield of gasoline
getCovariate | Utilities for formulas
getCovariateFormula | Utilities for formulas
getFixDF | Internal nlme functions
getFixDF,reStruct-method | Class "reStruct"
getGroups | Utilities for formulas
getGroups,data.frame,formula,ANY,ANY,ANY-method | Utilities for formulas
getGroups,reStruct,missing,ANY,missing,missing-method | Class "reStruct"
getGroupsFormula | Utilities for formulas
getGroupsFormula,ANY-method | Utilities for formulas
getResponse | Utilities for formulas
getResponse,glmm-method | Class "glmm"
getResponse,lme-method | Class "lme"
getResponse,reStruct-method | Class "reStruct"
getResponseFormula | Utilities for formulas
GLMM | Fit Generalized Linear Mixed Models via PQL
GLMM,ANY,ANY,missing,ANY-method | Fit Generalized Linear Mixed Models via PQL
GLMM,formula,ANY,ANY,formula-method | Fit Generalized Linear Mixed Models via PQL
GLMM,formula,ANY,ANY,list-method | Fit Generalized Linear Mixed Models via PQL
GLMM,formula,ANY,groupedData,missing-method | Fit Generalized Linear Mixed Models via PQL
GLMM,missing,ANY,groupedData,ANY-method | Fit Generalized Linear Mixed Models via PQL
glmm-class | Class "glmm"
glmmLa2LogLikComp | Internal nlme functions
glmmLa2RespWt | Internal nlme functions
glmmLa2Wt2 | Internal nlme functions
glmmStruct | Create a glmm object
glmmStruct,formula,list-method | Create a glmm object
Glucose | Glucose levels over time
Glucose2 | Glucose Levels Following Alcohol Ingestion
groupedData | Creation of groupedData objects
groupedData-class | Class "groupedData"
guImmun | Immunization in Guatemala
Gun | Methods for firing naval guns
guPrenat | Prenatal care in Guatemala

## -- H --

Hsb82 | High School and Beyond - 1982

## -- I --

IGF | Radioimmunoassay of IGF-I Protein
intervals | Confidence Intervals on Coefficients
intervals,lme-method | Class "lme"
intervals,lmList-method | Class "lmList"
isInitialized | Check for initialization
isInitialized,lmeLevelList-method | Check for initialization
isInitialized,pdBlocked-method | Check for initialization
isInitialized,pdCompSymm-method | Check for initialization
isInitialized,pdMat-method | Check for initialization
isInitialized,pdNatural-method | Check for initialization
isInitialized-methods | Check for initialization

## -- L --

lme | Fit linear mixed-effects models
lme,ANY,missing,ANY-method | Fit linear mixed-effects models
lme,formula,ANY,formula-method | Fit linear mixed-effects models
lme,formula,ANY,list-method | Fit linear mixed-effects models
lme,formula,data.frame,list-method | Fit linear mixed-effects models
lme,formula,groupedData,missing-method | Fit linear mixed-effects models
lme,missing,groupedData,ANY-method | Fit linear mixed-effects models
lme-class | Class "lme"
lmeControl | Control values for lme
LMEgradient | The gradient and Hessian in lme optimization-method
LMEgradient,lmeLevel,matrix,missing-method | The gradient and Hessian in lme optimization-method
LMEgradient,lmeLevel,missing,missing-method | The gradient and Hessian in lme optimization-method
LMEgradient,pdDiag,matrix,numeric-method | The gradient and Hessian in lme optimization-method
LMEgradient,pdIdent,matrix,numeric-method | The gradient and Hessian in lme optimization-method
LMEgradient,pdLogChol,matrix,numeric-method | The gradient and Hessian in lme optimization-method
LMEgradient,pdNatural,matrix,numeric-method | The gradient and Hessian in lme optimization-method
LMEgradient,reStruct,missing,missing-method | Class "reStruct"
LMEgradient-methods | The gradient and Hessian in lme optimization-method
LMEhessian | The gradient and Hessian in lme optimization-method
LMEhessian,lmeLevel,missing,missing,missing-method | The gradient and Hessian in lme optimization-method
LMEhessian,pdDiag,matrix,array,numeric-method | The gradient and Hessian in lme optimization-method
LMEhessian,pdLogChol,matrix,array,numeric-method | The gradient and Hessian in lme optimization-method
LMEhessian,reStruct,missing,missing,missing-method | The gradient and Hessian in lme optimization-method
LMEhessian-methods | The gradient and Hessian in lme optimization-method
lmeLevel | Construct an lmeLevel object
lmeLevel,missing,missing,integer,matrix-method | Construct an lmeLevel object
lmeLevel,pdMat,factor,integer,matrix-method | Construct an lmeLevel object
lmeLevel-class | Class "lmeLevel"
lmeLevelList-class | Some internal classes
LMEoptimize<-,glmm,list-method | Optimize linear mixed-effects
LMEoptimize<-,reStruct,list-method | Optimize linear mixed-effects
lmList | List of lm Objects with a Common Model
lmList,formula,data.frame-method | List of lm Objects with a Common Model
lmList,formula,groupedData-method | Class "groupedData"
lmList,missing,groupedData-method | Class "groupedData"
lmList-class | Class "lmList"
logDet | Logarithm of the determinant
logDet,pdBlocked,missing-method | Logarithm of the determinant
logDet,pdCompSymm,missing-method | Logarithm of the determinant
logDet,pdDiag,missing-method | Logarithm of the determinant
logDet,pdIdent,missing-method | Logarithm of the determinant
logDet,pdLogChol,missing-method | Logarithm of the determinant
logDet,pdMat-method | Logarithm of the determinant
logDet,pdNatural,missing-method | Logarithm of the determinant
logDet-methods | Logarithm of the determinant
logLik,glmm-method | Class "glmm"
logLik,lme-method | Class "lme"
logLik,reStruct-method | Class "reStruct"

## -- M --

Machines | Productivity Scores for Machines and Workers
MathAchieve | Mathematics achievement scores
MathAchSchool | School demographic data for MathAchieve
matrix<-,pdMat,matrix-method | Assign the matrix
matrix<--methods | Assign the matrix
Meat | Tenderness of meat
Milk | Protein content of cows' milk
model.matrix,reStruct-method | Class "reStruct"
model.matrix<-,reStruct,matrix-method | Assign the model.matrix
model.matrix<-,reStruct-method | Class "reStruct"
Muscle | Contraction of heart muscle sections

## -- N --

Names | Extract or assign Names
Names,ANY-method | Extract or assign Names
names,pdMat-method | Class pdMat, positive-definite matrices
Names-methods | Extract or assign Names
Names<-,ANY-method | Extract or assign Names
names<-,pdMat-method | Class pdMat, positive-definite matrices
Names<--methods | Extract or assign Names
nffGroupedData-class | Class "nffGroupedData"
nfGroupedData-class | Class "nfGroupedData"
nfnGroupedData-class | Class "nfnGroupedData"
Nitrendipene | Assay of nitrendipene
nmGroupedData-class | Class "nmGroupedData"

## -- O --

Oats | Split-plot Experiment on Varieties of Oats
Orthodont | Growth curve data on an orthdontic measurement
Ovary | Counts of Ovarian Follicles
Oxboys | Heights of Boys in Oxford
Oxide | Variability in Semiconductor Manufacturing

## -- P --

PBG | Effect of Phenylbiguanide on Blood Pressure
pdBlocked | Class "pdBlocked", blocked pd matrices
pdBlocked-class | Class "pdBlocked", blocked pd matrices
pdCompSymm | Class "pdCompSymm"
pdCompSymm,formula,missing,missing,missing-method | Class "pdCompSymm"
pdCompSymm-class | Class "pdCompSymm"
pdDiag | Class "pdDiag"
pdDiag,formula,missing,missing,missing-method | Class "pdDiag"
pdDiag-class | Class "pdDiag"
pdFactor | Square-root factor
pdFactor,pdMat-method | Square-root factor
pdfactor-class | Factors of positive-definite matrices
pdFactor-methods | Square-root factor
pdgradient | Evaluated the pdmatrix gradient
pdgradient,pdIdent-method | Evaluated the pdmatrix gradient
pdgradient,pdLogChol-method | Evaluated the pdmatrix gradient
pdgradient,pdMat-method | Evaluated the pdmatrix gradient
pdgradient-methods | Evaluated the pdmatrix gradient
pdgradNumeric | Evaluate the pdmatrix gradient numerically
pdIdent | Class "pdIdent"
pdIdent,formula,missing,missing,missing-method | Class "pdIdent"
pdIdent-class | Class "pdIdent"
pdLogChol | Class "pdLogChol", positive-definite matrices
pdLogChol,formula,missing,missing,missing-method | Class "pdLogChol", positive-definite matrices
pdLogChol-class | Class "pdLogChol", positive-definite matrices
pdMat-class | Class pdMat, positive-definite matrices
pdMatrix | Return the positive-definite matrix
pdMatrix,pdMat-method | Return the positive-definite matrix
pdmatrix-class | Positive-definite matrices
pdMatrix-methods | Return the positive-definite matrix
pdNatural | Class "pdNatural", positive-definite matrices
pdNatural,formula,missing,missing,missing-method | Class "pdNatural", positive-definite matrices
pdNatural,pdMat,missing,missing,missing-method | Class "pdNatural", positive-definite matrices
pdNatural-class | Class "pdNatural", positive-definite matrices
Phenobarb | Phenobarbitol Kinetics
Pixel | X-ray pixel intensities over time
plot,groupedData,missing-method | Class "groupedData"
plot,lme-method | Class "lme"
plot,lmList-method | Class "lmList"
pooledSD | Extract pooled standard deviation
pooledSD,lmList-method | Class "lmList"

## -- Q --

Quinidine | Quinidine Kinetics

## -- R --

Rail | Evaluation of Stress in Railway Rails
random.effects | Extract Random Effects
ranef | Extract Random Effects
ranef,ANY-method | Extract Random Effects
ranef,lme-method | Class "lme"
ranef,reStruct-method | Extract Random Effects
ranef-methods | Extract Random Effects
RatPupWeight | The weight of rat pups
Relaxin | Assay for Relaxin
Remifentanil | Pharmacokinetics of remifentanil
residuals,lme-method | Class "lme"
response<-,reStruct,matrix-method | Modify the response
response<-,reStruct,numeric-method | Class "reStruct"
reStruct | Create an reStruct object
reStruct,formula,list,data.frame,missing,logical-method | Create an reStruct object
reStruct,formula,list,data.frame,numeric,logical-method | Create an reStruct object
reStruct-class | Class "reStruct"

## -- S --

s3bbx | Covariates in the Rodriguez and Goldman simulation
s3bby | Responses simulated by Rodriguez and Goldman
show,glmm-method | Class "glmm"
show,groupedData-method | Class "groupedData"
show,lme-method | Class "lme"
show,lmList-method | Class "lmList"
show,pdMat-method | Class pdMat, positive-definite matrices
show,summary.glmm-method | Some internal classes
show,summary.lme-method | Some internal classes
show,summary.reStruct-method | Class "summary.reStruct"
show,VarCorr-method | Class "VarCorr"
solve,pdBlocked,missing-method | Methods for Function solve
solve,pdDiag,missing-method | Methods for Function solve
solve,pdIdent,missing-method | Methods for Function solve
solve,pdLogChol,missing-method | Methods for Function solve
solve,pdMat,missing-method | Methods for Function solve
solve,pdMat-method | Class pdMat, positive-definite matrices
solve,pdNatural,missing-method | Methods for Function solve
solve-methods | Methods for Function solve
Soybean | Growth of soybean plants
splitFormula | Utilities for formulas
Spruce | Growth of Spruce Trees
subFormula | Utilities for formulas
summary,glmm-method | Class "glmm"
summary,groupedData-method | Class "groupedData"
summary,lme-method | Class "lme"
summary,pdMat-method | Class pdMat, positive-definite matrices
summary,reStruct-method | Class "reStruct"
summary.glmm-class | Some internal classes
summary.lme-class | Some internal classes
summary.pdMat-class | Some internal classes
summary.reStruct-class | Class "summary.reStruct"

## -- T --

Tetracycline1 | Pharmacokinetics of tetracycline
Tetracycline2 | Pharmacokinetics of tetracycline

## -- U --

update,lme-method | Class "lme"
update,lmList-method | Class "lmList"

## -- V --

VarCorr | Extract variance and correlation components
VarCorr,glmm-method | Class "glmm"
VarCorr,lme-method | Class "lme"
VarCorr,reStruct-method | Class "reStruct"
VarCorr-class | Class "VarCorr"

## -- W --

Wafer | Modeling of Analog MOS Circuits
weighted<-,reStruct,matrix-method | Modify the weights
weighted<-,reStruct,numeric-method | Class "reStruct"
Wheat | Yields by growing conditions
Wheat2 | Wheat Yield Trials

## -- misc --

[,groupedData,ANY,ANY,logical-method | Class "groupedData"
[,groupedData,ANY,ANY,missing-method | Class "groupedData"
[,groupedData,ANY,missing,logical-method | Class "groupedData"
[,groupedData,ANY,missing,missing-method | Class "groupedData"
[,groupedData,missing,ANY,logical-method | Class "groupedData"
[,groupedData,missing,ANY,missing-method | Class "groupedData"
[<-,groupedData,ANY,ANY-method | Class "groupedData"
[<-,groupedData,ANY,missing-method | Class "groupedData"
[<-,groupedData,missing-method | Class "groupedData"
[[,groupedData,ANY,ANY-method | Class "groupedData"
[[,groupedData,ANY,missing-method | Class "groupedData"