Linear mixed-effects models using S4 classes

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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
Chem97	Scores on A-level Chemistry in 1997
coef,GLMM-method	Class "GLMM"
coef,lme-method	Class "lme"
coef,lmList-method	Class "lmList"
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,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
Contraception	Contraceptive use in Bangladesh
convertFromS3groupedData	Creation of groupedData objects

-- D --

deviance,GLMM-method	Class "GLMM"
deviance,lme-method	Class "lme"
deviance,ssclme-method	Class "lme"
Dialyzer	High-Flux Hemodialyzer

-- E --

Earthquake	Earthquake Intensity
egsingle	US Sustaining Effects study
ergoStool	Ergometrics experiment with stool types
Exam	Exam scores from inner London

-- F --

Fatigue	Cracks caused by metal fatigue
fitted,lme-method	Class "lme"
fixed.effects	Extract Fixed Effects
fixef	Extract Fixed Effects
fixef,ANY-method	Extract Fixed Effects
fixef,GLMM-method	Class "GLMM"
fixef,lme-method	Extract Fixed Effects
fixef,ssclme-method	Extract Fixed Effects
formula,groupedData-method	Class "groupedData"
formula,lme-method	Class "lme"
formula,lmList-method	Class "lmList"

-- G --

Gasoline	Refinery yield of gasoline
Gcsemv	GCSE exam score
getCovariate	Utilities for formulas
getCovariateFormula	Utilities for formulas
getGroups	Utilities for formulas
getGroups,data.frame,formula-method	Utilities for formulas
getGroups,groupedData-method	Utilities for formulas
getGroupsFormula	Utilities for formulas
getGroupsFormula,ANY-method	Utilities for formulas
getResponse	Utilities for formulas
getResponseFormula	Utilities for formulas
GLMM	Fit Generalized Linear Mixed Models via PQL
GLMM,ANY,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,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,ANY,ANY-method	Fit Generalized Linear Mixed Models via PQL
GLMM-class	Class "GLMM"
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,lmList-method	Class "lmList"

-- L --

lme	Fit linear mixed-effects models
lme,ANY,ANY,formula-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,list-method	Fit linear mixed-effects models
lme,formula,groupedData,missing-method	Fit linear mixed-effects models
lme,missing,ANY,ANY-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
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"
logLik,GLMM-method	Class "GLMM"
logLik,lme-method	Class "lme"

-- M --

Machines	Productivity Scores for Machines and Workers
MathAchieve	Mathematics achievement scores
MathAchSchool	School demographic data for MathAchieve
Meat	Tenderness of meat
Milk	Protein content of cows' milk
Mmmec	Malignant melanoma deaths in Europe
Muscle	Contraction of heart muscle sections

-- N --

Names	Extract or assign Names
Names,ANY-method	Extract or assign Names
Names-methods	Extract or assign Names
Names<-,ANY-method	Extract or assign Names
Names<--methods	Extract or assign Names
Nitrendipene	Assay of nitrendipene

-- 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
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,GLMM-method	Class "GLMM"
ranef,lme-method	Class "lme"
ranef,reStruct-method	Extract Random Effects
ranef,ssclme-method	Class "lme"
ranef-methods	Extract Random Effects
RatPupWeight	The weight of rat pups
Relaxin	Assay for Relaxin
Remifentanil	Pharmacokinetics of remifentanil
residuals,lme-method	Class "lme"

-- 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,ssclme-method	Class "lme"
show,summary.GLMM-method	Class "summary.GLMM"
show,summary.lme-method	Class "summary.lme"
show,summary.ssclme-method	Class "summary.lme"
show,VarCorr-method	Class "VarCorr"
Socatt	Social Attitudes Survey
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,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,ssclme-method	Class "lme"
summary.GLMM-class	Class "summary.GLMM"
summary.lme-class	Class "summary.lme"
summary.ssclme-class	Class "summary.lme"

-- 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,lme-method	Class "lme"
VarCorr,ssclme-method	Class "lme"
VarCorr-class	Class "VarCorr"
vcov,lme-method	Class "lme"
vcov,ssclme-method	Class "lme"

-- W --

Wafer	Modeling of Analog MOS Circuits
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"