Linear mixed-effects models using S4 classes

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

-- A --

anova,lme-method Class "lme"

-- B --

BIC Bayesian Information Criterion
BIC,logLik-method Bayesian Information Criterion

-- C --

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,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
corFactor Extract the correlation factor
corMatrix Generate the correlation matrix
corMatrix,pdMat-method Generate the correlation matrix
corrmatrix-class Class "corrmatrix"

-- D --

dim,pdMat-method Class pdMat, positive-definite matrices

-- E --

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

-- F --

family-class Class "family"
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 --

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
groupedData-class Class "groupedData"
guImmun Immunization in Guatemala
guPrenat Prenatal care in Guatemala

-- H --

Hsb82 High School and Beyond - 1982

-- I --

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-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 --

matrix<-,pdMat,matrix-method Assign the matrix
matrix<--methods Assign the matrix
model.matrix,reStruct-method Class "reStruct"
model.matrix<-,reStruct,matrix-method Assign the model.matrix
model.matrix<-,reStruct-method Class "reStruct"

-- 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"
nmGroupedData-class Class "nmGroupedData"

-- P --

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
plot,lme-method Class "lme"
plot,lmList-method Class "lmList"
pooledSD Extract pooled standard deviation
pooledSD,lmList-method Class "lmList"

-- R --

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
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,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
splitFormula Utilities for formulas
subFormula Utilities for formulas
summary,glmm-method Class "glmm"
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"

-- 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 --

weighted<-,reStruct,matrix-method Modify the weights
weighted<-,reStruct,numeric-method Class "reStruct"