Entry: BIC
Aliases: BIC BIC,logLik-method
Keywords: models
Description: Bayesian Information Criterion
URL: ../../../library/lme4/html/BIC.html

Entry: coefGets
Aliases: coef<- coef<--methods coef<-,lmeLevel,numeric-method coef<-,pdCompSymm,numeric-method coef<-,pdDiag,numeric-method coef<-,pdIdent,numeric-method coef<-,pdLogChol,numeric-method coef<-,pdNatural,numeric-method coef<-,reStruct,numeric-method
Keywords: manip
Description: Assign parameters
URL: ../../../library/lme4/html/coefGets.html

Entry: coerce-methods
Aliases: coerce-methods coerce,lme,reStruct-method coerce,matrix,pdmatrix-method coerce,pdCompSymm,pdmatrix-method coerce,pdDiag,pdmatrix-method coerce,pdIdent,corrmatrix-method coerce,pdIdent,pdmatrix-method coerce,pdLogChol,pdmatrix-method coerce,pdMat,corrmatrix-method coerce,pdMat,matrix-method coerce,pdNatural,corrmatrix-method coerce,pdNatural,pdmatrix-method coerce,pdfactor,pdmatrix-method coerce,pdmatrix,corrmatrix-method coerce,pdmatrix,pdfactor-method coerce<-,lme,reStruct-method coerce<-,pdDiag,pdmatrix-method coerce<-,pdIdent,pdmatrix-method coerce<-,pdLogChol,pdmatrix-method coerce<-,pdMat,matrix-method coerce<-,pdMat,pdfactor-method coerce<-,pdNatural,corrmatrix-method coerce<-,pdNatural,pdmatrix-method coerce<-,pdmatrix,pdfactor-method
Keywords: manip methods
Description: Coercion methods and assignments
URL: ../../../library/lme4/html/coerce-methods.html

Entry: corFactor
Aliases: corFactor
Keywords: models
Description: Extract the correlation factor
URL: ../../../library/lme4/html/corFactor.html

Entry: corMatrix
Aliases: corMatrix corMatrix,pdMat-method
Keywords: models
Description: Generate the correlation matrix
URL: ../../../library/lme4/html/corMatrix.html

Entry: corrmatrix-class
Aliases: corrmatrix-class
Keywords: classes
Description: Class "corrmatrix"
URL: ../../../library/lme4/html/corrmatrix-class.html

Entry: EMstepsGets
Aliases: EMsteps<- EMsteps<-,reStruct,list-method
Keywords: models
Description: Perform EM iterations
URL: ../../../library/lme4/html/EMstepsGets.html

Entry: EMupdateGets
Aliases: EMupdate<- EMupdate<--methods EMupdate<-,pdDiag,numeric,matrix-method EMupdate<-,pdIdent,numeric,matrix-method EMupdate<-,pdLogChol,numeric,matrix-method EMupdate<-,lmeLevel,missing,matrix-method
Keywords: models
Description: Update an object in the EM algorithm
URL: ../../../library/lme4/html/EMupdateGets.html

Entry: family-class
Aliases: family-class
Keywords: classes
Description: Class "family"
URL: ../../../library/lme4/html/family-class.html

Entry: fixed.effects
Aliases: fixed.effects fixef fixef<- fixef,ANY-method fixef,reStruct-method
Keywords: models
Description: Extract Fixed Effects
URL: ../../../library/lme4/html/fixed.effects.html

Entry: formulas
Aliases: getCovariate getCovariateFormula getGroups getGroups,data.frame,formula,ANY,ANY,ANY-method getGroupsFormula getGroupsFormula,ANY-method getResponse getResponseFormula subFormula splitFormula
Keywords: models
Description: Utilities for formulas
URL: ../../../library/lme4/html/formulas.html

Entry: glmm-class
Aliases: glmm-class VarCorr,glmm-method fixef<-,glmm,numeric-method getResponse,glmm-method logLik,glmm-method show,glmm-method summary,glmm-method
Keywords: classes
Description: Class "glmm"
URL: ../../../library/lme4/html/glmm-class.html

Entry: GLMM
Aliases: GLMM GLMM,ANY,ANY,missing,ANY-method GLMM,missing,ANY,groupedData,ANY-method GLMM,formula,ANY,groupedData,missing-method GLMM,formula,ANY,ANY,formula-method GLMM,formula,ANY,ANY,list-method
Keywords: models
Description: Fit Generalized Linear Mixed Models via PQL
URL: ../../../library/lme4/html/GLMM.html

Entry: glmmStruct
Aliases: glmmStruct glmmStruct,formula,list-method
Keywords: models
Description: Create a glmm object
URL: ../../../library/lme4/html/glmmStruct.html

Entry: groupedData-class
Aliases: groupedData-class formula,groupedData-method
Keywords: classes
Description: Class "groupedData"
URL: ../../../library/lme4/html/groupedData-class.html

Entry: guImmun
Aliases: guImmun
Keywords: datasets
Description: Immunization in Guatemala
URL: ../../../library/lme4/html/guImmun.html

Entry: guPrenat
Aliases: guPrenat
Keywords: datasets
Description: Prenatal care in Guatemala
URL: ../../../library/lme4/html/guPrenat.html

Entry: Hsb82
Aliases: Hsb82
Keywords: datasets
Description: High School and Beyond - 1982
URL: ../../../library/lme4/html/Hsb82.html

Entry: intervals
Aliases: intervals
Keywords: models
Description: Confidence Intervals on Coefficients
URL: ../../../library/lme4/html/intervals.html

Entry: isInitialized
Aliases: isInitialized isInitialized-methods isInitialized,pdBlocked-method isInitialized,pdCompSymm-method isInitialized,pdMat-method isInitialized,pdNatural-method isInitialized,lmeLevelList-method
Keywords: manip
Description: Check for initialization
URL: ../../../library/lme4/html/isInitialized.html

Entry: lme-class
Aliases: lme-class VarCorr,lme-method anova,lme-method coef,lme-method fitted,lme-method fixef,lme-method formula,lme-method getResponse,lme-method intervals,lme-method logLik,lme-method plot,lme-method ranef,lme-method residuals,lme-method show,lme-method summary,lme-method update,lme-method
Keywords: classes
Description: Class "lme"
URL: ../../../library/lme4/html/lme-class.html

Entry: lme
Aliases: lme lme,formula,data.frame,list-method lme,ANY,missing,ANY-method lme,missing,groupedData,ANY-method lme,formula,groupedData,missing-method lme,formula,ANY,formula-method lme,formula,ANY,list-method
Keywords: models methods
Description: Fit linear mixed-effects models
URL: ../../../library/lme4/html/lme.html

Entry: lmeControl
Aliases: lmeControl
Keywords: models
Description: Control values for lme
URL: ../../../library/lme4/html/lmeControl.html

Entry: LMEgradient
Aliases: LMEgradient LMEgradient-methods LMEgradient,pdDiag,matrix,numeric-method LMEgradient,pdIdent,matrix,numeric-method LMEgradient,pdLogChol,matrix,numeric-method LMEgradient,pdNatural,matrix,numeric-method LMEgradient,lmeLevel,matrix,missing-method LMEgradient,lmeLevel,missing,missing-method LMEhessian LMEhessian-methods LMEhessian,pdDiag,matrix,array,numeric-method LMEhessian,pdLogChol,matrix,array,numeric-method LMEhessian,lmeLevel,missing,missing,missing-method LMEhessian,reStruct,missing,missing,missing-method
Keywords: models
Description: The gradient and Hessian in lme optimization-method
URL: ../../../library/lme4/html/LMEgradient.html

Entry: lmeLevel-class
Aliases: lmeLevel-class coef,lmeLevel-method
Keywords: classes
Description: Class "lmeLevel"
URL: ../../../library/lme4/html/lmeLevel-class.html

Entry: lmeLevel
Aliases: lmeLevel lmeLevel,pdMat,factor,integer,matrix-method lmeLevel,missing,missing,integer,matrix-method
Keywords: models
Description: Construct an lmeLevel object
URL: ../../../library/lme4/html/lmeLevel.html

Entry: LMEoptimizeGets
Aliases: LMEoptimize<- LMEoptimize<-,reStruct,list-method LMEoptimize<-,glmm,list-method
Keywords: models
Description: Optimize linear mixed-effects
URL: ../../../library/lme4/html/LMEoptimizeGets.html

Entry: lmList-class
Aliases: lmList-class coef,lmList-method formula,lmList-method intervals,lmList-method plot,lmList-method pooledSD,lmList-method show,lmList-method update,lmList-method
Keywords: classes
Description: Class "lmList"
URL: ../../../library/lme4/html/lmList-class.html

Entry: lmList
Aliases: lmList lmList,formula,data.frame-method
Keywords: models
Description: List of lm Objects with a Common Model
URL: ../../../library/lme4/html/lmList.html

Entry: logDet
Aliases: logDet logDet-methods logDet,pdBlocked,missing-method logDet,pdCompSymm,missing-method logDet,pdDiag,missing-method logDet,pdIdent,missing-method logDet,pdLogChol,missing-method logDet,pdMat-method logDet,pdNatural,missing-method
Keywords: algebra array
Description: Logarithm of the determinant
URL: ../../../library/lme4/html/logDet.html

Entry: matrixGets
Aliases: matrix<- matrix<--methods matrix<-,pdMat,matrix-method
Keywords: manip algebra array methods
Description: Assign the matrix
URL: ../../../library/lme4/html/matrixGets.html

Entry: model.matrixGets
Aliases: model.matrix<- model.matrix<-,reStruct,matrix-method
Keywords: manip models
Description: Assign the model.matrix
URL: ../../../library/lme4/html/model.matrixGets.html

Entry: Names
Aliases: Names Names<- Names-methods Names<--methods Names,ANY-method Names<-,ANY-method
Keywords: attribute
Description: Extract or assign Names
URL: ../../../library/lme4/html/Names.html

Entry: nffGroupedData-class
Aliases: nffGroupedData-class
Keywords: classes
Description: Class "nffGroupedData"
URL: ../../../library/lme4/html/nffGroupedData-class.html

Entry: nfGroupedData-class
Aliases: nfGroupedData-class
Keywords: classes
Description: Class "nfGroupedData"
URL: ../../../library/lme4/html/nfGroupedData-class.html

Entry: nfnGroupedData-class
Aliases: nfnGroupedData-class
Keywords: classes
Description: Class "nfnGroupedData"
URL: ../../../library/lme4/html/nfnGroupedData-class.html

Entry: nlme-internal
Aliases: getFixDF glmmLa2LogLikComp glmmLa2RespWt glmmLa2Wt2
Keywords: models
Description: Internal nlme functions
URL: ../../../library/lme4/html/nlme-internal.html

Entry: nlmeInternal-class
Aliases: lmeLevelList-class summary.glmm-class show,summary.glmm-method summary.lme-class show,summary.lme-method summary.pdMat-class
Keywords: classes
Description: Some internal classes
URL: ../../../library/lme4/html/nlmeInternal-class.html

Entry: nmGroupedData-class
Aliases: nmGroupedData-class
Keywords: classes
Description: Class "nmGroupedData"
URL: ../../../library/lme4/html/nmGroupedData-class.html

Entry: pdBlocked-class
Aliases: pdBlocked-class pdBlocked
Keywords: classes
Description: Class "pdBlocked", blocked pd matrices
URL: ../../../library/lme4/html/pdBlocked-class.html

Entry: pdCompSymm-class
Aliases: pdCompSymm-class pdCompSymm pdCompSymm,formula,missing,missing,missing-method
Keywords: classes
Description: Class "pdCompSymm"
URL: ../../../library/lme4/html/pdCompSymm-class.html

Entry: pdDiag-class
Aliases: pdDiag-class pdDiag pdDiag,formula,missing,missing,missing-method
Keywords: classes
Description: Class "pdDiag"
URL: ../../../library/lme4/html/pdDiag-class.html

Entry: pdfactor-class
Aliases: pdfactor-class
Keywords: classes
Description: Factors of positive-definite matrices
URL: ../../../library/lme4/html/pdfactor-class.html

Entry: pdFactor
Aliases: pdFactor pdFactor-methods pdFactor,pdMat-method
Keywords: models
Description: Square-root factor
URL: ../../../library/lme4/html/pdFactor.html

Entry: pdgradient
Aliases: pdgradient pdgradient-methods pdgradient,pdIdent-method pdgradient,pdLogChol-method pdgradient,pdMat-method
Keywords: array algebra models methods
Description: Evaluated the pdmatrix gradient
URL: ../../../library/lme4/html/pdgradient.html

Entry: pdgradNumeric
Aliases: pdgradNumeric
Keywords: array algebra models
Description: Evaluate the pdmatrix gradient numerically
URL: ../../../library/lme4/html/pdgradNumeric.html

Entry: pdIdent-class
Aliases: pdIdent-class pdIdent pdIdent,formula,missing,missing,missing-method
Keywords: classes
Description: Class "pdIdent"
URL: ../../../library/lme4/html/pdIdent-class.html

Entry: pdLogChol-class
Aliases: pdLogChol-class pdLogChol pdLogChol,formula,missing,missing,missing-method
Keywords: classes
Description: Class "pdLogChol", positive-definite matrices
URL: ../../../library/lme4/html/pdLogChol-class.html

Entry: pdMat-class
Aliases: pdMat-class coef,pdMat-method coerce,pdMat,pdfactor-method dim,pdMat-method formula,pdMat-method names,pdMat-method names<-,pdMat-method show,pdMat-method solve,pdMat-method summary,pdMat-method
Keywords: classes
Description: Class pdMat, positive-definite matrices
URL: ../../../library/lme4/html/pdMat-class.html

Entry: pdmatrix-class
Aliases: pdmatrix-class
Keywords: classes
Description: Positive-definite matrices
URL: ../../../library/lme4/html/pdmatrix-class.html

Entry: pdMatrix
Aliases: pdMatrix pdMatrix-methods pdMatrix,pdMat-method
Keywords: models
Description: Return the positive-definite matrix
URL: ../../../library/lme4/html/pdMatrix.html

Entry: pdNatural-class
Aliases: pdNatural-class pdNatural pdNatural,formula,missing,missing,missing-method pdNatural,pdMat,missing,missing,missing-method
Keywords: classes
Description: Class "pdNatural", positive-definite matrices
URL: ../../../library/lme4/html/pdNatural-class.html

Entry: pooledSD
Aliases: pooledSD
Keywords: models
Description: Extract pooled standard deviation
URL: ../../../library/lme4/html/pooledSD.html

Entry: random.effects
Aliases: random.effects ranef ranef-methods ranef,ANY-method ranef,reStruct-method
Keywords: models methods
Description: Extract Random Effects
URL: ../../../library/lme4/html/random.effects.html

Entry: responseGets
Aliases: response<- response<-,reStruct,matrix-method
Keywords: manip models
Description: Modify the response
URL: ../../../library/lme4/html/responseGets.html

Entry: reStruct-class
Aliases: reStruct-class LMEgradient,reStruct,missing,missing-method VarCorr,reStruct-method coef,reStruct-method fitted,reStruct-method fixef<-,reStruct,numeric-method getFixDF,reStruct-method getGroups,reStruct,missing,ANY,missing,missing-method getResponse,reStruct-method logLik,reStruct-method model.matrix,reStruct-method model.matrix<-,reStruct-method response<-,reStruct,numeric-method summary,reStruct-method weighted<-,reStruct,numeric-method
Keywords: classes
Description: Class "reStruct"
URL: ../../../library/lme4/html/reStruct-class.html

Entry: reStruct
Aliases: reStruct reStruct,formula,list,data.frame,missing,logical-method reStruct,formula,list,data.frame,numeric,logical-method
Keywords: models
Description: Create an reStruct object
URL: ../../../library/lme4/html/reStruct.html

Entry: s3bbx
Aliases: s3bbx
Keywords: datasets
Description: Covariates in the Rodriguez and Goldman simulation
URL: ../../../library/lme4/html/s3bbx.html

Entry: s3bby
Aliases: s3bby
Keywords: datasets
Description: Responses simulated by Rodriguez and Goldman
URL: ../../../library/lme4/html/s3bby.html

Entry: solve-methods
Aliases: solve-methods solve,pdBlocked,missing-method solve,pdDiag,missing-method solve,pdIdent,missing-method solve,pdLogChol,missing-method solve,pdMat,missing-method solve,pdNatural,missing-method
Keywords: manip algebra array methods
Description: Methods for Function solve
URL: ../../../library/lme4/html/solve-methods.html

Entry: summary.reStruct-class
Aliases: summary.reStruct-class show,summary.reStruct-method
Keywords: classes
Description: Class "summary.reStruct"
URL: ../../../library/lme4/html/summary.reStruct-class.html

Entry: VarCorr-class
Aliases: VarCorr-class show,VarCorr-method
Keywords: classes
Description: Class "VarCorr"
URL: ../../../library/lme4/html/VarCorr-class.html

Entry: VarCorr
Aliases: VarCorr
Keywords: models
Description: Extract variance and correlation components
URL: ../../../library/lme4/html/VarCorr.html

Entry: weightedGets
Aliases: weighted<- weighted<-,reStruct,matrix-method
Keywords: manip models
Description: Modify the weights
URL: ../../../library/lme4/html/weightedGets.html
