Package index • nlme

All functions
`ACF()`	Autocorrelation Function
`ACF(<gls>)`	Autocorrelation Function for gls Residuals
`ACF(<lme>)`	Autocorrelation Function for lme Residuals
`Alfalfa`	Split-Plot Experiment on Varieties of Alfalfa
`Assay`	Bioassay on Cell Culture Plate
`BodyWeight`	Rat weight over time for different diets
`Cefamandole`	Pharmacokinetics of Cefamandole
`coef<-`() `coefficients<-`()	Assign Values to Coefficients
`covariate<-`()	Assign Covariate Values
`covariate<-`(<varFunc>)	Assign varFunc Covariate
`Dialyzer`	High-Flux Hemodialyzer
`Dim()`	Extract Dimensions from an Object
`Dim(<corSpatial>)`	Dimensions of a corSpatial Object
`Dim(<corStruct>)`	Dimensions of a corStruct Object
`Dim(<pdMat>)`	Dimensions of a pdMat Object
`Earthquake`	Earthquake Intensity
`[`(<pdMat>) `[<-`(<pdMat>)	Subscript a pdMat Object
`Fatigue`	Cracks caused by metal fatigue
`Gasoline`	Refinery yield of gasoline
`Glucose`	Glucose levels over time
`Glucose2`	Glucose Levels Following Alcohol Ingestion
`Gun`	Methods for firing naval guns
`IGF`	Radioimmunoassay of IGF-I Protein
`Initialize()`	Initialize Object
`Initialize(<corStruct>)`	Initialize corStruct Object
`Initialize(<glsStruct>)`	Initialize a glsStruct Object
`Initialize(<lmeStruct>)`	Initialize an lmeStruct Object
`Initialize(<reStruct>)`	Initialize reStruct Object
`Initialize(<varFunc>)`	Initialize varFunc Object
`LDEsysMat()`	Generate system matrix for LDEs
`Machines`	Productivity Scores for Machines and Workers
`MathAchSchool`	School demographic data for MathAchieve
`MathAchieve`	Mathematics achievement scores
`matrix<-`()	Assign Matrix Values
`matrix<-`(<pdMat>) `matrix<-`(<pdBlocked>)	Assign Matrix to a pdMat or pdBlocked Object
`matrix<-`(<reStruct>)	Assign reStruct Matrices
`Meat`	Tenderness of meat
`Milk`	Protein content of cows' milk
`Muscle`	Contraction of heart muscle sections
`Names()` `Names<-`()	Names Associated with an Object
`Names(<formula>)`	Extract Names from a formula
`Names(<pdBlocked>)`	Names of a pdBlocked Object
`Names(<pdMat>)` `Names<-`(<pdMat>)	Names of a pdMat Object
`Names(<reStruct>)` `Names<-`(<reStruct>)	Names of an reStruct Object
`Nitrendipene`	Assay of nitrendipene
`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
`PBG`	Effect of Phenylbiguanide on Blood Pressure
`Phenobarb`	Phenobarbitol Kinetics
`Pixel`	X-ray pixel intensities over time
`Quinidine`	Quinidine Kinetics
`Rail`	Evaluation of Stress in Railway Rails
`RatPupWeight`	The weight of rat pups
`Relaxin`	Assay for Relaxin
`Remifentanil`	Pharmacokinetics of Remifentanil
`Soybean`	Growth of soybean plants
`Spruce`	Growth of Spruce Trees
`Tetracycline1`	Pharmacokinetics of tetracycline
`Tetracycline2`	Pharmacokinetics of tetracycline
`VarCorr()`	Extract variance and correlation components
`Variogram()`	Calculate Semi-variogram
`Variogram(<corExp>)`	Calculate Semi-variogram for a corExp Object
`Variogram(<corGaus>)`	Calculate Semi-variogram for a corGaus Object
`Variogram(<corLin>)`	Calculate Semi-variogram for a corLin Object
`Variogram(<corRatio>)`	Calculate Semi-variogram for a corRatio Object
`Variogram(<corSpatial>)`	Calculate Semi-variogram for a corSpatial Object
`Variogram(<corSpher>)`	Calculate Semi-variogram for a corSpher Object
`Variogram(<default>)`	Calculate Semi-variogram
`Variogram(<gls>)`	Calculate Semi-variogram for Residuals from a gls Object
`Variogram(<lme>)`	Calculate Semi-variogram for Residuals from an lme Object
`Wafer`	Modeling of Analog MOS Circuits
`Wheat`	Yields by growing conditions
`Wheat2`	Wheat Yield Trials
`allCoef()`	Extract Coefficients from a Set of Objects
`anova(<gls>)`	Compare Likelihoods of Fitted Objects
`anova(<lme>)` `print(<anova.lme>)`	Compare Likelihoods of Fitted Objects
`as.matrix(<corStruct>)`	Matrix of a corStruct Object
`as.matrix(<pdMat>)`	Matrix of a pdMat Object
`as.matrix(<reStruct>)`	Matrices of an reStruct Object
`asOneFormula()`	Combine Formulas of a Set of Objects
`asTable()`	Convert groupedData to a matrix
`augPred()`	Augmented Predictions
`balancedGrouped()`	Create a groupedData object from a matrix
`bdf`	Language scores
`coef(<corStruct>)` `coef<-`(<corStruct>)	Coefficients of a corStruct Object
`coef(<gnls>)`	Extract gnls Coefficients
`coef(<lmList>)`	Extract lmList Coefficients
`coef(<lme>)`	Extract lme Coefficients
`coef(<modelStruct>)` `coef<-`(<modelStruct>)	Extract modelStruct Object Coefficients
`coef(<pdMat>)` `coef<-`(<pdMat>)	pdMat Object Coefficients
`coef(<reStruct>)` `coef<-`(<reStruct>)	reStruct Object Coefficients
`coef(<varFunc>)` `coef<-`(<varIdent>)	varFunc Object Coefficients
`collapse()`	Collapse According to Groups
`collapse(<groupedData>)`	Collapse a groupedData Object
`compareFits()`	Compare Fitted Objects
`comparePred()`	Compare Predictions
`corAR1()`	AR(1) Correlation Structure
`corARMA()`	ARMA(p,q) Correlation Structure
`corCAR1()`	Continuous AR(1) Correlation Structure
`corClasses` `corStruct`	Correlation Structure Classes
`corCompSymm()`	Compound Symmetry Correlation Structure
`corExp()`	Exponential Correlation Structure
`corFactor()`	Factor of a Correlation Matrix
`corFactor(<corStruct>)`	Factor of a corStruct Object Matrix
`corGaus()`	Gaussian Correlation Structure
`corLin()`	Linear Correlation Structure
`corMatrix()`	Extract Correlation Matrix
`corMatrix(<corStruct>)`	Matrix of a corStruct Object
`corMatrix(<pdMat>)`	Extract Correlation Matrix from a pdMat Object
`corMatrix(<reStruct>)`	Extract Correlation Matrix from Components of an reStruct Object
`corNatural()`	General correlation in natural parameterization
`corRatio()`	Rational Quadratic Correlation Structure
`corSpatial()`	Spatial Correlation Structure
`corSpher()`	Spherical Correlation Structure
`corSymm()`	General Correlation Structure
`ergoStool`	Ergometrics experiment with stool types
`fdHess()`	Finite difference Hessian
`fitted(<glsStruct>)`	Calculate glsStruct Fitted Values
`fitted(<gnlsStruct>)`	Calculate gnlsStruct Fitted Values
`fitted(<lmList>)`	Extract lmList Fitted Values
`fitted(<lme>)`	Extract lme Fitted Values
`fitted(<lmeStruct>)`	Calculate lmeStruct Fitted Values
`fitted(<nlmeStruct>)`	Calculate nlmeStruct Fitted Values
`fixed.effects()` `fixef()`	Extract Fixed Effects
`fixef(<lmList>)`	Extract lmList Fixed Effects
`formula(<pdBlocked>)`	Extract pdBlocked Formula
`formula(<pdMat>)`	Extract pdMat Formula
`formula(<reStruct>)`	Extract reStruct Object Formula
`gapply()`	Apply a Function by Groups
`getCovariate()`	Extract Covariate from an Object
`getCovariate(<corStruct>)`	Extract corStruct Object Covariate
`getCovariate(<data.frame>)`	Extract Data Frame Covariate
`getCovariate(<varFunc>)`	Extract varFunc Covariate
`getCovariateFormula()`	Extract Covariates Formula
`getData()`	Extract Data from an Object
`getData(<gls>)`	Extract gls Object Data
`getData(<lmList>)`	Extract lmList Object Data
`getData(<lme>)`	Extract lme Object Data
`getGroups()`	Extract Grouping Factors from an Object
`getGroups(<corStruct>)`	Extract corStruct Groups
`getGroups(<data.frame>)`	Extract Groups from a Data Frame
`getGroups(<gls>)`	Extract gls Object Groups
`getGroups(<lmList>)`	Extract lmList Object Groups
`getGroups(<lme>)`	Extract lme Object Groups
`getGroups(<varFunc>)`	Extract varFunc Groups
`getGroupsFormula()`	Extract Grouping Formula
`getResponse()`	Extract Response Variable from an Object
`getResponseFormula()`	Extract Formula Specifying Response Variable
`getVarCov()`	Extract variance-covariance matrix
`gls()` `update(<gls>)`	Fit Linear Model Using Generalized Least Squares
`glsControl()`	Control Values for gls Fit
`glsObject`	Fitted gls Object
`glsStruct()`	Generalized Least Squares Structure
`gnls()`	Fit Nonlinear Model Using Generalized Least Squares
`gnlsControl()`	Control Values for gnls Fit
`gnlsObject`	Fitted gnls Object
`gnlsStruct()`	Generalized Nonlinear Least Squares Structure
`groupedData()` `update(<groupedData>)`	Construct a groupedData Object
`gsummary()`	Summarize by Groups
`intervals()`	Confidence Intervals on Coefficients
`intervals(<gls>)`	Confidence Intervals on gls Parameters
`intervals(<lmList>)`	Confidence Intervals on lmList Coefficients
`intervals(<lme>)`	Confidence Intervals on lme Parameters
`isBalanced()`	Check a Design for Balance
`isInitialized()`	Check if Object is Initialized
`lmList()` `update(<lmList>)` `print(<lmList>)`	List of lm Objects with a Common Model
`lmList(<groupedData>)`	lmList Fit from a groupedData Object
`lme()` `update(<lme>)`	Linear Mixed-Effects Models
`lme(<groupedData>)`	LME fit from groupedData Object
`lme(<lmList>)`	LME fit from lmList Object
`lmeControl()`	Specifying Control Values for lme Fit
`lmeObject`	Fitted lme Object
`lmeStruct()`	Linear Mixed-Effects Structure
`logDet()`	Extract the Logarithm of the Determinant
`logDet(<corStruct>)`	Extract corStruct Log-Determinant
`logDet(<pdMat>)`	Extract Log-Determinant from a pdMat Object
`logDet(<reStruct>)`	Extract reStruct Log-Determinants
`logLik(<corStruct>)`	Extract corStruct Log-Likelihood
`logLik(<glsStruct>)`	Log-Likelihood of a glsStruct Object
`logLik(<gnls>)`	Log-Likelihood of a gnls Object
`logLik(<gnlsStruct>)`	Log-Likelihood of a gnlsStruct Object
`logLik(<lmList>)`	Log-Likelihood of an lmList Object
`logLik(<lme>)`	Log-Likelihood of an lme Object
`logLik(<lmeStruct>)`	Log-Likelihood of an lmeStruct Object
`logLik(<reStruct>)`	Calculate reStruct Log-Likelihood
`logLik(<varFunc>)`	Extract varFunc logLik
`model.matrix(<reStruct>)`	reStruct Model Matrix
`needUpdate()`	Check if Update is Needed
`needUpdate(<modelStruct>)`	Check if a modelStruct Object Needs Updating
`nlme()`	Nonlinear Mixed-Effects Models
`nlme(<nlsList>)`	NLME fit from nlsList Object
`nlmeControl()`	Control Values for nlme Fit
`nlmeObject`	Fitted nlme Object
`nlmeStruct()`	Nonlinear Mixed-Effects Structure
`nlsList()` `update(<nlsList>)`	List of nls Objects with a Common Model
`nlsList(<selfStart>)`	nlsList Fit from a selfStart Function
`pairs(<compareFits>)`	Pairs Plot of compareFits Object
`pairs(<lmList>)`	Pairs Plot of an lmList Object
`pairs(<lme>)`	Pairs Plot of an lme Object
`pdBlocked()`	Positive-Definite Block Diagonal Matrix
`pdClasses`	Positive-Definite Matrix Classes
`pdCompSymm()`	Positive-Definite Matrix with Compound Symmetry Structure
`pdConstruct()`	Construct pdMat Objects
`pdConstruct(<pdBlocked>)`	Construct pdBlocked Objects
`pdDiag()`	Diagonal Positive-Definite Matrix
`pdFactor()`	Square-Root Factor of a Positive-Definite Matrix
`pdFactor(<reStruct>)`	Extract Square-Root Factor from Components of an reStruct Object
`pdIdent()`	Multiple of the Identity Positive-Definite Matrix
`pdLogChol()`	General Positive-Definite Matrix
`pdMat()`	Positive-Definite Matrix
`pdMatrix()`	Extract Matrix or Square-Root Factor from a pdMat Object
`pdMatrix(<reStruct>)`	Extract Matrix or Square-Root Factor from Components of an reStruct Object
`pdNatural()`	General Positive-Definite Matrix in Natural Parametrization
`pdSymm()`	General Positive-Definite Matrix
`phenoModel()`	Model function for the Phenobarb data
`plot(<ACF>)`	Plot an ACF Object
`plot(<Variogram>)`	Plot a Variogram Object
`plot(<augPred>)`	Plot an augPred Object
`plot(<compareFits>)`	Plot a compareFits Object
`plot(<gls>)`	Plot a gls Object
`plot(<intervals.lmList>)`	Plot lmList Confidence Intervals
`plot(<lmList>)`	Plot an lmList Object
`plot(<lme>)` `plot(<nls>)`	Plot an lme or nls object
`plot(<nffGroupedData>)`	Plot an nffGroupedData Object
`plot(<nfnGroupedData>)`	Plot an nfnGroupedData Object
`plot(<nmGroupedData>)`	Plot an nmGroupedData Object
`plot(<ranef.lmList>)`	Plot a ranef.lmList Object
`plot(<ranef.lme>)`	Plot a ranef.lme Object
`pooledSD()`	Extract Pooled Standard Deviation
`predict(<gls>)`	Predictions from a gls Object
`predict(<gnls>)`	Predictions from a gnls Object
`predict(<lmList>)`	Predictions from an lmList Object
`predict(<lme>)`	Predictions from an lme Object
`predict(<nlme>)`	Predictions from an nlme Object
`print(<summary.pdMat>)`	Print a summary.pdMat Object
`print(<varFunc>)`	Print a varFunc Object
`qqnorm(<gls>)`	Normal Plot of Residuals from a gls Object
`qqnorm(<lme>)`	Normal Plot of Residuals or Random Effects from an lme Object
`quinModel()`	Model function for the Quinidine data
`random.effects()` `ranef()`	Extract Random Effects
`ranef(<lmList>)`	Extract lmList Random Effects
`ranef(<lme>)`	Extract lme Random Effects
`reStruct()` `print(<reStruct>)`	Random Effects Structure
`recalc()`	Recalculate Condensed Linear Model Object
`recalc(<corStruct>)`	Recalculate for corStruct Object
`recalc(<modelStruct>)`	Recalculate for a modelStruct Object
`recalc(<reStruct>)`	Recalculate for an reStruct Object
`recalc(<varFunc>)`	Recalculate for varFunc Object
`residuals(<gls>)`	Extract gls Residuals
`residuals(<glsStruct>)`	Calculate glsStruct Residuals
`residuals(<gnlsStruct>)`	Calculate gnlsStruct Residuals
`residuals(<lmList>)`	Extract lmList Residuals
`residuals(<lme>)`	Extract lme Residuals
`residuals(<lmeStruct>)`	Calculate lmeStruct Residuals
`residuals(<nlmeStruct>)`	Calculate nlmeStruct Residuals
`simulate(<lme>)`	Simulate Results from `lme` Models
`solve(<pdMat>)`	Calculate Inverse of a Positive-Definite Matrix
`solve(<reStruct>)`	Apply Solve to an reStruct Object
`splitFormula()`	Split a Formula
`summary(<corStruct>)`	Summarize a corStruct Object
`summary(<gls>)`	Summarize a Generalized Least Squares `gls` Object
`summary(<lmList>)`	Summarize an lmList Object
`summary(<lme>)` `print(<summary.lme>)`	Summarize an lme Object
`summary(<modelStruct>)`	Summarize a modelStruct Object
`summary(<nlsList>)`	Summarize an nlsList Object
`summary(<pdMat>)`	Summarize a pdMat Object
`summary(<varFunc>)`	Summarize "varFunc" Object
`update(<modelStruct>)`	Update a modelStruct Object
`update(<varFunc>)`	Update varFunc Object
`varClasses`	Variance Function Classes
`varComb()`	Combination of Variance Functions
`varConstPower()`	Constant Plus Power Variance Function
`varConstProp()`	Constant Plus Proportion Variance Function
`varExp()`	Exponential Variance Function
`varFixed()`	Fixed Variance Function
`varFunc()`	Variance Function Structure
`varIdent()`	Constant Variance Function
`varPower()`	Power Variance Function
`varWeights()`	Extract Variance Function Weights
`varWeights(<glsStruct>)`	Variance Weights for glsStruct Object
`varWeights(<lmeStruct>)`	Variance Weights for lmeStruct Object

Reference

All functions