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
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
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
Meat                    Tenderness of meat
Milk                    Protein content of cows' milk
Muscle                  Contraction of heart muscle sections
Names                   Names Associated with an Object
Names.formula           Extract Names from a formula
Names.pdBlocked         Names of a pdBlocked Object
Names.pdMat             Names of a pdMat Object
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
[.pdMat                 Subscript a pdMat Object
allCoef                 Extract Coefficients from a Set of Objects
anova.gls               Compare Likelihoods of Fitted Objects
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          Coefficients of a corStruct Object
coef.gnls               Extract gnls Coefficients
coef.lmList             Extract lmList Coefficients
coef.lme                Extract lme Coefficients
coef.modelStruct        Extract modelStruct Object Coefficients
coef.pdMat              pdMat Object Coefficients
coef.reStruct           reStruct Object Coefficients
coef.varFunc            varFunc Object Coefficients
coef<-                  Assign Values to 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              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
covariate<-             Assign Covariate Values
covariate<-.varFunc     Assign varFunc Covariate
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           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                     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             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                  List of lm Objects with a Common Model
lmList.groupedData      lmList Fit from a groupedData Object
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
matrix<-                Assign Matrix Values
matrix<-.pdMat          Assign Matrix to a pdMat or pdBlocked Object
matrix<-.reStruct       Assign reStruct Matrices
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                 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 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          Extract Random Effects
ranef.lmList            Extract lmList Random Effects
ranef.lme               Extract lme Random Effects
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             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
