ACF                      Autocorrelation Function
ACF.gls                  Autocorrelation Function for gls Residuals
ACF.lme                  Autocorrelation Function for lme Residuals
AIC                      Akaike Information Criterion
AIC.lme                  Akaike Information Criterion
AIC.logLik               AIC of a logLik Object
Alfalfa                  Split-Plot Experiment on Varieties of Alfalfa
Assay                    Bioassay on Cell Culture Plate
BIC                      Bayesian Information Criterion
BIC.logLik               BIC of a logLik Object
BodyWeight               Rat weight over time for different diets
Cefamandole              Pharmacokinetics of Cefamandole
Coef                     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                  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
MEEM                     EM iterations for mixed-effects
MEdecomp                 Decompose a mixed-effects model
MEdims                   Calculate dimensions in mixed-effects
MEestimate               Estimate mixed-effects parameters
Machines                 Productivity Scores for Machines and Workers
MathAchSchool            School demographic data for MathAchieve
MathAchieve              Mathematics achievement scores
Matrix                   Assign Matrix Values
Matrix.pdMat             Assign Matrix to a pdMat Object
Matrix.reStruct          Assign reStruct Matrices
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
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
coef.corStruct           Coefficients of a corStruct Object
coef.gls                 Extract gls Coefficients
coef.gnls                Extract gnls Coefficients
coef.lmList              Extract lmList Coefficients
coef.lme                 Extract lme Coefficients
coef.modelStruct         Extract modelStruct Object Coefficients
coef.pdCompSymm          pdCompSymm Object Coefficients
coef.pdDiag              pdDiag Object Coefficients
coef.pdIdent             pdIdent Object Coefficients
coef.pdMat               pdMat Object Coefficients
coef.reStruct            reStruct Object Coefficients
coef.varFunc             varFunc Object Coefficients
collapse                 Collapse According to Groups
collapse.groupedData     Collapse a groupedData Object
compareFits              Compare Fitted Objects
comparePred              Compare Predictions
contr.SAS                Contrast Matrices
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
ergoStool                Ergometrics experiment with stool types
fdHess                   Finite difference Hessian
fitted.gls               Extract gls Fitted Values
fitted.glsStruct         Calculate glsStruct Fitted Values
fitted.gnls              Extract gnls 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
fixed.effects.lmList     Extract lmList Fixed Effects
fixed.effects.lme        Extract lme Fixed Effects
formula.corStruct        Extract corStruct Object Formula
formula.gls              Extract gls Object Formula
formula.gnls             Extract gnls Object Formula
formula.groupedData      Extract groupedData Formula
formula.lmList           Extract lmList Object Formula
formula.lme              Extract lme Object Formula
formula.modelStruct      Extract modelStruct Object Formula
formula.nlme             Extract nlme Object Formula
formula.nls              Extract Model Formula from nls Object
formula.nlsList          Extract nlsList Object Formula
formula.pdBlocked        Extract pdBlocked Formula
formula.pdMat            Extract pdMat Formula
formula.reStruct         Extract reStruct Object Formula
formula.varFunc          Extract varFunc 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
getResponse.data.frame   Extract Response from a Data Frame
getResponse.gls          Extract gls Object Response
getResponse.lmList       Extract lmList Object Response
getResponse.lme          Extract lme Object Response
getResponseFormula       Extract Formula Specifying Response Variable
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
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
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
isInitialized.reStruct   Check if an reStruct 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               Control Values for lme Fit
lmeObject                Fitted lme Object
lmeScale                 Scale for lme Optimization
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.gls               Log-Likelihood of a gls Object
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.lm                Extract Log-Likelihood from an lm 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                  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
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 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.anova.lme          Print an anova.lme Object
print.corStruct          Print a corStruct Object
print.gls                Print a gls Object
print.groupedData        Print a groupedData Object
print.lmList             Print an lmList Object
print.lme                Print an lme Object
print.modelStruct        Print a modelStruct Object
print.pdMat              Print a pdMat Object
print.reStruct           Print an reStruct Object
print.summary.corStruct  Print a summary.corStruct Object
print.summary.gls        Print a summary.gls Object
print.summary.lmList     Print a summary.lmList Object
print.summary.lme        Print a summary.lme Object
print.summary.modelStruct
                         Print a summary.modelStruct Object
print.summary.pdMat      Print a summary.pdMat Object
print.summary.varFunc    Print a summary.varFunc Object
print.varFunc            Print a varFunc Object
pruneLevels              Prune Factor Levels
qqnorm.gls               Normal Plot of Residuals from a gls Object
qqnorm.lme               Normal Plot of Residuals or Random Effects from
                         an lme Object
random.effects           Extract Random Effects
random.effects.lmList    Extract lmList Random Effects
random.effects.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.gnls           Extract gnls 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 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 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.gls               Update a gls Object
update.gnls              Update a gnls Object
update.groupedData       Update a groupedData Object
update.lmList            Update an lmList Object
update.lme               Update an lme Object
update.modelStruct       Update a modelStruct Object
update.nlme              Update an nlme Object
update.nlsList           Update an nlsList Object
update.varFunc           Update varFunc Object
varClasses               Variance Function Classes
varComb                  Combination of Variance Functions
varConstPower            Constant Plus Power 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
