# Linear and Nonlinear Mixed Effects Models

## Documentation for package ‘nlme’ version 3.1-128

- DESCRIPTION file.

## Help Pages

A B C D E F G I L M N O P Q R S T U V W misc

## -- A --

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
allCoef | Extract Coefficients from a Set of Objects
anova.gls | Compare Likelihoods of Fitted Objects
anova.lme | Compare Likelihoods of Fitted Objects
as.data.frame.groupedData | Construct a groupedData Object
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
Assay | Bioassay on Cell Culture Plate
asTable | Convert groupedData to a matrix
asTable.groupedData | Convert groupedData to a matrix
augPred | Augmented Predictions
augPred.gls | Augmented Predictions
augPred.lme | Augmented Predictions
augPred.lmList | Augmented Predictions

## -- B --

balancedGrouped | Create a groupedData object from a matrix
bdf | Language scores
BodyWeight | Rat weight over time for different diets

## -- C --

Cefamandole | Pharmacokinetics of Cefamandole
coef.corAR1 | Coefficients of a corStruct Object
coef.corARMA | ARMA(p,q) Correlation Structure
coef.corARMAd | Coefficients of a corStruct Object
coef.corCAR1 | Coefficients of a corStruct Object
coef.corCompSymm | Coefficients of a corStruct Object
coef.corHF | Coefficients of a corStruct Object
coef.corIdent | Coefficients of a corStruct Object
coef.corLin | Coefficients of a corStruct Object
coef.corNatural | Coefficients of a corStruct Object
coef.corSpatial | Coefficients of a corStruct Object
coef.corSpher | Coefficients of a corStruct Object
coef.corStruct | Coefficients of a corStruct Object
coef.corSymm | Coefficients of a corStruct Object
coef.gnls | Extract gnls Coefficients
coef.lme | Extract lme Coefficients
coef.lmList | Extract lmList Coefficients
coef.modelStruct | Extract modelStruct Object Coefficients
coef.pdBlocked | pdMat Object Coefficients
coef.pdCompSymm | pdMat Object Coefficients
coef.pdDiag | pdMat Object Coefficients
coef.pdIdent | pdMat Object Coefficients
coef.pdMat | pdMat Object Coefficients
coef.pdNatural | pdMat Object Coefficients
coef.pdSymm | pdMat Object Coefficients
coef.reStruct | reStruct Object Coefficients
coef.summary.nlsList | Coefficients of a corStruct Object
coef.varComb | varFunc Object Coefficients
coef.varConstPower | varFunc Object Coefficients
coef.varExp | varFunc Object Coefficients
coef.varFixed | varFunc Object Coefficients
coef.varFunc | varFunc Object Coefficients
coef.varIdent | varFunc Object Coefficients
coef.varPower | varFunc Object Coefficients
coef<- | Assign Values to Coefficients
coef<-.corAR1 | Coefficients of a corStruct Object
coef<-.corARMA | Coefficients of a corStruct Object
coef<-.corCAR1 | Coefficients of a corStruct Object
coef<-.corCompSymm | Coefficients of a corStruct Object
coef<-.corHF | Coefficients of a corStruct Object
coef<-.corIdent | Coefficients of a corStruct Object
coef<-.corLin | Coefficients of a corStruct Object
coef<-.corNatural | Coefficients of a corStruct Object
coef<-.corSpatial | Coefficients of a corStruct Object
coef<-.corSpher | Coefficients of a corStruct Object
coef<-.corStruct | Coefficients of a corStruct Object
coef<-.corSymm | Coefficients of a corStruct Object
coef<-.modelStruct | Extract modelStruct Object Coefficients
coef<-.pdBlocked | pdMat Object Coefficients
coef<-.pdMat | pdMat Object Coefficients
coef<-.reStruct | reStruct Object Coefficients
coef<-.varComb | varFunc Object Coefficients
coef<-.varConstPower | varFunc Object Coefficients
coef<-.varExp | varFunc Object Coefficients
coef<-.varFixed | varFunc Object Coefficients
coef<-.varIdent | varFunc Object Coefficients
coef<-.varPower | varFunc Object Coefficients
coefficients<- | Assign Values to Coefficients
collapse | Collapse According to Groups
collapse.groupedData | Collapse a groupedData Object
compareFits | Compare Fitted Objects
comparePred | Compare Predictions
comparePred.gls | Compare Predictions
comparePred.lme | Compare Predictions
comparePred.lmList | 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.compSymm | Factor of a corStruct Object Matrix
corFactor.corAR1 | Factor of a corStruct Object Matrix
corFactor.corARMA | Factor of a corStruct Object Matrix
corFactor.corCAR1 | Factor of a corStruct Object Matrix
corFactor.corNatural | Factor of a corStruct Object Matrix
corFactor.corSpatial | Factor of a corStruct Object Matrix
corFactor.corStruct | Factor of a corStruct Object Matrix
corFactor.corSymm | Factor of a corStruct Object Matrix
corGaus | Gaussian Correlation Structure
corIdent | Correlation Structure Classes
corLin | Linear Correlation Structure
corMatrix | Extract Correlation Matrix
corMatrix.compSymm | Matrix of a corStruct Object
corMatrix.corAR1 | Matrix of a corStruct Object
corMatrix.corARMA | Matrix of a corStruct Object
corMatrix.corCAR1 | Matrix of a corStruct Object
corMatrix.corCompSymm | Matrix of a corStruct Object
corMatrix.corIdent | Matrix of a corStruct Object
corMatrix.corNatural | Matrix of a corStruct Object
corMatrix.corSpatial | Matrix of a corStruct Object
corMatrix.corStruct | Matrix of a corStruct Object
corMatrix.corSymm | Matrix of a corStruct Object
corMatrix.pdBlocked | Extract Correlation Matrix from a pdMat Object
corMatrix.pdCompSymm | Extract Correlation Matrix from a pdMat Object
corMatrix.pdDiag | Extract Correlation Matrix from a pdMat Object
corMatrix.pdIdent | Extract Correlation Matrix from a pdMat Object
corMatrix.pdMat | Extract Correlation Matrix from a pdMat Object
corMatrix.pdSymm | 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
corStruct | Correlation Structure Classes
corSymm | General Correlation Structure
covariate<- | Assign Covariate Values
covariate<-.varFunc | Assign varFunc Covariate

## -- D --

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.default | Extract Dimensions from an Object
Dim.pdCompSymm | Dimensions of a pdMat Object
Dim.pdDiag | Dimensions of a pdMat Object
Dim.pdIdent | Dimensions of a pdMat Object
Dim.pdMat | Dimensions of a pdMat Object
Dim.pdNatural | Dimensions of a pdMat Object
Dim.pdSymm | Dimensions of a pdMat Object

## -- E --

Earthquake | Earthquake Intensity
ergoStool | Ergometrics experiment with stool types

## -- F --

Fatigue | Cracks caused by metal fatigue
fdHess | Finite difference Hessian
fitted.glsStruct | Calculate glsStruct Fitted Values
fitted.gnlsStruct | Calculate gnlsStruct Fitted Values
fitted.lme | Extract lme Fitted Values
fitted.lmeStruct | Calculate lmeStruct Fitted Values
fitted.lmList | Extract lmList Fitted Values
fitted.nlmeStruct | Calculate nlmeStruct Fitted Values
fixed.effects | Extract Fixed Effects
fixed.effects.lmList | Extract lmList 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

## -- G --

gapply | Apply a Function by Groups
Gasoline | Refinery yield of gasoline
getCovariate | Extract Covariate from an Object
getCovariate.corSpatial | Extract corStruct Object Covariate
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.gnls | Extract gls Object Data
getData.lme | Extract lme Object Data
getData.lmList | Extract lmList Object Data
getData.nlme | Extract lme Object Data
getData.nls | 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.lme | Extract lme Object Groups
getGroups.lmList | Extract lmList Object Groups
getGroups.varFunc | Extract varFunc Groups
getGroupsFormula | Extract Grouping Formula
getGroupsFormula.default | Extract Grouping Formula
getGroupsFormula.gls | Extract Grouping Formula
getGroupsFormula.lme | Extract Grouping Formula
getGroupsFormula.lmList | Extract Grouping Formula
getGroupsFormula.reStruct | Extract Grouping Formula
getResponse | Extract Response Variable from an Object
getResponse.data.frame | Extract Response Variable from an Object
getResponseFormula | Extract Formula Specifying Response Variable
getVarCov | Extract variance-covariance matrix
getVarCov.gls | Extract variance-covariance matrix
getVarCov.lme | 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
Glucose | Glucose levels over time
Glucose2 | Glucose Levels Following Alcohol Ingestion
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
Gun | Methods for firing naval guns

## -- I --

IGF | Radioimmunoassay of IGF-I Protein
Initialize | Initialize Object
Initialize.corAR1 | Initialize corStruct Object
Initialize.corARMA | Initialize corStruct Object
Initialize.corCAR1 | Initialize corStruct Object
Initialize.corCompSymm | Initialize corStruct Object
Initialize.corHF | Initialize corStruct Object
Initialize.corIdent | Initialize corStruct Object
Initialize.corLin | Initialize corStruct Object
Initialize.corNatural | Initialize corStruct Object
Initialize.corSpatial | Initialize corStruct Object
Initialize.corSpher | Initialize corStruct Object
Initialize.corStruct | Initialize corStruct Object
Initialize.corSymm | Initialize corStruct Object
Initialize.glsStruct | Initialize a glsStruct Object
Initialize.gnlsStruct | Generalized Nonlinear Least Squares Structure
Initialize.lmeStruct | Initialize an lmeStruct Object
Initialize.reStruct | Initialize reStruct Object
Initialize.varComb | Initialize varFunc Object
Initialize.varConstPower | Initialize varFunc Object
Initialize.varExp | Initialize varFunc Object
Initialize.varFixed | Initialize varFunc Object
Initialize.varFunc | Initialize varFunc Object
Initialize.varIdent | Initialize varFunc Object
Initialize.varPower | Initialize varFunc Object
intervals | Confidence Intervals on Coefficients
intervals.gls | Confidence Intervals on gls Parameters
intervals.lme | Confidence Intervals on lme Parameters
intervals.lmList | Confidence Intervals on lmList Coefficients
isBalanced | Check a Design for Balance
isBalanced.groupedData | Check a Design for Balance
isInitialized | Check if Object is Initialized
isInitialized.pdBlocked | Check if Object is Initialized
isInitialized.pdMat | Check if Object is Initialized

## -- L --

LDEsysMat | Generate system matrix for LDEs
lme | Linear Mixed-Effects Models
lme.formula | 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
lmList | List of lm Objects with a Common Model
lmList.formula | List of lm Objects with a Common Model
lmList.groupedData | lmList Fit from a groupedData Object
logDet | Extract the Logarithm of the Determinant
logDet.corIdent | Extract corStruct Log-Determinant
logDet.corStruct | Extract corStruct Log-Determinant
logDet.pdBlocked | Extract Log-Determinant from a pdMat Object
logDet.pdCompSymm | Extract Log-Determinant from a pdMat Object
logDet.pdDiag | Extract Log-Determinant from a pdMat Object
logDet.pdIdent | Extract Log-Determinant from a pdMat Object
logDet.pdMat | Extract Log-Determinant from a pdMat Object
logDet.pdNatural | Extract Log-Determinant from a pdMat Object
logDet.pdSymm | Extract Log-Determinant from a pdMat Object
logDet.reStruct | Extract reStruct Log-Determinants
logLik.corStruct | Extract corStruct Log-Likelihood
logLik.gls | Log-Likelihood of an lme 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.lme | Log-Likelihood of an lme Object
logLik.lmeStruct | Log-Likelihood of an lmeStruct Object
logLik.lmeStructInt | Log-Likelihood of an lmeStruct Object
logLik.lmList | Log-Likelihood of an lmList Object
logLik.reStruct | Calculate reStruct Log-Likelihood
logLik.varComb | Extract varFunc logLik
logLik.varFunc | Extract varFunc logLik

## -- M --

Machines | Productivity Scores for Machines and Workers
MathAchieve | Mathematics achievement scores
MathAchSchool | School demographic data for MathAchieve
matrix<- | Assign Matrix Values
matrix<-.pdBlocked | Assign Matrix to a pdMat or pdBlocked Object
matrix<-.pdMat | Assign Matrix to a pdMat or pdBlocked Object
matrix<-.reStruct | Assign reStruct Matrices
Meat | Tenderness of meat
Milk | Protein content of cows' milk
model.matrix.reStruct | reStruct Model Matrix
Muscle | Contraction of heart muscle sections

## -- N --

Names | Names Associated with an Object
Names.formula | Extract Names from a formula
Names.listForm | 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
Names<- | Names Associated with an Object
Names<-.pdBlocked | Names of a pdBlocked Object
Names<-.pdMat | Names of a pdMat Object
Names<-.reStruct | Names of an reStruct Object
needUpdate | Check if Update is Needed
needUpdate.corStruct | Check if a modelStruct Object Needs Updating
needUpdate.default | Check if Update is Needed
needUpdate.modelStruct | Check if a modelStruct Object Needs Updating
needUpdate.reStruct | Check if a modelStruct Object Needs Updating
needUpdate.varComb | Check if Update is Needed
needUpdate.varIdent | Check if Update is Needed
nfGroupedData | Construct a groupedData Object
Nitrendipene | Assay of nitrendipene
nlme | Nonlinear Mixed-Effects Models
nlme.formula | 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.formula | List of nls Objects with a Common Model
nlsList.selfStart | nlsList Fit from a selfStart Function
nmGroupedData | Construct a groupedData Object

## -- O --

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

## -- P --

pairs.compareFits | Pairs Plot of compareFits Object
pairs.lme | Pairs Plot of an lme Object
pairs.lmList | Pairs Plot of an lmList Object
PBG | Effect of Phenylbiguanide on Blood Pressure
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
pdConstruct.pdCompSymm | Construct pdMat Objects
pdConstruct.pdDiag | Construct pdMat Objects
pdConstruct.pdIdent | Construct pdMat Objects
pdConstruct.pdLogChol | Construct pdMat Objects
pdConstruct.pdMat | Construct pdMat Objects
pdConstruct.pdNatural | Construct pdMat Objects
pdConstruct.pdSymm | Construct pdMat Objects
pdDiag | Diagonal Positive-Definite Matrix
pdFactor | Square-Root Factor of a Positive-Definite Matrix
pdFactor.pdBlocked | Square-Root Factor of a Positive-Definite Matrix
pdFactor.pdCompSymm | Square-Root Factor of a Positive-Definite Matrix
pdFactor.pdDiag | Square-Root Factor of a Positive-Definite Matrix
pdFactor.pdIdent | Square-Root Factor of a Positive-Definite Matrix
pdFactor.pdLogChol | Square-Root Factor of a Positive-Definite Matrix
pdFactor.pdMat | Square-Root Factor of a Positive-Definite Matrix
pdFactor.pdNatural | Square-Root Factor of a Positive-Definite Matrix
pdFactor.pdSymm | 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.pdBlocked | Extract Matrix or Square-Root Factor from a pdMat Object
pdMatrix.pdCompSymm | Extract Matrix or Square-Root Factor from a pdMat Object
pdMatrix.pdDiag | Extract Matrix or Square-Root Factor from a pdMat Object
pdMatrix.pdIdent | Extract Matrix or Square-Root Factor from a pdMat Object
pdMatrix.pdMat | Extract Matrix or Square-Root Factor from a pdMat Object
pdMatrix.pdNatural | Extract Matrix or Square-Root Factor from a pdMat Object
pdMatrix.pdSymm | 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
Phenobarb | Phenobarbitol Kinetics
phenoModel | Model function for the Phenobarb data
Pixel | X-ray pixel intensities over time
plot.ACF | Plot an ACF 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.lme | Plot an lme or nls object
plot.lmList | Plot an lmList Object
plot.nffGroupedData | Plot an nffGroupedData Object
plot.nfnGroupedData | Plot an nfnGroupedData Object
plot.nls | Plot an lme or nls object
plot.nmGroupedData | Plot an nmGroupedData Object
plot.pdMat | Positive-Definite Matrix
plot.ranef.lme | Plot a ranef.lme Object
plot.ranef.lmList | Plot a ranef.lmList Object
plot.simulate.lme | Simulate Results from 'lme' Models
plot.Variogram | Plot a Variogram Object
pooledSD | Extract Pooled Standard Deviation
predict.gls | Predictions from a gls Object
predict.gnls | Predictions from a gnls Object
predict.lme | Predictions from an lme Object
predict.lmList | Predictions from an lmList Object
predict.nlme | Predictions from an nlme Object
print.anova.lme | Compare Likelihoods of Fitted Objects
print.compareFits | Compare Fitted Objects
print.corNatural | General correlation in natural parameterization
print.intervals.gls | Confidence Intervals on gls Parameters
print.intervals.lme | Confidence Intervals on lme Parameters
print.intervals.lmList | Confidence Intervals on lmList Coefficients
print.lmList | List of lm Objects with a Common Model
print.ranef | Extract Random Effects
print.ranef.lme | Extract lme Random Effects
print.reStruct | Random Effects Structure
print.simulate.lme | Simulate Results from 'lme' Models
print.summary.lme | Summarize an lme Object
print.summary.pdMat | Print a summary.pdMat Object
print.varComb | Print a varFunc Object
print.VarCorr.lme | Extract variance and correlation components
print.VarCov | Extract variance-covariance matrix
print.varFunc | Print a varFunc Object

## -- Q --

qqnorm.gls | Normal Plot of Residuals from a gls Object
qqnorm.lm | Normal Plot of Residuals or Random Effects from an lme Object
qqnorm.lme | Normal Plot of Residuals or Random Effects from an lme Object
qqnorm.lmList | Normal Plot of Residuals or Random Effects from an lme Object
qqnorm.nls | Normal Plot of Residuals or Random Effects from an lme Object
Quinidine | Quinidine Kinetics
quinModel | Model function for the Quinidine data

## -- R --

Rail | Evaluation of Stress in Railway Rails
random.effects | Extract Random Effects
random.effects.lme | Extract lme Random Effects
random.effects.lmList | Extract lmList Random Effects
ranef | Extract Random Effects
ranef.lme | Extract lme Random Effects
ranef.lmList | Extract lmList Random Effects
RatPupWeight | The weight of rat pups
recalc | Recalculate Condensed Linear Model Object
recalc.corAR1 | Recalculate for corStruct Object
recalc.corARMA | Recalculate for corStruct Object
recalc.corCAR1 | Recalculate for corStruct Object
recalc.corCompSymm | Recalculate for corStruct Object
recalc.corHF | Recalculate for corStruct Object
recalc.corIdent | Recalculate for corStruct Object
recalc.corNatural | Recalculate for corStruct Object
recalc.corSpatial | Recalculate for corStruct Object
recalc.corStruct | Recalculate for corStruct Object
recalc.corSymm | Recalculate for corStruct Object
recalc.modelStruct | Recalculate for a modelStruct Object
recalc.reStruct | Recalculate for an reStruct Object
recalc.varFunc | Recalculate for varFunc Object
recalc.varIdent | Recalculate for varFunc Object
Relaxin | Assay for Relaxin
Remifentanil | Pharmacokinetics of remifentanil
residuals.gls | Extract gls Residuals
residuals.glsStruct | Calculate glsStruct Residuals
residuals.gnls | Extract gls Residuals
residuals.gnlsStruct | Calculate gnlsStruct Residuals
residuals.lme | Extract lme Residuals
residuals.lmeStruct | Calculate lmeStruct Residuals
residuals.lmList | Extract lmList Residuals
residuals.nlmeStruct | Calculate nlmeStruct Residuals
reStruct | Random Effects Structure

## -- S --

simulate.lme | Simulate Results from 'lme' Models
solve.pdBlocked | Calculate Inverse of a Positive-Definite Matrix
solve.pdDiag | Calculate Inverse of a Positive-Definite Matrix
solve.pdIdent | Calculate Inverse of a Positive-Definite Matrix
solve.pdLogChol | Calculate Inverse of a Positive-Definite Matrix
solve.pdMat | Calculate Inverse of a Positive-Definite Matrix
solve.pdNatural | Calculate Inverse of a Positive-Definite Matrix
solve.pdSymm | Calculate Inverse of a Positive-Definite Matrix
solve.reStruct | Apply Solve to an reStruct Object
Soybean | Growth of soybean plants
splitFormula | Split a Formula
Spruce | Growth of Spruce Trees
summary.corAR1 | Summarize a corStruct Object
summary.corARMA | Summarize a corStruct Object
summary.corCAR1 | Summarize a corStruct Object
summary.corCompSymm | Summarize a corStruct Object
summary.corExp | Summarize a corStruct Object
summary.corGaus | Summarize a corStruct Object
summary.corIdent | Summarize a corStruct Object
summary.corLin | Summarize a corStruct Object
summary.corNatural | Summarize a corStruct Object
summary.corRatio | Summarize a corStruct Object
summary.corSpher | Summarize a corStruct Object
summary.corStruct | Summarize a corStruct Object
summary.corSymm | Summarize a corStruct Object
summary.gls | Summarize a Generalized Least Squares 'gls' Object
summary.lme | Summarize an lme Object
summary.lmList | Summarize an lmList Object
summary.modelStruct | Summarize a modelStruct Object
summary.nlsList | Summarize an nlsList Object
summary.pdBlocked | Summarize a pdMat Object
summary.pdCompSymm | Summarize a pdMat Object
summary.pdDiag | Summarize a pdMat Object
summary.pdIdent | Summarize a pdMat Object
summary.pdLogChol | Summarize a pdMat Object
summary.pdMat | Summarize a pdMat Object
summary.pdNatural | Summarize a pdMat Object
summary.pdSymm | Summarize a pdMat Object
summary.reStruct | Summarize a modelStruct Object
summary.varComb | Summarize varFunc Object
summary.varConstPower | Summarize varFunc Object
summary.varExp | Summarize varFunc Object
summary.varFixed | Summarize varFunc Object
summary.varFunc | Summarize varFunc Object
summary.varIdent | Summarize varFunc Object
summary.varPower | Summarize varFunc Object

## -- T --

Tetracycline1 | Pharmacokinetics of tetracycline
Tetracycline2 | Pharmacokinetics of tetracycline

## -- U --

update.corStruct | Update a modelStruct Object
update.gls | Fit Linear Model Using Generalized Least Squares
update.groupedData | Construct a groupedData Object
update.lme | Linear Mixed-Effects Models
update.lmList | List of lm Objects with a Common Model
update.modelStruct | Update a modelStruct Object
update.nlsList | List of nls Objects with a Common Model
update.reStruct | Update a modelStruct Object
update.varComb | Update varFunc Object
update.varConstPower | Update varFunc Object
update.varExp | Update varFunc Object
update.varExpon | Update varFunc Object
update.varFunc | Update varFunc Object
update.varPower | Update varFunc Object

## -- V --

varClasses | Variance Function Classes
varComb | Combination of Variance Functions
varConstPower | Constant Plus Power Variance Function
VarCorr | Extract variance and correlation components
VarCorr.lme | Extract variance and correlation components
VarCorr.pdBlocked | Extract variance and correlation components
VarCorr.pdMat | Extract variance and correlation components
varExp | Exponential Variance Function
varFixed | Fixed Variance Function
varFunc | Variance Function Structure
varIdent | Constant Variance Function
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
varPower | Power Variance Function
varWeights | Extract Variance Function Weights
varWeights.glsStruct | Variance Weights for glsStruct Object
varWeights.lmeStruct | Variance Weights for lmeStruct Object
varWeights.varComb | Extract Variance Function Weights
varWeights.varFunc | Extract Variance Function Weights

## -- W --

Wafer | Modeling of Analog MOS Circuits
Wheat | Yields by growing conditions
Wheat2 | Wheat Yield Trials

## -- misc --

[.groupedData | Construct a groupedData Object
[.pdBlocked | Subscript a pdMat Object
[.pdMat | Subscript a pdMat Object
[.reStruct | Random Effects Structure
[<-.pdMat | Subscript a pdMat Object