Man pages for nlme
Linear and Nonlinear Mixed Effects Models

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.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
augPred	Augmented Predictions
balancedGrouped	Create a groupedData object from a matrix
bdf	Language scores
BodyWeight	Rat weight over time for different diets
Cefamandole	Pharmacokinetics of Cefamandole
Coef	Assign Values to Coefficients
coef.corStruct	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.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
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...
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
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
ergoStool	Ergometrics experiment with stool types
Extract.pdMat	Subscript a pdMat Object
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
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
Gasoline	Refinery yield of gasoline
getCovariate	Extract Covariate from an Object
getCovariate.corStruct	Extract corStruct Object Covariate
getCovariate.data.frame	Extract Data Frame Covariate
getCovariateFormula	Extract Covariates Formula
getCovariate.varFunc	Extract varFunc Covariate
getData	Extract Data from an Object
getData.gls	Extract gls Object Data
getData.lme	Extract lme Object Data
getData.lmList	Extract lmList Object Data
getGroups	Extract Grouping Factors from an Object
getGroups.corStruct	Extract corStruct Groups
getGroups.data.frame	Extract Groups from a Data Frame
getGroupsFormula	Extract Grouping Formula
getGroups.gls	Extract gls Object Groups
getGroups.lme	Extract lme Object Groups
getGroups.lmList	Extract lmList Object Groups
getGroups.varFunc	Extract varFunc Groups
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
gls-internal	Auxiliary functions used by gls
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
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
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
isInitialized	Check if Object is Initialized
LDEsysMat	Generate system matrix for LDEs
lme	Linear Mixed-Effects Models
lmeControl	Specifying Control Values for lme Fit
lme.groupedData	LME fit from groupedData Object
lme.lmList	LME fit from lmList Object
lmeObject	Fitted lme Object
lmeStruct	Linear Mixed-Effects Structure
lmList	List of lm Objects with a Common Model
lmList.groupedData	lmList Fit from a groupedData Object
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.lme	Log-Likelihood of an lme Object
logLik.lmeStruct	Log-Likelihood of an lmeStruct Object
logLik.lmList	Log-Likelihood of an lmList Object
logLik.reStruct	Calculate reStruct Log-Likelihood
logLik.varFunc	Extract varFunc logLik
Machines	Productivity Scores for Machines and Workers
MathAchieve	Mathematics achievement scores
MathAchSchool	School demographic data for MathAchieve
Matrix	Assign Matrix Values
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
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
needUpdate	Check if Update is Needed
needUpdate.modelStruct	Check if a modelStruct Object Needs Updating
Nitrendipene	Assay of nitrendipene
nlme	Nonlinear Mixed-Effects Models
nlmeControl	Control Values for nlme Fit
nlme-deprecated	Deprecated Functions in Package 'nlme'
nlme.nlsList	NLME fit from nlsList Object
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
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
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
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...
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...
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.nmGroupedData	Plot an nmGroupedData Object
plot.ranef.lme	Plot a ranef.lme Object
plot.ranef.lmList	Plot a ranef.lmList Object
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.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
Quinidine	Quinidine Kinetics
quinModel	Model function for the Quinidine data
Rail	Evaluation of Stress in Railway Rails
random.effects	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.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
Relaxin	Assay for Relaxin
Remifentanil	Pharmacokinetics of Remifentanil
residuals.gls	Extract gls Residuals
residuals.glsStruct	Calculate glsStruct 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
simulate.lme	Simulate Results from 'lme' Models
solve.pdMat	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.corStruct	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.pdMat	Summarize a pdMat Object
summary.varFunc	Summarize "varFunc" Object
Tetracycline1	Pharmacokinetics of tetracycline
Tetracycline2	Pharmacokinetics of tetracycline
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
VarCorr	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
Wafer	Modeling of Analog MOS Circuits
Wheat	Yields by growing conditions
Wheat2	Wheat Yield Trials