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 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 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 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 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 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 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 Control Values for lme Fit lme.groupedData LME fit from groupedData Object lme.lmList LME fit from lmList Object lmeObject Fitted lme Object lmeScale Scale for lme Optimization 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 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.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 Object pdIdent Multiple of the Identity Positive-Definite Matrix pdLogChol General Positive-Definite Matrix pdMat Positive-Definite Matrix [.pdMat Subscript a pdMat Object 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 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 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 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