| Subscript a pdMat Object | [.pdBlocked [.pdMat [<-.pdMat |
| Autocorrelation Function | ACF |
| Autocorrelation Function for gls Residuals | ACF.gls |
| Autocorrelation Function for lme Residuals | ACF.lme |
| Split-Plot Experiment on Varieties of Alfalfa | Alfalfa |
| Extract Coefficients from a Set of Objects | allCoef |
| Compare Likelihoods of Fitted Objects | anova.gls |
| Compare Likelihoods of Fitted Objects | anova.lme print.anova.lme |
| Matrix of a corStruct Object | as.matrix.corStruct |
| Matrix of a pdMat Object | as.matrix.pdMat |
| Matrices of an reStruct Object | as.matrix.reStruct |
| Combine Formulas of a Set of Objects | asOneFormula |
| Bioassay on Cell Culture Plate | Assay |
| Convert groupedData to a matrix | asTable asTable.groupedData |
| Augmented Predictions | augPred augPred.gls augPred.lme augPred.lmList |
| Create a groupedData object from a matrix | balancedGrouped |
| Language scores | bdf |
| Rat weight over time for different diets | BodyWeight |
| Pharmacokinetics of Cefamandole | Cefamandole |
| Assign Values to Coefficients | coef<- coefficients<- |
| Coefficients of a corStruct Object | coef.corAR1 coef.corARMAd coef.corCAR1 coef.corCompSymm coef.corHF coef.corLin coef.corNatural coef.corSpatial coef.corSpher coef.corStruct coef.corSymm coef.summary.nlsList coef<-.corAR1 coef<-.corARMA coef<-.corCAR1 coef<-.corCompSymm coef<-.corHF coef<-.corLin coef<-.corNatural coef<-.corSpatial coef<-.corSpher coef<-.corStruct coef<-.corSymm |
| Extract gnls Coefficients | coef.gnls |
| Extract lme Coefficients | coef.lme |
| Extract lmList Coefficients | coef.lmList |
| Extract modelStruct Object Coefficients | coef.modelStruct coef<-.modelStruct |
| pdMat Object Coefficients | coef.pdBlocked coef.pdCompSymm coef.pdDiag coef.pdIdent coef.pdMat coef.pdNatural coef.pdSymm coef<-.pdBlocked coef<-.pdMat |
| reStruct Object Coefficients | coef.reStruct coef<-.reStruct |
| varFunc Object Coefficients | coef.varComb coef.varConstPower coef.varConstProp coef.varExp coef.varFixed coef.varFunc coef.varIdent coef.varPower coef<-.varComb coef<-.varConstPower coef<-.varConstProp coef<-.varExp coef<-.varFixed coef<-.varIdent coef<-.varPower |
| Collapse According to Groups | collapse |
| Collapse a groupedData Object | collapse.groupedData |
| Compare Fitted Objects | compareFits print.compareFits |
| Compare Predictions | comparePred comparePred.gls comparePred.lme comparePred.lmList |
| AR(1) Correlation Structure | corAR1 |
| ARMA(p,q) Correlation Structure | coef.corARMA corARMA |
| Continuous AR(1) Correlation Structure | corCAR1 |
| Correlation Structure Classes | corClasses corStruct |
| Compound Symmetry Correlation Structure | corCompSymm |
| Exponential Correlation Structure | corExp |
| Factor of a Correlation Matrix | corFactor |
| Factor of a corStruct Object Matrix | corFactor.corAR1 corFactor.corARMA corFactor.corCAR1 corFactor.corCompSymm corFactor.corNatural corFactor.corSpatial corFactor.corStruct corFactor.corSymm |
| Gaussian Correlation Structure | corGaus |
| Linear Correlation Structure | corLin |
| Extract Correlation Matrix | corMatrix |
| Matrix of a corStruct Object | corMatrix.corAR1 corMatrix.corARMA corMatrix.corCAR1 corMatrix.corCompSymm corMatrix.corNatural corMatrix.corSpatial corMatrix.corStruct corMatrix.corSymm |
| Extract Correlation Matrix from a pdMat Object | corMatrix.pdBlocked corMatrix.pdCompSymm corMatrix.pdDiag corMatrix.pdIdent corMatrix.pdMat corMatrix.pdSymm |
| Extract Correlation Matrix from Components of an reStruct Object | corMatrix.reStruct |
| General correlation in natural parameterization | corNatural print.corNatural |
| Rational Quadratic Correlation Structure | corRatio |
| Spatial Correlation Structure | corSpatial |
| Spherical Correlation Structure | corSpher |
| General Correlation Structure | corSymm |
| Assign Covariate Values | covariate<- |
| Assign varFunc Covariate | covariate<-.varFunc |
| High-Flux Hemodialyzer | Dialyzer |
| Extract Dimensions from an Object | Dim Dim.default |
| Dimensions of a corSpatial Object | Dim.corSpatial |
| Dimensions of a corStruct Object | Dim.corStruct |
| Dimensions of a pdMat Object | Dim.pdCompSymm Dim.pdDiag Dim.pdIdent Dim.pdMat Dim.pdNatural Dim.pdSymm |
| Earthquake Intensity | Earthquake |
| Ergometrics experiment with stool types | ergoStool |
| Cracks caused by metal fatigue | Fatigue |
| Finite difference Hessian | fdHess |
| Calculate glsStruct Fitted Values | fitted.glsStruct |
| Calculate gnlsStruct Fitted Values | fitted.gnlsStruct |
| Extract lme Fitted Values | fitted.lme |
| Calculate lmeStruct Fitted Values | fitted.lmeStruct |
| Extract lmList Fitted Values | fitted.lmList |
| Calculate nlmeStruct Fitted Values | fitted.nlmeStruct |
| Extract Fixed Effects | fixed.effects fixef |
| Extract lmList Fixed Effects | fixed.effects.lmList fixef.lmList |
| Extract pdBlocked Formula | formula.pdBlocked |
| Extract pdMat Formula | formula.pdMat |
| Extract reStruct Object Formula | formula.reStruct |
| Apply a Function by Groups | gapply |
| Refinery yield of gasoline | Gasoline |
| Extract Covariate from an Object | getCovariate |
| Extract corStruct Object Covariate | getCovariate.corSpatial getCovariate.corStruct |
| Extract Data Frame Covariate | getCovariate.data.frame |
| Extract varFunc Covariate | getCovariate.varFunc |
| Extract Covariates Formula | getCovariateFormula |
| Extract Data from an Object | getData |
| Extract gls Object Data | getData.gls getData.gnls |
| Extract lme Object Data | getData.lme getData.nlme getData.nls |
| Extract lmList Object Data | getData.lmList |
| Extract Grouping Factors from an Object | getGroups |
| Extract corStruct Groups | getGroups.corStruct |
| Extract Groups from a Data Frame | getGroups.data.frame |
| Extract gls Object Groups | getGroups.gls |
| Extract lme Object Groups | getGroups.lme |
| Extract lmList Object Groups | getGroups.lmList |
| Extract varFunc Groups | getGroups.varFunc |
| Extract Grouping Formula | getGroupsFormula getGroupsFormula.default getGroupsFormula.gls getGroupsFormula.lme getGroupsFormula.lmList getGroupsFormula.reStruct |
| Extract Response Variable from an Object | getResponse getResponse.data.frame |
| Extract Formula Specifying Response Variable | getResponseFormula |
| Extract variance-covariance matrix | getVarCov getVarCov.gls getVarCov.lme print.VarCov |
| Fit Linear Model Using Generalized Least Squares | gls update.gls |
| Control Values for gls Fit | glsControl |
| Fitted gls Object | glsObject |
| Generalized Least Squares Structure | glsStruct |
| Glucose levels over time | Glucose |
| Glucose Levels Following Alcohol Ingestion | Glucose2 |
| Fit Nonlinear Model Using Generalized Least Squares | gnls |
| Control Values for gnls Fit | gnlsControl |
| Fitted gnls Object | gnlsObject |
| Generalized Nonlinear Least Squares Structure | gnlsStruct Initialize.gnlsStruct |
| Construct a groupedData Object | as.data.frame.groupedData groupedData update.groupedData [.groupedData |
| Summarize by Groups | gsummary |
| Methods for firing naval guns | Gun |
| Radioimmunoassay of IGF-I Protein | IGF |
| Initialize Object | Initialize |
| Initialize corStruct Object | Initialize.corAR1 Initialize.corARMA Initialize.corCAR1 Initialize.corCompSymm Initialize.corHF Initialize.corLin Initialize.corNatural Initialize.corSpatial Initialize.corSpher Initialize.corStruct Initialize.corSymm |
| Initialize a glsStruct Object | Initialize.glsStruct |
| Initialize an lmeStruct Object | Initialize.lmeStruct |
| Initialize reStruct Object | Initialize.reStruct |
| Initialize varFunc Object | Initialize.varComb Initialize.varConstPower Initialize.varConstProp Initialize.varExp Initialize.varFixed Initialize.varFunc Initialize.varIdent Initialize.varPower |
| Confidence Intervals on Coefficients | intervals |
| Confidence Intervals on gls Parameters | intervals.gls print.intervals.gls |
| Confidence Intervals on lme Parameters | intervals.lme print.intervals.lme |
| Confidence Intervals on lmList Coefficients | intervals.lmList print.intervals.lmList |
| Check a Design for Balance | isBalanced isBalanced.groupedData |
| Check if Object is Initialized | isInitialized isInitialized.pdBlocked isInitialized.pdMat |
| Generate system matrix for LDEs | LDEsysMat |
| Linear Mixed-Effects Models | lme lme.formula update.lme |
| LME fit from groupedData Object | lme.groupedData |
| LME fit from lmList Object | lme.lmList |
| Specifying Control Values for lme Fit | lmeControl |
| Fitted lme Object | lmeObject |
| Linear Mixed-Effects Structure | lmeStruct |
| List of lm Objects with a Common Model | lmList lmList.formula print.lmList update.lmList |
| lmList Fit from a groupedData Object | lmList.groupedData |
| Extract the Logarithm of the Determinant | logDet |
| Extract corStruct Log-Determinant | logDet.corStruct |
| Extract Log-Determinant from a pdMat Object | logDet.pdBlocked logDet.pdCompSymm logDet.pdDiag logDet.pdIdent logDet.pdMat logDet.pdNatural logDet.pdSymm |
| Extract reStruct Log-Determinants | logDet.reStruct |
| Extract corStruct Log-Likelihood | logLik.corStruct |
| Log-Likelihood of a glsStruct Object | logLik.glsStruct |
| Log-Likelihood of a gnls Object | logLik.gnls |
| Log-Likelihood of a gnlsStruct Object | logLik.gnlsStruct |
| Log-Likelihood of an lme Object | logLik.gls logLik.lme |
| Log-Likelihood of an lmeStruct Object | logLik.lmeStruct logLik.lmeStructInt |
| Log-Likelihood of an lmList Object | logLik.lmList |
| Calculate reStruct Log-Likelihood | logLik.reStruct |
| Extract varFunc logLik | logLik.varComb logLik.varFunc |
| Productivity Scores for Machines and Workers | Machines |
| Mathematics achievement scores | MathAchieve |
| School demographic data for MathAchieve | MathAchSchool |
| Assign Matrix Values | matrix<- |
| Assign Matrix to a pdMat or pdBlocked Object | matrix<-.pdBlocked matrix<-.pdMat |
| Assign reStruct Matrices | matrix<-.reStruct |
| Tenderness of meat | Meat |
| Protein content of cows' milk | Milk |
| reStruct Model Matrix | model.matrix.reStruct |
| Contraction of heart muscle sections | Muscle |
| Names Associated with an Object | Names Names<- |
| Extract Names from a formula | Names.formula Names.listForm |
| Names of a pdBlocked Object | Names.pdBlocked Names<-.pdBlocked |
| Names of a pdMat Object | Names.pdMat Names<-.pdMat |
| Names of an reStruct Object | Names.reStruct Names<-.reStruct |
| Check if Update is Needed | needUpdate needUpdate.default needUpdate.varComb needUpdate.varIdent |
| Check if a modelStruct Object Needs Updating | needUpdate.corStruct needUpdate.modelStruct needUpdate.reStruct |
| Assay of nitrendipene | Nitrendipene |
| Nonlinear Mixed-Effects Models | nlme nlme.formula |
| NLME fit from nlsList Object | nlme.nlsList |
| Control Values for nlme Fit | nlmeControl |
| Fitted nlme Object | nlmeObject |
| Nonlinear Mixed-Effects Structure | nlmeStruct |
| List of nls Objects with a Common Model | nlsList nlsList.formula update.nlsList |
| nlsList Fit from a selfStart Function | nlsList.selfStart |
| Split-plot Experiment on Varieties of Oats | Oats |
| Growth curve data on an orthdontic measurement | Orthodont |
| Counts of Ovarian Follicles | Ovary |
| Heights of Boys in Oxford | Oxboys |
| Variability in Semiconductor Manufacturing | Oxide |
| Pairs Plot of compareFits Object | pairs.compareFits |
| Pairs Plot of an lme Object | pairs.lme |
| Pairs Plot of an lmList Object | pairs.lmList |
| Effect of Phenylbiguanide on Blood Pressure | PBG |
| Positive-Definite Block Diagonal Matrix | pdBlocked |
| Positive-Definite Matrix Classes | pdClasses |
| Positive-Definite Matrix with Compound Symmetry Structure | pdCompSymm |
| Construct pdMat Objects | pdConstruct pdConstruct.pdCompSymm pdConstruct.pdDiag pdConstruct.pdIdent pdConstruct.pdLogChol pdConstruct.pdMat pdConstruct.pdNatural pdConstruct.pdSymm |
| Construct pdBlocked Objects | pdConstruct.pdBlocked |
| Diagonal Positive-Definite Matrix | pdDiag |
| Square-Root Factor of a Positive-Definite Matrix | pdFactor pdFactor.pdBlocked pdFactor.pdCompSymm pdFactor.pdDiag pdFactor.pdIdent pdFactor.pdLogChol pdFactor.pdMat pdFactor.pdNatural pdFactor.pdSymm |
| Extract Square-Root Factor from Components of an reStruct Object | pdFactor.reStruct |
| Multiple of the Identity Positive-Definite Matrix | pdIdent |
| General Positive-Definite Matrix | pdLogChol |
| Positive-Definite Matrix | pdMat plot.pdMat |
| Extract Matrix or Square-Root Factor from a pdMat Object | pdMatrix pdMatrix.pdBlocked pdMatrix.pdCompSymm pdMatrix.pdDiag pdMatrix.pdIdent pdMatrix.pdMat pdMatrix.pdNatural pdMatrix.pdSymm |
| Extract Matrix or Square-Root Factor from Components of an reStruct Object | pdMatrix.reStruct |
| General Positive-Definite Matrix in Natural Parametrization | pdNatural |
| General Positive-Definite Matrix | pdSymm |
| Phenobarbitol Kinetics | Phenobarb |
| Model function for the Phenobarb data | phenoModel |
| X-ray pixel intensities over time | Pixel |
| Plot an ACF Object | plot.ACF |
| Plot an augPred Object | plot.augPred |
| Plot a compareFits Object | plot.compareFits |
| Plot a gls Object | plot.gls |
| Plot lmList Confidence Intervals | plot.intervals.lmList |
| Plot an lme or nls object | plot.lme plot.nls |
| Plot an lmList Object | plot.lmList |
| Plot an nffGroupedData Object | plot.nffGroupedData |
| Plot an nfnGroupedData Object | plot.nfnGroupedData |
| Plot an nmGroupedData Object | plot.nmGroupedData |
| Plot a ranef.lme Object | plot.ranef.lme |
| Plot a ranef.lmList Object | plot.ranef.lmList |
| Plot a Variogram Object | plot.Variogram |
| Extract Pooled Standard Deviation | pooledSD |
| Predictions from a gls Object | predict.gls |
| Predictions from a gnls Object | predict.gnls |
| Predictions from an lme Object | predict.lme |
| Predictions from an lmList Object | predict.lmList |
| Predictions from an nlme Object | predict.nlme |
| Print a summary.pdMat Object | print.summary.pdMat |
| Print a varFunc Object | print.varComb print.varFunc |
| Normal Plot of Residuals from a gls Object | qqnorm.gls |
| Normal Plot of Residuals or Random Effects from an lme Object | qqnorm.lm qqnorm.lme qqnorm.lmList qqnorm.nls |
| Quinidine Kinetics | Quinidine |
| Model function for the Quinidine data | quinModel |
| Evaluation of Stress in Railway Rails | Rail |
| Extract Random Effects | print.ranef random.effects ranef |
| Extract lme Random Effects | print.ranef.lme random.effects.lme ranef.lme |
| Extract lmList Random Effects | random.effects.lmList ranef.lmList |
| The weight of rat pups | RatPupWeight |
| Recalculate Condensed Linear Model Object | recalc |
| Recalculate for corStruct Object | recalc.corAR1 recalc.corARMA recalc.corCAR1 recalc.corCompSymm recalc.corHF recalc.corNatural recalc.corSpatial recalc.corStruct recalc.corSymm |
| Recalculate for a modelStruct Object | recalc.modelStruct |
| Recalculate for an reStruct Object | recalc.reStruct |
| Recalculate for varFunc Object | recalc.varFunc recalc.varIdent |
| Assay for Relaxin | Relaxin |
| Pharmacokinetics of Remifentanil | Remifentanil |
| Extract gls Residuals | residuals.gls residuals.gnls |
| Calculate glsStruct Residuals | residuals.glsStruct |
| Calculate gnlsStruct Residuals | residuals.gnlsStruct |
| Extract lme Residuals | residuals.lme |
| Calculate lmeStruct Residuals | residuals.lmeStruct |
| Extract lmList Residuals | residuals.lmList |
| Calculate nlmeStruct Residuals | residuals.nlmeStruct |
| Random Effects Structure | print.reStruct reStruct [.reStruct |
| Simulate Results from 'lme' Models | plot.simulate.lme print.simulate.lme simulate.lme |
| Calculate Inverse of a Positive-Definite Matrix | solve.pdBlocked solve.pdDiag solve.pdIdent solve.pdLogChol solve.pdMat solve.pdNatural solve.pdSymm |
| Apply Solve to an reStruct Object | solve.reStruct |
| Growth of soybean plants | Soybean |
| Split a Formula | splitFormula |
| Growth of Spruce Trees | Spruce |
| Summarize a corStruct Object | summary.corAR1 summary.corARMA summary.corCAR1 summary.corCompSymm summary.corExp summary.corGaus summary.corLin summary.corNatural summary.corRatio summary.corSpher summary.corStruct summary.corSymm |
| Summarize a Generalized Least Squares 'gls' Object | summary.gls |
| Summarize an lme Object | print.summary.lme summary.lme |
| Summarize an lmList Object | summary.lmList |
| Summarize a modelStruct Object | summary.modelStruct summary.reStruct |
| Summarize an nlsList Object | summary.nlsList |
| Summarize a pdMat Object | summary.pdBlocked summary.pdCompSymm summary.pdDiag summary.pdIdent summary.pdLogChol summary.pdMat summary.pdNatural summary.pdSymm |
| Summarize "varFunc" Object | summary.varComb summary.varConstPower summary.varConstProp summary.varExp summary.varFixed summary.varFunc summary.varIdent summary.varPower |
| Pharmacokinetics of tetracycline | Tetracycline1 |
| Pharmacokinetics of tetracycline | Tetracycline2 |
| Update a modelStruct Object | update.corStruct update.modelStruct update.reStruct |
| Update varFunc Object | update.varComb update.varConstPower update.varConstProp update.varExp update.varExpon update.varFunc update.varPower |
| Variance Function Classes | varClasses |
| Combination of Variance Functions | varComb |
| Constant Plus Power Variance Function | varConstPower |
| Constant Plus Proportion Variance Function | varConstProp |
| Extract variance and correlation components | print.VarCorr.lme VarCorr VarCorr.lme VarCorr.pdBlocked VarCorr.pdMat |
| Exponential Variance Function | varExp |
| Fixed Variance Function | varFixed |
| Variance Function Structure | varFunc |
| Constant Variance Function | varIdent |
| Calculate Semi-variogram | Variogram |
| Calculate Semi-variogram for a corExp Object | Variogram.corExp |
| Calculate Semi-variogram for a corGaus Object | Variogram.corGaus |
| Calculate Semi-variogram for a corLin Object | Variogram.corLin |
| Calculate Semi-variogram for a corRatio Object | Variogram.corRatio |
| Calculate Semi-variogram for a corSpatial Object | Variogram.corSpatial |
| Calculate Semi-variogram for a corSpher Object | Variogram.corSpher |
| Calculate Semi-variogram | Variogram.default |
| Calculate Semi-variogram for Residuals from a gls Object | Variogram.gls |
| Calculate Semi-variogram for Residuals from an lme Object | Variogram.lme |
| Power Variance Function | varPower |
| Extract Variance Function Weights | varWeights varWeights.varComb varWeights.varFunc |
| Variance Weights for glsStruct Object | varWeights.glsStruct |
| Variance Weights for lmeStruct Object | varWeights.lmeStruct |
| Modeling of Analog MOS Circuits | Wafer |
| Yields by growing conditions | Wheat |
| Wheat Yield Trials | Wheat2 |
