nlme v3.1-86
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Linear and Nonlinear Mixed Effects Models
Fit and compare Gaussian linear and nonlinear mixed-effects models.
Functions in nlme
| Name | Description | |
| ACF | Autocorrelation Function | |
| BIC.logLik | BIC of a logLik Object | |
| Oats | Split-plot Experiment on Varieties of Oats | |
| getResponseFormula | Extract Formula Specifying Response Variable | |
| corFactor.corStruct | Factor of a corStruct Object Matrix | |
| Variogram.default | Calculate Semi-variogram | |
| Dialyzer | High-Flux Hemodialyzer | |
| Gun | Methods for firing naval guns | |
| Covariate | Assign Covariate Values | |
| Ovary | Counts of Ovarian Follicles | |
| Covariate.varFunc | Assign varFunc Covariate | |
| Orthodont | Growth curve data on an orthdontic measurement | |
| coef.pdMat | pdMat Object Coefficients | |
| Coef | Assign Values to Coefficients | |
| collapse | Collapse According to Groups | |
| IGF | Radioimmunoassay of IGF-I Protein | |
| Soybean | Growth of soybean plants | |
| Glucose | Glucose levels over time | |
| getGroups.corStruct | Extract corStruct Groups | |
| getGroups | Extract Grouping Factors from an Object | |
| coef.modelStruct | Extract modelStruct Object Coefficients | |
| Tetracycline1 | Pharmacokinetics of tetracycline | |
| glsControl | Control Values for gls Fit | |
| random.effects | Extract Random Effects | |
| Initialize.varFunc | Initialize varFunc Object | |
| Cefamandole | Pharmacokinetics of Cefamandole | |
| BodyWeight | Rat weight over time for different diets | |
| Fatigue | Cracks caused by metal fatigue | |
| getGroups.gls | Extract gls Object Groups | |
| needUpdate.modelStruct | Check if a modelStruct Object Needs Updating | |
| plot.augPred | Plot an augPred Object | |
| varFixed | Fixed Variance Function | |
| Remifentanil | Pharmacokinetics of remifentanil | |
| Dim.pdMat | Dimensions of a pdMat Object | |
| Earthquake | Earthquake Intensity | |
| corExp | Exponential Correlation Structure | |
| Gasoline | Refinery yield of gasoline | |
| recalc.reStruct | Recalculate for an reStruct Object | |
| isBalanced | Check a Design for Balance | |
| logDet | Extract the Logarithm of the Determinant | |
| lmeScale | Scale for lme Optimization | |
| getGroupsFormula | Extract Grouping Formula | |
| Initialize.reStruct | Initialize reStruct Object | |
| lmList | List of lm Objects with a Common Model | |
| intervals | Confidence Intervals on Coefficients | |
| logDet.reStruct | Extract reStruct Log-Determinants | |
| gnlsStruct | Generalized Nonlinear Least Squares Structure | |
| residuals.lme | Extract lme Residuals | |
| fixef.lmList | Extract lmList Fixed Effects | |
| glsStruct | Generalized Least Squares Structure | |
| getGroups.lme | Extract lme Object Groups | |
| ACF.gls | Autocorrelation Function for gls Residuals | |
| logLik.varFunc | Extract varFunc logLik | |
| as.matrix.pdMat | Matrix of a pdMat Object | |
| Oxide | Variability in Semiconductor Manufacturing | |
| bdf | Language scores | |
| residuals.glsStruct | Calculate glsStruct Residuals | |
| lmeStruct | Linear Mixed-Effects Structure | |
| corClasses | Correlation Structure Classes | |
| update.varFunc | Update varFunc Object | |
| asTable | Convert groupedData to a matrix | |
| plot.lmList | Plot an lmList Object | |
| Initialize.corStruct | Initialize corStruct Object | |
| varWeights | Extract Variance Function Weights | |
| plot.gls | Plot a gls Object | |
| recalc | Recalculate Condensed Linear Model Object | |
| summary.pdMat | Summarize a pdMat Object | |
| residuals.gnlsStruct | Calculate gnlsStruct Residuals | |
| fitted.lmList | Extract lmList Fitted Values | |
| solve.pdMat | Calculate Inverse of a Positive-Definite Matrix | |
| getGroups.data.frame | Extract Groups from a Data Frame | |
| pairs.compareFits | Pairs Plot of compareFits Object | |
| Variogram.corGaus | Calculate Semi-variogram for a corGaus Object | |
| varComb | Combination of Variance Functions | |
| [.pdMat | Subscript a pdMat Object | |
| balancedGrouped | Create a groupedData object from a matrix | |
| Names.reStruct | Names of an reStruct Object | |
| varFunc | Variance Function Structure | |
| varClasses | Variance Function Classes | |
| getCovariateFormula | Extract Covariates Formula | |
| splitFormula | Split a Formula | |
| getData | Extract Data from an Object | |
| Muscle | Contraction of heart muscle sections | |
| corMatrix.pdMat | Extract Correlation Matrix from a pdMat Object | |
| plot.compareFits | Plot a compareFits Object | |
| recalc.corStruct | Recalculate for corStruct Object | |
| Tetracycline2 | Pharmacokinetics of tetracycline | |
| getData.lmList | Extract lmList Object Data | |
| Nitrendipene | Assay of nitrendipene | |
| isInitialized | Check if Object is Initialized | |
| intervals.gls | Confidence Intervals on gls Parameters | |
| logLik.lmList | Log-Likelihood of an lmList Object | |
| ranef.lmList | Extract lmList Random Effects | |
| corFactor | Factor of a Correlation Matrix | |
| varPower | Power Variance Function | |
| MathAchieve | Mathematics achievement scores | |
| getResponse | Extract Response Variable from an Object | |
| predict.gnls | Predictions from a gnls Object | |
| summary.corStruct | Summarize a corStruct Object | |
| summary.modelStruct | Summarize a modelStruct Object | |
| recalc.modelStruct | Recalculate for a modelStruct Object | |
| corSymm | General Correlation Structure | |
| getGroups.lmList | Extract lmList Object Groups | |
| Initialize | Initialize Object | |
| getCovariate | Extract Covariate from an Object | |
| Initialize.lmeStruct | Initialize an lmeStruct Object | |
| summary.lme | Summarize an lme Object | |
| pdMat | Positive-Definite Matrix | |
| formula.pdMat | Extract pdMat Formula | |
| coef.gnls | Extract gnls Coefficients | |
| corAR1 | AR(1) Correlation Structure | |
| coef.varFunc | varFunc Object Coefficients | |
| Oxboys | Heights of Boys in Oxford | |
| pdLogChol | General Positive-Definite Matrix | |
| recalc.varFunc | Recalculate for varFunc Object | |
| Dim.corStruct | Dimensions of a corStruct Object | |
| Dim | Extract Dimensions from an Object | |
| Variogram.corExp | Calculate Semi-variogram for a corExp Object | |
| formula.reStruct | Extract reStruct Object Formula | |
| formula.pdBlocked | Extract pdBlocked Formula | |
| intervals.lmList | Confidence Intervals on lmList Coefficients | |
| varWeights.lmeStruct | Variance Weights for lmeStruct Object | |
| lmeObject | Fitted lme Object | |
| residuals.nlmeStruct | Calculate nlmeStruct Residuals | |
| phenoModel | Model function for the Phenobarb data | |
| getGroups.varFunc | Extract varFunc Groups | |
| residuals.gls | Extract gls Residuals | |
| fitted.glsStruct | Calculate glsStruct Fitted Values | |
| BIC | Bayesian Information Criterion | |
| Variogram.corSpher | Calculate Semi-variogram for a corSpher Object | |
| model.matrix.reStruct | reStruct Model Matrix | |
| pooledSD | Extract Pooled Standard Deviation | |
| summary.varFunc | Summarize varFunc Object | |
| plot.ranef.lme | Plot a ranef.lme Object | |
| corMatrix.corStruct | Matrix of a corStruct Object | |
| plot.ACF | Plot an ACF Object | |
| qqnorm.gls | Normal Plot of Residuals from a gls Object | |
| gsummary | Summarize by Groups | |
| fdHess | Finite difference Hessian | |
| Variogram.lme | Calculate Semi-variogram for Residuals from an lme Object | |
| varIdent | Constant Variance Function | |
| Variogram.corLin | Calculate Semi-variogram for a corLin Object | |
| RatPupWeight | The weight of rat pups | |
| gnls | Fit Nonlinear Model Using Generalized Least Squares | |
| corSpatial | Spatial Correlation Structure | |
| gnlsObject | Fitted gnls Object | |
| lmeControl | Control Values for lme Fit | |
| pdMatrix | Extract Matrix or Square-Root Factor from a pdMat Object | |
| summary.lmList | Summarize an lmList Object | |
| logDet.corStruct | Extract corStruct Log-Determinant | |
| plot.nfnGroupedData | Plot an nfnGroupedData Object | |
| getData.lme | Extract lme Object Data | |
| fixed.effects | Extract Fixed Effects | |
| nlmeStruct | Nonlinear Mixed-Effects Structure | |
| plot.intervals.lmList | Plot lmList Confidence Intervals | |
| update.modelStruct | Update a modelStruct Object | |
| varWeights.glsStruct | Variance Weights for glsStruct Object | |
| Pixel | X-ray pixel intensities over time | |
| simulate.lme | Simulate results from lme models | |
| glsObject | Fitted gls Object | |
| predict.gls | Predictions from a gls Object | |
| corGaus | Gaussian Correlation Structure | |
| plot.ranef.lmList | Plot a ranef.lmList Object | |
| getVarCov | Extract variance-covariance matrix | |
| coef.lmList | Extract lmList Coefficients | |
| Phenobarb | Phenobarbitol Kinetics | |
| varConstPower | Constant Plus Power Variance Function | |
| VarCorr | Extract variance and correlation components | |
| Variogram | Calculate Semi-variogram | |
| nlmeObject | Fitted nlme Object | |
| predict.lme | Predictions from an lme Object | |
| Dim.corSpatial | Dimensions of a corSpatial Object | |
| ergoStool | Ergometrics experiment with stool types | |
| nlsList | List of nls Objects with a Common Model | |
| quinModel | Model function for the Quinidine data | |
| logLik.reStruct | Calculate reStruct Log-Likelihood | |
| compareFits | Compare Fitted Objects | |
| Rail | Evaluation of Stress in Railway Rails | |
| logLik.glsStruct | Log-Likelihood of a glsStruct Object | |
| ranef.lme | Extract lme Random Effects | |
| getCovariate.varFunc | Extract varFunc Covariate | |
| PBG | Effect of Phenylbiguanide on Blood Pressure | |
| pdFactor.reStruct | Extract Square-Root Factor from Components of an reStruct Object | |
| fitted.gnlsStruct | Calculate gnlsStruct Fitted Values | |
| Names.pdMat | Names of a pdMat Object | |
| coef.corStruct | Coefficients of a corStruct Object | |
| fitted.nlmeStruct | Calculate nlmeStruct Fitted Values | |
| varExp | Exponential Variance Function | |
| predict.nlme | Predictions from an nlme Object | |
| ACF.lme | Autocorrelation Function for lme Residuals | |
| Assay | Bioassay on Cell Culture Plate | |
| lmList.groupedData | lmList Fit from a groupedData Object | |
| Variogram.corRatio | Calculate Semi-variogram for a corRatio Object | |
| lme.lmList | LME fit from lmList Object | |
| nlmeControl | Control Values for nlme Fit | |
| gapply | Apply a Function by Groups | |
| logLik.lmeStruct | Log-Likelihood of an lmeStruct Object | |
| LDEsysMat | Generate system matrix for LDEs | |
| print.summary.pdMat | Print a summary.pdMat Object | |
| corLin | Linear Correlation Structure | |
| collapse.groupedData | Collapse a groupedData Object | |
| residuals.lmList | Extract lmList Residuals | |
| coef.reStruct | reStruct Object Coefficients | |
| pdSymm | General Positive-Definite Matrix | |
| needUpdate | Check if Update is Needed | |
| groupedData | Construct a groupedData Object | |
| plot.nmGroupedData | Plot an nmGroupedData Object | |
| Glucose2 | Glucose Levels Following Alcohol Ingestion | |
| reStruct | Random Effects Structure | |
| plot.nffGroupedData | Plot an nffGroupedData Object | |
| solve.reStruct | Apply Solve to an reStruct Object | |
| logLik.gnls | Log-Likelihood of a gnls Object | |
| Wafer | Modeling of Analog MOS Circuits | |
| Meat | Tenderness of meat | |
| Matrix.reStruct | Assign reStruct Matrices | |
| logLik.corStruct | Extract corStruct Log-Likelihood | |
| pdClasses | Positive-Definite Matrix Classes | |
| lme | Linear Mixed-Effects Models | |
| print.varFunc | Print a varFunc Object | |
| Names.formula | Extract Names from a formula | |
| corRatio | Rational Quadratic Correlation Structure | |
| residuals.lmeStruct | Calculate lmeStruct Residuals | |
| corARMA | ARMA(p,q) Correlation Structure | |
| pdDiag | Diagonal Positive-Definite Matrix | |
| Wheat2 | Wheat Yield Trials | |
| allCoef | Extract Coefficients from a Set of Objects | |
| MathAchSchool | School demographic data for MathAchieve | |
| augPred | Augmented Predictions | |
| pdIdent | Multiple of the Identity Positive-Definite Matrix | |
| summary.nlsList | Summarize an nlsList Object | |
| asOneFormula | Combine Formulas of a Set of Objects | |
| plot.lme | Plot an lme or nls object | |
| pdMatrix.reStruct | Extract Matrix or Square-Root Factor from Components of an reStruct Object | |
| plot.Variogram | Plot a Variogram Object | |
| Milk | Protein content of cows' milk | |
| Initialize.glsStruct | Initialize a glsStruct Object | |
| logDet.pdMat | Extract Log-Determinant from a pdMat Object | |
| lme.groupedData | LME fit from groupedData Object | |
| logLik.lme | Log-Likelihood of an lme Object | |
| Alfalfa | Split-Plot Experiment on Varieties of Alfalfa | |
| gls | Fit Linear Model Using Generalized Least Squares | |
| pdConstruct | Construct pdMat Objects | |
| logLik.gnlsStruct | Log-Likelihood of a gnlsStruct Object | |
| coef.lme | Extract lme Coefficients | |
| corCompSymm | Compound Symmetry Correlation Structure | |
| Matrix | Assign Matrix Values | |
| Variogram.corSpatial | Calculate Semi-variogram for a corSpatial Object | |
| getCovariate.corStruct | Extract corStruct Object Covariate | |
| pairs.lme | Pairs Plot of an lme Object | |
| as.matrix.reStruct | Matrices of an reStruct Object | |
| corNatural | General correlation in natural parameterization | |
| pdCompSymm | Positive-Definite Matrix with Compound Symmetry Structure | |
| pairs.lmList | Pairs Plot of an lmList Object | |
| getData.gls | Extract gls Object Data | |
| nlsList.selfStart | nlsList Fit from a selfStart Function | |
| Quinidine | Quinidine Kinetics | |
| corMatrix.reStruct | Extract Correlation Matrix from Components of an reStruct Object | |
| corSpher | Spherical Correlation Structure | |
| Matrix.pdMat | Assign Matrix to a pdMat Object | |
| Names.pdBlocked | Names of a pdBlocked Object | |
| Spruce | Growth of Spruce Trees | |
| pdConstruct.pdBlocked | Construct pdBlocked Objects | |
| nlme.nlsList | NLME fit from nlsList Object | |
| fitted.lmeStruct | Calculate lmeStruct Fitted Values | |
| summary.gls | Summarize a gls Object | |
| pdFactor | Square-Root Factor of a Positive-Definite Matrix | |
| getCovariate.data.frame | Extract Data Frame Covariate | |
| nlme | Nonlinear Mixed-Effects Models | |
| pdBlocked | Positive-Definite Block Diagonal Matrix | |
| fitted.lme | Extract lme Fitted Values | |
| intervals.lme | Confidence Intervals on lme Parameters | |
| comparePred | Compare Predictions | |
| predict.lmList | Predictions from an lmList Object | |
| corMatrix | Extract Correlation Matrix | |
| corCAR1 | Continuous AR(1) Correlation Structure | |
| anova.lme | Compare Likelihoods of Fitted Objects | |
| Relaxin | Assay for Relaxin | |
| qqnorm.lme | Normal Plot of Residuals or Random Effects from an lme Object | |
| Variogram.gls | Calculate Semi-variogram for Residuals from a gls Object | |
| pdNatural | General Positive-Definite Matrix in Natural Parametrization | |
| gnlsControl | Control Values for gnls Fit | |
| anova.gls | Compare Likelihoods of Fitted Objects | |
| Wheat | Yields by growing conditions | |
| Machines | Productivity Scores for Machines and Workers | |
| as.matrix.corStruct | Matrix of a corStruct Object | |
| Names | Names Associated with an Object | |
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Details
| Date | 2007-10-04 |
| Priority | recommended |
| LazyLoad | yes |
| LazyData | yes |
| License | GPL (>=2) |
| Packaged | Thu Oct 4 23:25:21 2007; hornik |
| depends | base (>= 2.4.0) , graphics , R (>= 2.4.0) , stats |
| imports | lattice |
| Contributors | Deepayan Sarkar, Jose Pinheiro, Douglas Bates, Saikat DebRoy |
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