*COLOR(red){nlme}パッケージ(線形・非線形混合効果モデル)中のオブジェクト一覧 [#a8b1d359]

Title:         Linear and Nonlinear Mixed Effects Models

*COLOR(red){nlme}パッケージ中のオブジェクト一覧 [#a8b1d359]

|ACF|                     自己相関関数|
|ACF.gls|                 gls 残差の自己相関関数|
|ACF.lme|                 lme 残差の自己相関関数|
|Alfalfa|                 Split-Plot Experiment on Varieties of Alfalfa|
|Assay|                   Bioassay on Cell Culture Plate|
|BIC|                     Bayesian Information Criterion|
|BIC.logLik|             logLik オブジェクトの BIC|
|BodyWeight|              Rat weight over time for different diets|
|Cefamandole|             Pharmacokinetics of Cefamandole|
|Dialyzer|                High-Flux Hemodialyzer|
|Dim|                     オブジェクトの次元の抽出|
|Dim.corSpatial|          corSpatial オブジェクトの次元|
|Dim.corStruct|           corStruct オブジェクトの次元|
|Dim.pdMat|               pdMat オブジェクトの次元|
|Earthquake|              震度|
|Fatigue|                 金属疲労による亀裂|
|Gasoline|                Refinery yield of gasoline|
|Glucose|                 Glucose levels over time|
|Glucose2|                Glucose Levels Following Alcohol Ingestion|
|Gun|                     Methods for firing naval guns|
|IGF|                     Radioimmunoassay of IGF-I Protein|
|Initialize|              オブジェクトの初期化|
|Initialize.corStruct|    corStruct オブジェクトの初期化|
|Initialize.glsStruct|    glsStruct オブジェクトの初期化|
|Initialize.lmeStruct|    Initialize an lmeStruct オブジェクトの初期化|
|Initialize.reStruct|     reStruct オブジェクトの初期化|
|Initialize.varFunc|      varFunc オブジェクトの初期化|
|LDEsysMat|               Generate system matrix for LDEs|
|Machines|                Productivity Scores for Machines and Workers|
|MathAchSchool|           School demographic data for MathAchieve|
|MathAchieve|             Mathematics achievement scores|
|Meat|                    Tenderness of meat|
|Milk|                    Protein content of cows' milk|
|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|
|Nitrendipene|            Assay of nitrendipene|
|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|
|PBG|                     Effect of Phenylbiguanide on Blood Pressure|
|Phenobarb|               Phenobarbitol Kinetics|
|Pixel|                   X-ray pixel intensities over time|
|Quinidine|               Quinidine Kinetics|
|Rail|                    Evaluation of Stress in Railway Rails|
|RatPupWeight|            The weight of rat pups|
|Relaxin|                 Assay for Relaxin|
|Remifentanil|            Pharmacokinetics of remifentanil|
|Soybean|                 Growth of soybean plants|
|Spruce|                  Growth of Spruce Trees|
|Tetracycline1|           Pharmacokinetics of tetracycline|
|Tetracycline2|           Pharmacokinetics of tetracycline|
|VarCorr|                 Extract variance and correlation components|
|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|
|Wafer|                   Modeling of Analog MOS Circuits|
|Wheat|                   Yields by growing conditions|
|Wheat2|                  Wheat Yield Trials|
|[.pdMat|                 Subscript a pdMat Object|
|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|
|asTable|                 Convert groupedData to a matrix|
|augPred|                 Augmented Predictions|
|balancedGrouped|         Create a groupedData object from a matrix|
|bdf|                     Language scores|
|coef.corStruct|          Coefficients of a corStruct Object|
|coef.gnls|               Extract gnls Coefficients|
|coef.lmList|             Extract lmList Coefficients|
|coef.lme|                Extract lme Coefficients|
|coef.modelStruct|        Extract modelStruct Object Coefficients|
|coef.pdMat|              pdMat Object Coefficients|
|coef.reStruct|           reStruct Object Coefficients|
|coef.varFunc|            varFunc Object Coefficients|
|coef<-|                  Assign Values to 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|
|ergoStool|               Ergometrics experiment with stool types|
|fdHess|                  Finite difference Hessian|
|fitted.glsStruct|        Calculate glsStruct Fitted Values|
|fitted.gnlsStruct|       Calculate gnlsStruct Fitted Values|
|fitted.lmList|           Extract lmList Fitted Values|
|fitted.lme|              Extract lme Fitted Values|
|fitted.lmeStruct|        Calculate lmeStruct 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|
|getCovariate|            Extract Covariate from an Object|
|getCovariate.corStruct|  Extract corStruct Object Covariate|
|| 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.lmList|          Extract lmList Object Data|
|getData.lme|             Extract lme Object Data|
|getGroups|               Extract Grouping Factors from an Object|
|getGroups.corStruct|     Extract corStruct Groups|
||    Extract Groups from a Data Frame|
|getGroups.gls|           Extract gls Object Groups|
|getGroups.lmList|        Extract lmList Object Groups|
|getGroups.lme|           Extract lme Object Groups|
|getGroups.varFunc|       Extract varFunc Groups|
|getGroupsFormula|        Extract Grouping Formula|
|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|
|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|
|intervals|               Confidence Intervals on Coefficients|
|intervals.gls|           Confidence Intervals on gls Parameters|
|intervals.lmList|        Confidence Intervals on lmList Coefficients|
|intervals.lme|           Confidence Intervals on lme Parameters|
|isBalanced|              Check a Design for Balance|
|isInitialized |          Check if Object is Initialized|
|lmList|                  List of lm Objects with a Common Model|
|lmList.groupedData|      lmList Fit from a groupedData Object|
|lme|                     Linear Mixed-Effects Models|
|lme.groupedData|         LME fit from groupedData Object|
|lme.lmList|              LME fit from lmList Object|
|lmeControl|              Control Values for lme Fit|
|lmeObject|               Fitted lme Object|
|lmeScale|                Scale for lme Optimization|
|lmeStruct|               Linear Mixed-Effects Structure|
|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.lmList|           Log-Likelihood of an lmList Object|
|logLik.lme|              Log-Likelihood of an lme Object|
|logLik.lmeStruct|        Log-Likelihood of an lmeStruct Object|
|logLik.reStruct|         Calculate reStruct Log-Likelihood|
|logLik.varFunc|          Extract varFunc logLik|
|matrix<-|                Assign Matrix Values|
|matrix<-.pdMat|          Assign Matrix to a pdMat Object|
|matrix<-.reStruct|       Assign reStruct Matrices|
|model.matrix.reStruct|   reStruct Model Matrix|
|needUpdate|              Check if Update is Needed|
|needUpdate.modelStruct|  Check if a modelStruct Object Needs Updating|
|nlme|                    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.selfStart|       nlsList Fit from a selfStart Function|
|pairs.compareFits|       Pairs Plot of compareFits Object|
|pairs.lmList|            Pairs Plot of an lmList Object|
|pairs.lme|               Pairs Plot of an lme Object|
|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|
|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|
|phenoModel|              Model function for the Phenobarb data|
|plot.ACF|                Plot an ACF Object|
|plot.Variogram|          Plot a Variogram 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.lmList|             Plot an lmList Object|
|plot.lme|                Plot an lme or nls object|
|plot.nffGroupedData|     Plot an nffGroupedData Object|
|plot.nfnGroupedData|     Plot an nfnGroupedData Object|
|plot.nmGroupedData|      Plot an nmGroupedData Object|
|plot.ranef.lmList|       Plot a ranef.lmList Object|
|plot.ranef.lme|          Plot a ranef.lme Object|
|pooledSD|                Extract Pooled Standard Deviation|
|predict.gls|             Predictions from a gls Object|
|predict.gnls|            Predictions from a gnls Object|
|predict.lmList|          Predictions from an lmList Object|
|predict.lme|             Predictions from an lme 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|
|quinModel|               Model function for the Quinidine data|
|random.effects|          Extract Random Effects|
|ranef.lmList|            Extract lmList Random Effects|
|ranef.lme|               Extract lme Random Effects|
|reStruct|                Random Effects Structure|
|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|
|residuals.gls|           Extract gls Residuals|
|residuals.glsStruct|     Calculate glsStruct Residuals|
|residuals.gnlsStruct|    Calculate gnlsStruct Residuals|
|residuals.lmList|        Extract lmList Residuals|
|residuals.lme|           Extract lme Residuals|
|residuals.lmeStruct|     Calculate lmeStruct Residuals|
|residuals.nlmeStruct|    Calculate nlmeStruct Residuals|
|simulate.lme|            Simulate results from lme models|
|solve.pdMat|             Calculate Inverse of a Positive-Definite Matrix|
|solve.reStruct|          Apply Solve to an reStruct Object|
|splitFormula|            Split a Formula|
|summary.corStruct|       Summarize a corStruct Object|
|summary.gls|             Summarize a gls Object|
|summary.lmList|          Summarize an lmList Object|
|summary.lme|             Summarize an lme Object|
|summary.modelStruct|     Summarize a modelStruct Object|
|summary.nlsList|         Summarize an nlsList Object|
|summary.pdMat|           Summarize a pdMat Object|
|summary.varFunc|         Summarize varFunc Object|
|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|
|varExp|                  Exponential Variance Function|
|varFixed|                Fixed Variance Function|
|varFunc|                 Variance Function Structure|
|varIdent|                Constant Variance Function|
|varPower|                Power Variance Function|
|varWeights|              Extract Variance Function Weights|
|varWeights.glsStruct|    Variance Weights for glsStruct Object|
|varWeights.lmeStruct|    Variance Weights for lmeStruct Object|

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