Linear and Nonlinear Mixed Effects Models
Autocorrelation Function for gls Residuals
Extract Correlation Matrix from a pdMat Object
Extract Correlation Matrix
Extract Correlation Matrix from Components of an reStruct Object
General correlation in natural parameterization
Rational Quadratic Correlation Structure
Spatial Correlation Structure
Spherical Correlation Structure
General Correlation Structure
Assign Covariate Values
Assign varFunc Covariate
Extract reStruct Object Formula
Extract gls Object Data
Log-Likelihood of a gnls Object
Matrix of a pdMat Object
Plot a ranef.lmList Object
Matrices of an reStruct Object
Combine Formulas of a Set of Objects
Extract lme Object Data
Autocorrelation Function for lme Residuals
Autocorrelation Function
Extract Coefficients from a Set of Objects
Compare Likelihoods of Fitted Objects
Compare Likelihoods of Fitted Objects
Matrix of a corStruct Object
Convert groupedData to a matrix
Augmented Predictions
Create a groupedData object from a matrix
Coefficients of a corStruct Object
Extract gnls Coefficients
Extract lme Coefficients
Extract lmList Coefficients
Extract lmList Object Data
Extract modelStruct Object Coefficients
pdMat Object Coefficients
Assign Values to Coefficients
reStruct Object Coefficients
Correlation Structure Classes
varFunc Object Coefficients
Collapse a groupedData Object
Collapse According to Groups
Compare Fitted Objects
Compare Predictions
AR(1) Correlation Structure
ARMA(p,q) Correlation Structure
Continuous AR(1) Correlation Structure
Compound Symmetry Correlation Structure
Exponential Correlation Structure
Factor of a corStruct Object Matrix
Factor of a Correlation Matrix
Gaussian Correlation Structure
Linear Correlation Structure
Matrix of a corStruct Object
Dimensions of a corSpatial Object
Dimensions of a corStruct Object
Dimensions of a pdMat Object
Extract Dimensions from an Object
Subscript a pdMat Object
Extract Data from an Object
Finite difference Hessian
Calculate glsStruct Fitted Values
Calculate gnlsStruct Fitted Values
Extract lme Fitted Values
Calculate lmeStruct Fitted Values
Extract lmList Fitted Values
Calculate nlmeStruct Fitted Values
Extract Fixed Effects
Extract lmList Fixed Effects
Extract pdBlocked Formula
Extract pdMat Formula
Apply a Function by Groups
Extract corStruct Object Covariate
Extract Data Frame Covariate
Extract Covariate from an Object
Extract varFunc Covariate
Extract Covariates Formula
Extract corStruct Groups
Extract Groups from a Data Frame
Extract gls Object Groups
Extract lme Object Groups
Extract Formula Specifying Response Variable
Extract lmList Object Groups
Extract Grouping Factors from an Object
Extract varFunc Groups
Extract Grouping Formula
Extract Response Variable from an Object
Fit Nonlinear Model Using Generalized Least Squares
Extract variance-covariance matrix
Auxiliary functions used by gls
Fit Linear Model Using Generalized Least Squares
Control Values for gls Fit
Fitted gls Object
Generalized Least Squares Structure
Control Values for gnls Fit
Fitted gnls Object
Generalized Nonlinear Least Squares Structure
Construct a groupedData Object
Summarize by Groups
Initialize corStruct Object
Initialize a glsStruct Object
Initialize an lmeStruct Object
Initialize Object
Initialize reStruct Object
Initialize varFunc Object
Confidence Intervals on gls Parameters
Confidence Intervals on lme Parameters
Confidence Intervals on lmList Coefficients
Confidence Intervals on Coefficients
Check a Design for Balance
Check if Object is Initialized
Generate system matrix for LDEs
LME fit from groupedData Object
LME fit from lmList Object
Linear Mixed-Effects Models
Specifying Control Values for lme Fit
Fitted lme Object
Linear Mixed-Effects Structure
lmList Fit from a groupedData Object
List of lm Objects with a Common Model
Extract corStruct Log-Determinant
Extract Log-Determinant from a pdMat Object
Extract the Logarithm of the Determinant
Extract reStruct Log-Determinants
Extract corStruct Log-Likelihood
Log-Likelihood of a glsStruct Object
Log-Likelihood of a gnlsStruct Object
Log-Likelihood of an lme Object
Log-Likelihood of an lmeStruct Object
Log-Likelihood of an lmList Object
Extract Random Effects
Calculate reStruct Log-Likelihood
Extract varFunc logLik
Assign Matrix to a pdMat or pdBlocked Object
Assign Matrix Values
Assign reStruct Matrices
Extract lme Random Effects
reStruct Model Matrix
Extract Names from a formula
Names of a pdBlocked Object
Names of a pdMat Object
Names Associated with an Object
Names of an reStruct Object
Check if a modelStruct Object Needs Updating
Check if Update is Needed
Deprecated Functions in Package nlme
NLME fit from nlsList Object
Nonlinear Mixed-Effects Models
Control Values for nlme Fit
Fitted nlme Object
Calculate Inverse of a Positive-Definite Matrix
Nonlinear Mixed-Effects Structure
List of nls Objects with a Common Model
nlsList Fit from a selfStart Function
Pairs Plot of compareFits Object
Pairs Plot of an lme Object
Pairs Plot of an lmList Object
Positive-Definite Block Diagonal Matrix
Positive-Definite Matrix Classes
Positive-Definite Matrix with Compound Symmetry Structure
Construct pdBlocked Objects
Construct pdMat Objects
Diagonal Positive-Definite Matrix
Square-Root Factor of a Positive-Definite Matrix
Extract Square-Root Factor from Components of an reStruct Object
Multiple of the Identity Positive-Definite Matrix
General Positive-Definite Matrix
Positive-Definite Matrix
Extract Matrix or Square-Root Factor from a pdMat Object
Extract Matrix or Square-Root Factor from Components of an reStruct Ob...
General Positive-Definite Matrix in Natural Parametrization
General Positive-Definite Matrix
Model function for the Phenobarb data
Plot an ACF Object
Plot an augPred Object
Apply Solve to an reStruct Object
Plot a compareFits Object
Plot a gls Object
Plot lmList Confidence Intervals
Plot an lme or nls object
Plot an lmList Object
Plot an nffGroupedData Object
Plot an nfnGroupedData Object
Plot an nmGroupedData Object
Plot a ranef.lme Object
Plot a Variogram Object
Extract Pooled Standard Deviation
Predictions from a gls Object
Predictions from a gnls Object
Predictions from an lme Object
Split a Formula
Predictions from an lmList Object
Predictions from an nlme Object
Print a summary.pdMat Object
Print a varFunc Object
Normal Plot of Residuals from a gls Object
Normal Plot of Residuals or Random Effects from an lme Object
Model function for the Quinidine data
Extract lmList Random Effects
Recalculate for corStruct Object
Recalculate for a modelStruct Object
Recalculate Condensed Linear Model Object
Summarize a corStruct Object
Recalculate for an reStruct Object
Recalculate for varFunc Object
Extract gls Residuals
Calculate glsStruct Residuals
Calculate gnlsStruct Residuals
Extract lme Residuals
Calculate lmeStruct Residuals
Extract lmList Residuals
Calculate nlmeStruct Residuals
Random Effects Structure
Simulate Results from lme Models
Summarize a Generalized Least Squares gls Object
Summarize an lme Object
Summarize an lmList Object
Summarize a modelStruct Object
Variance Function Structure
Constant Variance Function
Summarize an nlsList Object
Summarize a pdMat Object
Summarize "varFunc" Object
Update a modelStruct Object
Update varFunc Object
Variance Function Classes
Combination of Variance Functions
Constant Plus Power Variance Function
Constant Plus Proportion Variance Function
Extract variance and correlation components
Exponential Variance Function
Fixed Variance Function
Calculate Semi-variogram for a corExp Object
Calculate Semi-variogram for a corGaus Object
Calculate Semi-variogram for a corLin Object
Calculate Semi-variogram for a corRatio Object
Calculate Semi-variogram for a corSpatial Object
Calculate Semi-variogram for a corSpher Object
Calculate Semi-variogram
Calculate Semi-variogram for Residuals from a gls Object
Calculate Semi-variogram for Residuals from an lme Object
Calculate Semi-variogram
Power Variance Function
Variance Weights for glsStruct Object
Variance Weights for lmeStruct Object
Extract Variance Function Weights
Fit and compare Gaussian linear and nonlinear mixed-effects models.