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nlme (version 3.1-61)
Linear and nonlinear mixed effects models
Description
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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3.1-2 (1999/12/23)
3.1-1
Install
install.packages('nlme')
Monthly Downloads
143,317
Version
3.1-61
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-61)
Search all functions
Initialize.varFunc
Initialize varFunc Object
Initialize.corStruct
Initialize corStruct Object
as.matrix.reStruct
Matrices of an reStruct Object
corNatural
General correlation in natural parameterization
getCovariateFormula
Extract Covariates Formula
getCovariate.data.frame
Extract Data Frame Covariate
corFactor
Factor of a Correlation Matrix
pdClasses
Positive-Definite Matrix Classes
getData
Extract Data from an Object
needUpdate
Check if Update is Needed
VarCorr
Extract variance and correlation components
corMatrix
Extract Correlation Matrix
coef.varFunc
varFunc Object Coefficients
getGroups.data.frame
Extract Groups from a Data Frame
getResponseFormula
Extract Formula Specifying Response Variable
intervals.lmList
Confidence Intervals on lmList Coefficients
fitted.glsStruct
Calculate glsStruct Fitted Values
getGroups.corStruct
Extract corStruct Groups
getGroups
Extract Grouping Factors from an Object
gsummary
Summarize by Groups
allCoef
Extract Coefficients from a Set of Objects
corExp
Exponential Correlation Structure
Names.pdMat
Names of a pdMat Object
predict.lmList
Predictions from an lmList Object
pairs.lmList
Pairs Plot of an lmList Object
logLik.lmList
Log-Likelihood of an lmList Object
logDet
Extract the Logarithm of the Determinant
fixed.effects
Extract Fixed Effects
Names
Names Associated with an Object
getVarCov
Extract variance-covariance matrix
formula.pdBlocked
Extract pdBlocked Formula
corSymm
General Correlation Structure
recalc.varFunc
Recalculate for varFunc Object
model.matrix.reStruct
reStruct Model Matrix
Names.reStruct
Names of an reStruct Object
fdHess
Finite difference Hessian
Initialize.reStruct
Initialize reStruct Object
asTable
Convert groupedData to a matrix
corARMA
ARMA(p,q) Correlation Structure
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
coef.gnls
Extract gnls Coefficients
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getData.lmList
Extract lmList Object Data
collapse
Collapse According to Groups
getGroups.lmList
Extract lmList Object Groups
Matrix
Assign Matrix Values
gapply
Apply a Function by Groups
Covariate
Assign Covariate Values
BIC.logLik
BIC of a logLik Object
corCompSymm
Compound Symmetry Correlation Structure
coef.lme
Extract lme Coefficients
corSpatial
Spatial Correlation Structure
corClasses
Correlation Structure Classes
corCAR1
Continuous AR(1) Correlation Structure
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
Initialize.lmeStruct
Initialize an lmeStruct Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
corAR1
AR(1) Correlation Structure
formula.pdMat
Extract pdMat Formula
pdMat
Positive-Definite Matrix
logLik.reStruct
Calculate reStruct Log-Likelihood
random.effects
Extract Random Effects
getGroups.lme
Extract lme Object Groups
getCovariate.varFunc
Extract varFunc Covariate
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
plot.nmGroupedData
Plot an nmGroupedData Object
lmList.groupedData
lmList Fit from a groupedData Object
Names.formula
Extract Names from a formula
pairs.compareFits
Pairs Plot of compareFits Object
logLik.varFunc
Extract varFunc logLik
fixef.lmList
Extract lmList Fixed Effects
coef.pdMat
pdMat Object Coefficients
logLik.gnls
Log-Likelihood of a gnls Object
corRatio
Rational Quadratic Correlation Structure
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
Dim.corSpatial
Dimensions of a corSpatial Object
getData.gls
Extract gls Object Data
formula.reStruct
Extract reStruct Object Formula
lmeScale
Scale for lme Optimization
corSpher
Spherical Correlation Structure
plot.Variogram
Plot a Variogram Object
comparePred
Compare Predictions
print.varFunc
Print a varFunc Object
logLik.corStruct
Extract corStruct Log-Likelihood
compareFits
Compare Fitted Objects
as.matrix.pdMat
Matrix of a pdMat Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
corMatrix.corStruct
Matrix of a corStruct Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
ACF.lme
Autocorrelation Function for lme Residuals
ACF
Autocorrelation Function
getResponse
Extract Response Variable from an Object
getCovariate.corStruct
Extract corStruct Object Covariate
corLin
Linear Correlation Structure
balancedGrouped
Create a groupedData object from a matrix
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.lme
Log-Likelihood of an lme Object
glsControl
Control Values for gls Fit
getGroupsFormula
Extract Grouping Formula
nlmeStruct
Nonlinear Mixed-Effects Structure
Variogram.default
Calculate Semi-variogram
ranef.lmList
Extract lmList Random Effects
logDet.pdMat
Extract Log-Determinant from a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
augPred
Augmented Predictions
predict.gnls
Predictions from a gnls Object
gnlsObject
Fitted gnls Object
getData.lme
Extract lme Object Data
pooledSD
Extract Pooled Standard Deviation
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
getCovariate
Extract Covariate from an Object
predict.gls
Predictions from a gls Object
Coef
Assign Values to Coefficients
LDEsysMat
Generate system matrix for LDEs
summary.lme
Summarize an lme Object
summary.varFunc
Summarize varFunc Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
pairs.lme
Pairs Plot of an lme Object
varComb
Combination of Variance Functions
coef.reStruct
reStruct Object Coefficients
nlsList
List of nls Objects with a Common Model
corFactor.corStruct
Factor of a corStruct Object Matrix
[.pdMat
Subscript a pdMat Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
Variogram
Calculate Semi-variogram
plot.lmList
Plot an lmList Object
quinModel
Model function for the Quinidine data
lme.groupedData
LME fit from groupedData Object
lmeStruct
Linear Mixed-Effects Structure
Dim.corStruct
Dimensions of a corStruct Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
predict.nlme
Predictions from an nlme Object
update.varFunc
Update varFunc Object
plot.nffGroupedData
Plot an nffGroupedData Object
getGroups.gls
Extract gls Object Groups
collapse.groupedData
Collapse a groupedData Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
fitted.lmList
Extract lmList Fitted Values
nlmeControl
Control Values for nlme Fit
logDet.corStruct
Extract corStruct Log-Determinant
gnlsStruct
Generalized Nonlinear Least Squares Structure
nlme
Nonlinear Mixed-Effects Models
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
plot.intervals.lmList
Plot lmList Confidence Intervals
ACF.gls
Autocorrelation Function for gls Residuals
pdConstruct
Construct pdMat Objects
Initialize
Initialize Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
asOneFormula
Combine Formulas of a Set of Objects
pdSymm
General Positive-Definite Matrix
Covariate.varFunc
Assign varFunc Covariate
pdLogChol
General Positive-Definite Matrix
lmList
List of lm Objects with a Common Model
intervals.gls
Confidence Intervals on gls Parameters
varFunc
Variance Function Structure
varExp
Exponential Variance Function
phenoModel
Model function for the Phenobarb data
summary.nlsList
Summarize an nlsList Object
plot.gls
Plot a gls Object
coef.modelStruct
Extract modelStruct Object Coefficients
summary.gls
Summarize a gls Object
predict.lme
Predictions from an lme Object
summary.pdMat
Summarize a pdMat Object
pdBlocked
Positive-Definite Block Diagonal Matrix
coef.corStruct
Coefficients of a corStruct Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
residuals.lmList
Extract lmList Residuals
update.modelStruct
Update a modelStruct Object
varPower
Power Variance Function
plot.augPred
Plot an augPred Object
isBalanced
Check a Design for Balance
recalc.corStruct
Recalculate for corStruct Object
varConstPower
Constant Plus Power Variance Function
varWeights
Extract Variance Function Weights
plot.nfnGroupedData
Plot an nfnGroupedData Object
Matrix.pdMat
Assign Matrix to a pdMat Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
nlmeObject
Fitted nlme Object
nlsList.selfStart
nlsList Fit from a selfStart Function
plot.ranef.lmList
Plot a ranef.lmList Object
residuals.lmeStruct
Calculate lmeStruct Residuals
gnlsControl
Control Values for gnls Fit
Dim
Extract Dimensions from an Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
varClasses
Variance Function Classes
summary.corStruct
Summarize a corStruct Object
BIC
Bayesian Information Criterion
groupedData
Construct a groupedData Object
plot.lme
Plot an lme or nls object
summary.lmList
Summarize an lmList Object
anova.lme
Compare Likelihoods of Fitted Objects
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
lme
Linear Mixed-Effects Models
residuals.gls
Extract gls Residuals
solve.reStruct
Apply Solve to an reStruct Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
isInitialized
Check if Object is Initialized
recalc.modelStruct
Recalculate for a modelStruct Object
logDet.reStruct
Extract reStruct Log-Determinants
Dim.pdMat
Dimensions of a pdMat Object
recalc
Recalculate Condensed Linear Model Object
Initialize.glsStruct
Initialize a glsStruct Object
varIdent
Constant Variance Function
lmeControl
Control Values for lme Fit
lmeObject
Fitted lme Object
lme.lmList
LME fit from lmList Object
coef.lmList
Extract lmList Coefficients
nlme.nlsList
NLME fit from nlsList Object
getGroups.varFunc
Extract varFunc Groups
fitted.lmeStruct
Calculate lmeStruct Fitted Values
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Matrix.reStruct
Assign reStruct Matrices
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
pdDiag
Diagonal Positive-Definite Matrix
fitted.lme
Extract lme Fitted Values
varWeights.glsStruct
Variance Weights for glsStruct Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
corGaus
Gaussian Correlation Structure
Variogram.corLin
Calculate Semi-variogram for a corLin Object
plot.ranef.lme
Plot a ranef.lme Object
gls
Fit Linear Model Using Generalized Least Squares
anova.gls
Compare Likelihoods of Fitted Objects
plot.compareFits
Plot a compareFits Object
print.summary.pdMat
Print a summary.pdMat Object
plot.ACF
Plot an ACF Object
intervals
Confidence Intervals on Coefficients
glsObject
Fitted gls Object
intervals.lme
Confidence Intervals on lme Parameters
glsStruct
Generalized Least Squares Structure
splitFormula
Split a Formula
residuals.nlmeStruct
Calculate nlmeStruct Residuals
recalc.reStruct
Recalculate for an reStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.lme
Extract lme Residuals
residuals.glsStruct
Calculate glsStruct Residuals
ranef.lme
Extract lme Random Effects
simulate.lme
simulate lme models
summary.modelStruct
Summarize a modelStruct Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
varFixed
Fixed Variance Function
varWeights.lmeStruct
Variance Weights for lmeStruct Object
reStruct
Random Effects Structure
PBG
Effect of Phenylbiguanide on Blood Pressure
Dialyzer
High-Flux Hemodialyzer
Soybean
Growth of soybean plants
Gasoline
Refinery yield of gasoline
MathAchSchool
School demographic data for MathAchieve
Quinidine
Quinidine Kinetics
Relaxin
Assay for Relaxin
Glucose2
Glucose Levels Following Alcohol Ingestion
Nitrendipene
Assay of nitrendipene
Oats
Split-plot Experiment on Varieties of Oats
Muscle
Contraction of heart muscle sections
Wheat
Yields by growing conditions
Meat
Tenderness of meat
Glucose
Glucose levels over time
IGF
Radioimmunoassay of IGF-I Protein
BodyWeight
Rat weight over time for different diets
Machines
Productivity Scores for Machines and Workers
Gun
Methods for firing naval guns
Phenobarb
Phenobarbitol Kinetics
Wheat2
Wheat Yield Trials
Cefamandole
Pharmacokinetics of Cefamandole
Tetracycline1
Pharmacokinetics of tetracycline
Earthquake
Earthquake Intensity
Rail
Evaluation of Stress in Railway Rails
RatPupWeight
The weight of rat pups
Tetracycline2
Pharmacokinetics of tetracycline
Oxboys
Heights of Boys in Oxford
bdf
Language scores
Orthodont
Growth curve data on an orthdontic measurement
Milk
Protein content of cows' milk
Oxide
Variability in Semiconductor Manufacturing
Ovary
Counts of Ovarian Follicles
Assay
Bioassay on Cell Culture Plate
Pixel
X-ray pixel intensities over time
Remifentanil
Pharmacokinetics of remifentanil
ergoStool
Ergometrics experiment with stool types
Spruce
Growth of Spruce Trees
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Fatigue
Cracks caused by metal fatigue
MathAchieve
Mathematics achievement scores
Wafer
Modeling of Analog MOS Circuits