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nlme (version 3.1-170)
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
144,137
Version
3.1-170
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
July 15th, 2026
Functions in nlme (3.1-170)
Search all functions
Dim
Extract Dimensions from an Object
Dim.corSpatial
Dimensions of a corSpatial Object
Fatigue
Cracks caused by metal fatigue
Dim.corStruct
Dimensions of a corStruct Object
Gasoline
Refinery yield of gasoline
Glucose
Glucose levels over time
Earthquake
Earthquake Intensity
Dim.pdMat
Dimensions of a pdMat Object
[.pdMat
Subscript a pdMat Object
Dialyzer
High-Flux Hemodialyzer
Gun
Methods for firing naval guns
LDEsysMat
Generate system matrix for LDEs
Initialize
Initialize Object
IGF
Radioimmunoassay of IGF-I Protein
Glucose2
Glucose Levels Following Alcohol Ingestion
Initialize.lmeStruct
Initialize an lmeStruct Object
Initialize.reStruct
Initialize reStruct Object
Initialize.varFunc
Initialize varFunc Object
MathAchieve
Mathematics achievement scores
Matrix
Assign Matrix Values
MathAchSchool
School demographic data for MathAchieve
Machines
Productivity Scores for Machines and Workers
Milk
Protein content of cows' milk
Meat
Tenderness of meat
Initialize.glsStruct
Initialize a glsStruct Object
Matrix.reStruct
Assign reStruct Matrices
Initialize.corStruct
Initialize corStruct Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Nitrendipene
Assay of nitrendipene
Oats
Split-plot Experiment on Varieties of Oats
Names
Names Associated with an Object
Muscle
Contraction of heart muscle sections
Pixel
X-ray pixel intensities over time
Quinidine
Quinidine Kinetics
Oxide
Variability in Semiconductor Manufacturing
Ovary
Counts of Ovarian Follicles
Relaxin
Assay for Relaxin
Remifentanil
Pharmacokinetics of Remifentanil
Orthodont
Growth curve data on an orthdontic measurement
Names.formula
Extract Names from a formula
Names.pdBlocked
Names of a pdBlocked Object
Rail
Evaluation of Stress in Railway Rails
Oxboys
Heights of Boys in Oxford
Variogram
Calculate Semi-variogram
VarCorr
Extract variance and correlation components
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Tetracycline2
Pharmacokinetics of tetracycline
Tetracycline1
Pharmacokinetics of tetracycline
Names.pdMat
Names of a pdMat Object
Phenobarb
Phenobarbitol Kinetics
PBG
Effect of Phenylbiguanide on Blood Pressure
Names.reStruct
Names of an reStruct Object
Soybean
Growth of soybean plants
Spruce
Growth of Spruce Trees
RatPupWeight
The weight of rat pups
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Wheat
Yields by growing conditions
anova.lme
Compare Likelihoods of Fitted Objects
Wafer
Modeling of Analog MOS Circuits
as.matrix.corStruct
Matrix of a corStruct Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Wheat2
Wheat Yield Trials
allCoef
Extract Coefficients from a Set of Objects
asOneFormula
Combine Formulas of a Set of Objects
Variogram.default
Calculate Semi-variogram
asTable
Convert groupedData to a matrix
as.matrix.pdMat
Matrix of a pdMat Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
anova.gls
Compare Likelihoods of Fitted Objects
bdf
Language scores
coef.corStruct
Coefficients of a corStruct Object
augPred
Augmented Predictions
coef.gnls
Extract gnls Coefficients
coef.lmList
Extract lmList Coefficients
as.matrix.reStruct
Matrices of an reStruct Object
balancedGrouped
Create a groupedData object from a matrix
comparePred
Compare Predictions
collapse
Collapse According to Groups
coef.varFunc
varFunc Object Coefficients
coef.modelStruct
Extract modelStruct Object Coefficients
coef.reStruct
reStruct Object Coefficients
coef.lme
Extract lme Coefficients
coef.pdMat
pdMat Object Coefficients
corCompSymm
Compound Symmetry Correlation Structure
collapse.groupedData
Collapse a groupedData Object
corFactor
Factor of a Correlation Matrix
corARMA
ARMA(p,q) Correlation Structure
corExp
Exponential Correlation Structure
corCAR1
Continuous AR(1) Correlation Structure
corMatrix
Extract Correlation Matrix
compareFits
Compare Fitted Objects
corLin
Linear Correlation Structure
corClasses
Correlation Structure Classes
corFactor.corStruct
Factor of a corStruct Object Matrix
corAR1
AR(1) Correlation Structure
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corSpher
Spherical Correlation Structure
corGaus
Gaussian Correlation Structure
corMatrix.corStruct
Matrix of a corStruct Object
corRatio
Rational Quadratic Correlation Structure
fdHess
Finite difference Hessian
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corNatural
General correlation in natural parameterization
corSymm
General Correlation Structure
ergoStool
Ergometrics experiment with stool types
corSpatial
Spatial Correlation Structure
fixed.effects
Extract Fixed Effects
fitted.lmList
Extract lmList Fitted Values
fixef.lmList
Extract lmList Fixed Effects
fitted.lme
Extract lme Fitted Values
formula.pdMat
Extract pdMat Formula
getCovariate.data.frame
Extract Data Frame Covariate
getCovariate
Extract Covariate from an Object
formula.reStruct
Extract reStruct Object Formula
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
fitted.lmeStruct
Calculate lmeStruct Fitted Values
fitted.glsStruct
Calculate glsStruct Fitted Values
getCovariateFormula
Extract Covariates Formula
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
formula.pdBlocked
Extract pdBlocked Formula
getData.lmList
Extract lmList Object Data
gapply
Apply a Function by Groups
getData
Extract Data from an Object
getData.lme
Extract lme Object Data
getCovariate.varFunc
Extract varFunc Covariate
getData.gls
Extract gls Object Data
getGroups.lme
Extract lme Object Groups
getResponse
Extract Response Variable from an Object
getCovariate.corStruct
Extract corStruct Object Covariate
getGroups.lmList
Extract lmList Object Groups
getGroups.gls
Extract gls Object Groups
getGroupsFormula
Extract Grouping Formula
getGroups.corStruct
Extract corStruct Groups
getGroups
Extract Grouping Factors from an Object
getGroups.data.frame
Extract Groups from a Data Frame
getGroups.varFunc
Extract varFunc Groups
getResponseFormula
Extract Formula Specifying Response Variable
glsStruct
Generalized Least Squares Structure
gnls
Fit Nonlinear Model Using Generalized Least Squares
gls
Fit Linear Model Using Generalized Least Squares
gls-internal
Auxiliary functions used by gls
getVarCov
Extract variance-covariance matrix
gnlsObject
Fitted gnls Object
glsControl
Control Values for gls Fit
gnlsControl
Control Values for gnls Fit
intervals.gls
Confidence Intervals on gls Parameters
glsObject
Fitted gls Object
gsummary
Summarize by Groups
gnlsStruct
Generalized Nonlinear Least Squares Structure
intervals.lmList
Confidence Intervals on lmList Coefficients
intervals.lme
Confidence Intervals on lme Parameters
lmList
List of lm Objects with a Common Model
isInitialized
Check if Object is Initialized
intervals
Confidence Intervals on Coefficients
isBalanced
Check a Design for Balance
groupedData
Construct a groupedData Object
logDet.corStruct
Extract corStruct Log-Determinant
lme.groupedData
LME fit from groupedData Object
lmList.groupedData
lmList Fit from a groupedData Object
logDet
Extract the Logarithm of the Determinant
lme.lmList
LME fit from lmList Object
lmeStruct
Linear Mixed-Effects Structure
logDet.pdMat
Extract Log-Determinant from a pdMat Object
lmeObject
Fitted lme Object
lme
Linear Mixed-Effects Models
lmeControl
Specifying Control Values for lme Fit
logLik.corStruct
Extract corStruct Log-Likelihood
logDet.reStruct
Extract reStruct Log-Determinants
logLik.gnls
Log-Likelihood of a gnls Object
logLik.lme
Log-Likelihood of an lme Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
logLik.lmList
Log-Likelihood of an lmList Object
logLik.varFunc
Extract varFunc logLik
nlmeStruct
Nonlinear Mixed-Effects Structure
model.matrix.reStruct
reStruct Model Matrix
nlme-deprecated
Deprecated Functions in Package
nlme
needUpdate
Check if Update is Needed
nlme.nlsList
NLME fit from nlsList Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
nlmeObject
Fitted nlme Object
nlmeControl
Control Values for nlme Fit
nlme
Nonlinear Mixed-Effects Models
nlsList
List of nls Objects with a Common Model
pdConstruct
Construct pdMat Objects
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdClasses
Positive-Definite Matrix Classes
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
pdDiag
Diagonal Positive-Definite Matrix
nlsList.selfStart
nlsList Fit from a selfStart Function
pdConstruct.pdBlocked
Construct pdBlocked Objects
phenoModel
Model function for the Phenobarb data
pdLogChol
General Positive-Definite Matrix
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdSymm
General Positive-Definite Matrix
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pdMat
Positive-Definite Matrix
plot.augPred
Plot an augPred Object
plot.compareFits
Plot a compareFits Object
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.lmList
Plot an lmList Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.nffGroupedData
Plot an nffGroupedData Object
plot.gls
Plot a gls Object
plot.lme
Plot an lme or nls object
plot.ACF
Plot an ACF Object
plot.Variogram
Plot a Variogram Object
pooledSD
Extract Pooled Standard Deviation
plot.ranef.lme
Plot a ranef.lme Object
plot.nmGroupedData
Plot an nmGroupedData Object
predict.lmList
Predictions from an lmList Object
predict.lme
Predictions from an lme Object
print.summary.pdMat
Print a summary.pdMat Object
plot.ranef.lmList
Plot a ranef.lmList Object
predict.nlme
Predictions from an nlme Object
predict.gnls
Predictions from a gnls Object
predict.gls
Predictions from a gls Object
reStruct
Random Effects Structure
qqnorm.gls
Normal Plot of Residuals from a gls Object
recalc
Recalculate Condensed Linear Model Object
ranef.lmList
Extract lmList Random Effects
recalc.corStruct
Recalculate for corStruct Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
ranef.lme
Extract lme Random Effects
quinModel
Model function for the Quinidine data
random.effects
Extract Random Effects
print.varFunc
Print a varFunc Object
residuals.glsStruct
Calculate glsStruct Residuals
residuals.lmeStruct
Calculate lmeStruct Residuals
recalc.varFunc
Recalculate for varFunc Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
recalc.reStruct
Recalculate for an reStruct Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
residuals.lme
Extract lme Residuals
recalc.modelStruct
Recalculate for a modelStruct Object
residuals.gls
Extract gls Residuals
residuals.lmList
Extract lmList Residuals
splitFormula
Split a Formula
summary.lmList
Summarize an lmList Object
summary.corStruct
Summarize a corStruct Object
summary.lme
Summarize an lme Object
summary.modelStruct
Summarize a modelStruct Object
summary.nlsList
Summarize an nlsList Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
summary.gls
Summarize a Generalized Least Squares
gls
Object
solve.reStruct
Apply Solve to an reStruct Object
simulate.lme
Simulate Results from
lme
Models
varClasses
Variance Function Classes
update.varFunc
Update varFunc Object
varConstProp
Constant Plus Proportion Variance Function
summary.pdMat
Summarize a pdMat Object
varExp
Exponential Variance Function
varComb
Combination of Variance Functions
summary.varFunc
Summarize "varFunc" Object
varFixed
Fixed Variance Function
varWeights
Extract Variance Function Weights
varFunc
Variance Function Structure
update.modelStruct
Update a modelStruct Object
varIdent
Constant Variance Function
varConstPower
Constant Plus Power Variance Function
varPower
Power Variance Function
varWeights.glsStruct
Variance Weights for glsStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
ACF.lme
Autocorrelation Function for lme Residuals
Covariate
Assign Covariate Values
ACF
Autocorrelation Function
Assay
Bioassay on Cell Culture Plate
BodyWeight
Rat weight over time for different diets
Covariate.varFunc
Assign varFunc Covariate
ACF.gls
Autocorrelation Function for gls Residuals
Coef
Assign Values to Coefficients
Cefamandole
Pharmacokinetics of Cefamandole
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa