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nlme (version 3.1-171)
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
143,039
Version
3.1-171
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
September 1st, 2026
Functions in nlme (3.1-171)
Search all functions
[.pdMat
Subscript a pdMat Object
Glucose
Glucose levels over time
Dim.corStruct
Dimensions of a corStruct Object
Dim.pdMat
Dimensions of a pdMat Object
Dialyzer
High-Flux Hemodialyzer
Dim
Extract Dimensions from an Object
Earthquake
Earthquake Intensity
Fatigue
Cracks caused by metal fatigue
Gasoline
Refinery yield of gasoline
Dim.corSpatial
Dimensions of a corSpatial Object
Initialize.glsStruct
Initialize a glsStruct Object
Initialize.corStruct
Initialize corStruct Object
Initialize.lmeStruct
Initialize an lmeStruct Object
LDEsysMat
Generate system matrix for LDEs
Gun
Methods for firing naval guns
IGF
Radioimmunoassay of IGF-I Protein
Initialize.reStruct
Initialize reStruct Object
Initialize.varFunc
Initialize varFunc Object
Initialize
Initialize Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Meat
Tenderness of meat
Matrix.reStruct
Assign reStruct Matrices
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Muscle
Contraction of heart muscle sections
Matrix
Assign Matrix Values
MathAchSchool
School demographic data for MathAchieve
Machines
Productivity Scores for Machines and Workers
Milk
Protein content of cows' milk
MathAchieve
Mathematics achievement scores
Names
Names Associated with an Object
Oxboys
Heights of Boys in Oxford
Names.formula
Extract Names from a formula
Names.pdMat
Names of a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
Ovary
Counts of Ovarian Follicles
Nitrendipene
Assay of nitrendipene
Oats
Split-plot Experiment on Varieties of Oats
Orthodont
Growth curve data on an orthdontic measurement
Oxide
Variability in Semiconductor Manufacturing
Names.reStruct
Names of an reStruct Object
Remifentanil
Pharmacokinetics of Remifentanil
Rail
Evaluation of Stress in Railway Rails
Relaxin
Assay for Relaxin
Spruce
Growth of Spruce Trees
RatPupWeight
The weight of rat pups
Pixel
X-ray pixel intensities over time
Phenobarb
Phenobarbitol Kinetics
Quinidine
Quinidine Kinetics
Soybean
Growth of soybean plants
PBG
Effect of Phenylbiguanide on Blood Pressure
Tetracycline1
Pharmacokinetics of tetracycline
VarCorr
Extract variance and correlation components
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Variogram
Calculate Semi-variogram
Tetracycline2
Pharmacokinetics of tetracycline
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Wheat
Yields by growing conditions
allCoef
Extract Coefficients from a Set of Objects
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
anova.lme
Compare Likelihoods of Fitted Objects
anova.gls
Compare Likelihoods of Fitted Objects
Wheat2
Wheat Yield Trials
Wafer
Modeling of Analog MOS Circuits
as.matrix.corStruct
Matrix of a corStruct Object
Variogram.default
Calculate Semi-variogram
as.matrix.reStruct
Matrices of an reStruct Object
coef.gnls
Extract gnls Coefficients
asOneFormula
Combine Formulas of a Set of Objects
coef.pdMat
pdMat Object Coefficients
bdf
Language scores
coef.varFunc
varFunc Object Coefficients
coef.reStruct
reStruct Object Coefficients
augPred
Augmented Predictions
asTable
Convert groupedData to a matrix
corAR1
AR(1) Correlation Structure
as.matrix.pdMat
Matrix of a pdMat Object
coef.corStruct
Coefficients of a corStruct Object
coef.lmList
Extract lmList Coefficients
comparePred
Compare Predictions
balancedGrouped
Create a groupedData object from a matrix
collapse.groupedData
Collapse a groupedData Object
compareFits
Compare Fitted Objects
collapse
Collapse According to Groups
coef.modelStruct
Extract modelStruct Object Coefficients
coef.lme
Extract lme Coefficients
corARMA
ARMA(p,q) Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
corExp
Exponential Correlation Structure
corClasses
Correlation Structure Classes
corCompSymm
Compound Symmetry Correlation Structure
corLin
Linear Correlation Structure
corMatrix
Extract Correlation Matrix
corFactor
Factor of a Correlation Matrix
corCAR1
Continuous AR(1) Correlation Structure
corGaus
Gaussian Correlation Structure
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corNatural
General correlation in natural parameterization
corMatrix.corStruct
Matrix of a corStruct Object
fdHess
Finite difference Hessian
corSpatial
Spatial Correlation Structure
corSpher
Spherical Correlation Structure
corSymm
General Correlation Structure
ergoStool
Ergometrics experiment with stool types
corRatio
Rational Quadratic Correlation Structure
fitted.lmList
Extract lmList Fitted Values
fitted.glsStruct
Calculate glsStruct Fitted Values
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.lme
Extract lme Fitted Values
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getCovariate
Extract Covariate from an Object
formula.reStruct
Extract reStruct Object Formula
formula.pdMat
Extract pdMat Formula
formula.pdBlocked
Extract pdBlocked Formula
fixed.effects
Extract Fixed Effects
getCovariate.data.frame
Extract Data Frame Covariate
fixef.lmList
Extract lmList Fixed Effects
getCovariate.corStruct
Extract corStruct Object Covariate
getCovariate.varFunc
Extract varFunc Covariate
getData.gls
Extract gls Object Data
getCovariateFormula
Extract Covariates Formula
getData
Extract Data from an Object
gapply
Apply a Function by Groups
getGroupsFormula
Extract Grouping Formula
getResponse
Extract Response Variable from an Object
getGroups.data.frame
Extract Groups from a Data Frame
getGroups.corStruct
Extract corStruct Groups
getData.lmList
Extract lmList Object Data
getGroups.gls
Extract gls Object Groups
getGroups.varFunc
Extract varFunc Groups
getGroups.lmList
Extract lmList Object Groups
getGroups.lme
Extract lme Object Groups
glsStruct
Generalized Least Squares Structure
glsControl
Control Values for gls Fit
gnlsControl
Control Values for gnls Fit
gnls
Fit Nonlinear Model Using Generalized Least Squares
gnlsObject
Fitted gnls Object
getResponseFormula
Extract Formula Specifying Response Variable
getGroups
Extract Grouping Factors from an Object
glsObject
Fitted gls Object
getData.lme
Extract lme Object Data
gls-internal
Auxiliary functions used by gls
gls
Fit Linear Model Using Generalized Least Squares
gsummary
Summarize by Groups
gnlsStruct
Generalized Nonlinear Least Squares Structure
getVarCov
Extract variance-covariance matrix
intervals.gls
Confidence Intervals on gls Parameters
intervals
Confidence Intervals on Coefficients
lmList
List of lm Objects with a Common Model
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
groupedData
Construct a groupedData Object
lmeControl
Specifying Control Values for lme Fit
lme.lmList
LME fit from lmList Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
lme
Linear Mixed-Effects Models
lmeObject
Fitted lme Object
lmList.groupedData
lmList Fit from a groupedData Object
lmeStruct
Linear Mixed-Effects Structure
logDet.corStruct
Extract corStruct Log-Determinant
logDet
Extract the Logarithm of the Determinant
lme.groupedData
LME fit from groupedData Object
logLik.gnls
Log-Likelihood of a gnls Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
logDet.reStruct
Extract reStruct Log-Determinants
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logLik.corStruct
Extract corStruct Log-Likelihood
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
logLik.lme
Log-Likelihood of an lme Object
logLik.varFunc
Extract varFunc logLik
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
model.matrix.reStruct
reStruct Model Matrix
needUpdate
Check if Update is Needed
nlme.nlsList
NLME fit from nlsList Object
nlme-deprecated
Deprecated Functions in Package
nlme
nlmeObject
Fitted nlme Object
nlmeStruct
Nonlinear Mixed-Effects Structure
nlme
Nonlinear Mixed-Effects Models
nlsList
List of nls Objects with a Common Model
nlmeControl
Control Values for nlme Fit
pairs.lmList
Pairs Plot of an lmList Object
pdClasses
Positive-Definite Matrix Classes
pdConstruct.pdBlocked
Construct pdBlocked Objects
pairs.compareFits
Pairs Plot of compareFits Object
pdDiag
Diagonal Positive-Definite Matrix
pdConstruct
Construct pdMat Objects
pdBlocked
Positive-Definite Block Diagonal Matrix
pairs.lme
Pairs Plot of an lme Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
nlsList.selfStart
nlsList Fit from a selfStart Function
pdMat
Positive-Definite Matrix
pdSymm
General Positive-Definite Matrix
phenoModel
Model function for the Phenobarb data
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdLogChol
General Positive-Definite Matrix
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.lmList
Plot an lmList Object
plot.gls
Plot a gls Object
plot.nffGroupedData
Plot an nffGroupedData Object
plot.augPred
Plot an augPred Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.Variogram
Plot a Variogram Object
plot.compareFits
Plot a compareFits Object
plot.ACF
Plot an ACF Object
plot.lme
Plot an lme or nls object
plot.ranef.lme
Plot a ranef.lme Object
predict.lmList
Predictions from an lmList Object
plot.ranef.lmList
Plot a ranef.lmList Object
plot.nmGroupedData
Plot an nmGroupedData Object
predict.gnls
Predictions from a gnls Object
predict.lme
Predictions from an lme Object
pooledSD
Extract Pooled Standard Deviation
print.summary.pdMat
Print a summary.pdMat Object
predict.gls
Predictions from a gls Object
predict.nlme
Predictions from an nlme Object
recalc
Recalculate Condensed Linear Model 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
ranef.lmList
Extract lmList Random Effects
random.effects
Extract Random Effects
recalc.corStruct
Recalculate for corStruct Object
ranef.lme
Extract lme Random Effects
reStruct
Random Effects Structure
quinModel
Model function for the Quinidine data
residuals.lmeStruct
Calculate lmeStruct Residuals
recalc.varFunc
Recalculate for varFunc Object
residuals.gls
Extract gls Residuals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
recalc.modelStruct
Recalculate for a modelStruct Object
residuals.lme
Extract lme Residuals
residuals.glsStruct
Calculate glsStruct Residuals
residuals.lmList
Extract lmList Residuals
recalc.reStruct
Recalculate for an reStruct Object
summary.modelStruct
Summarize a modelStruct Object
splitFormula
Split a Formula
solve.reStruct
Apply Solve to an reStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
summary.lmList
Summarize an lmList Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
summary.nlsList
Summarize an nlsList Object
summary.corStruct
Summarize a corStruct Object
simulate.lme
Simulate Results from
lme
Models
summary.gls
Summarize a Generalized Least Squares
gls
Object
summary.lme
Summarize an lme Object
varClasses
Variance Function Classes
update.varFunc
Update varFunc Object
summary.varFunc
Summarize "varFunc" Object
summary.pdMat
Summarize a pdMat Object
varComb
Combination of Variance Functions
varExp
Exponential Variance Function
update.modelStruct
Update a modelStruct Object
varConstPower
Constant Plus Power Variance Function
varFixed
Fixed Variance Function
varConstProp
Constant Plus Proportion Variance Function
varWeights
Extract Variance Function Weights
varWeights.glsStruct
Variance Weights for glsStruct Object
varIdent
Constant Variance Function
varPower
Power Variance Function
varFunc
Variance Function Structure
varWeights.lmeStruct
Variance Weights for lmeStruct Object
Coef
Assign Values to Coefficients
Covariate
Assign Covariate Values
BodyWeight
Rat weight over time for different diets
ACF
Autocorrelation Function
ACF.lme
Autocorrelation Function for lme Residuals
ACF.gls
Autocorrelation Function for gls Residuals
Assay
Bioassay on Cell Culture Plate
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Cefamandole
Pharmacokinetics of Cefamandole
Covariate.varFunc
Assign varFunc Covariate