Rdocumentation
powered by
Learn R Programming
⚠️
There's a newer version (3.1-168) of this package.
Take me there.
nlme (version 3.1-30)
Linear and nonlinear mixed effects models
Description
Fit and compare Gaussian linear and nonlinear mixed-effects models.
Copy Link
Link to current version
Version
Version
3.1-168
3.1-167
3.1-166
3.1-164
3.1-163
3.1-162
3.1-161
3.1-160
3.1-159
3.1-158
3.1-157
3.1-155
3.1-153
3.1-152
3.1-151
3.1-150
3.1-149
3.1-148
3.1-147
3.1-145
3.1-144
3.1-143
3.1-142
3.1-141
3.1-140
3.1-139
3.1-138
3.1-137
3.1-131.1
3.1-131
3.1-130
3.1-129
3.1-128
3.1-127
3.1-126
3.1-125
3.1-124
3.1-123
3.1-122
3.1-121
3.1-120
3.1-119
3.1-118
3.1-117
3.1-116
3.1-115
3.1-114
3.1-113
3.1-112
3.1-111
3.1-110
3.1-109
3.1-108
3.1-107
3.1-106
3.1-105
3.1-104
3.1-103
3.1-102
3.1-101
3.1-100
3.1-99
3.1-98
3.1-97
3.1-96
3.1-95
3.1-94
3.1-93
3.1-92
3.1-91
3.1-90
3.1-89
3.1-88
3.1-87
3.1-86
3.1-85
3.1-84
3.1-83
3.1-82
3.1-81
3.1-80
3.1-79
3.1-78
3.1-77
3.1-76
3.1-75
3.1-74
3.1-73
3.1-72
3.1-71
3.1-70
3.1-69
3.1-68.1
3.1-66
3.1-65
3.1-64
3.1-63
3.1-62
3.1-61
3.1-60
3.1-58
3.1-57
3.1-56
3.1-55
3.1-53
3.1-52
3.1-51
3.1-50
3.1-48
3.1-45
3.1-44
3.1-43
3.1-42
3.1-41
3.1-40
3.1-39
3.1-38
3.1-37
3.1-36
3.1-35
3.1-34
3.1-33
3.1-32
3.1-31
3.1-30
3.1-29
3.1-28
3.1-27
3.1-24
3.1-23
3.1-22
3.1-21
3.1-19
3.1-18
3.1-17
3.1-16
3.1-13
3.1-10
3.1-8
3.1-7
3.1-6
3.1-5
3.1-4
3.1-3
3.1-2 (1999/12/23)
3.1-1
Install
install.packages('nlme')
Monthly Downloads
84,769
Version
3.1-30
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-30)
Search all functions
MEestimate
Estimate mixed-effects parameters
Initialize.lmeStruct
Initialize an lmeStruct Object
corAR1
AR(1) Correlation Structure
logDet.corStruct
Extract corStruct Log-Determinant
Matrix
Assign Matrix Values
Variogram.corExp
Calculate Semi-variogram for a corExp Object
formula.nlsList
Extract nlsList Object Formula
BIC.logLik
BIC of a logLik Object
Initialize.glsStruct
Initialize a glsStruct Object
MEEM
EM iterations for mixed-effects
plot.ranef.lmList
Plot a ranef.lmList Object
Initialize
Initialize Object
print.lmList
Print an lmList Object
print.varFunc
Print a varFunc Object
Names
Names Associated with an Object
plot.intervals.lmList
Plot lmList Confidence Intervals
Initialize.reStruct
Initialize reStruct Object
lmeStruct
Linear Mixed-Effects Structure
ACF
Autocorrelation Function
corFactor
Factor of a Correlation Matrix
formula.corStruct
Extract corStruct Object Formula
plot.gls
Plot a gls Object
Dim
Extract Dimensions from an Object
Names.formula
Extract Names from a formula
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
lme.lmList
LME fit from lmList Object
predict.gnls
Predictions from a gnls Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
pdMat
Positive-Definite Matrix
fixed.effects
Extract Fixed Effects
predict.nlme
Predictions from an nlme Object
print.gls
Print a gls Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
Covariate
Assign Covariate Values
Names.reStruct
Names of an reStruct Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
plot.compareFits
Plot a compareFits Object
MEdims
Calculate dimensions in mixed-effects
[.pdMat
Subscript a pdMat Object
summary.lme
Summarize an lme Object
print.reStruct
Print an reStruct Object
Dim.corStruct
Dimensions of a corStruct Object
pdSymm
General Positive-Definite Matrix
summary.corStruct
Summarize a corStruct Object
print.summary.modelStruct
Print a summary.modelStruct Object
gnlsControl
Control Values for gnls Fit
ACF.gls
Autocorrelation Function for gls Residuals
Names.pdBlocked
Names of a pdBlocked Object
varExp
Exponential Variance Function
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pairs.lmList
Pairs Plot of an lmList Object
summary.pdMat
Summarize a pdMat Object
print.summary.varFunc
Print a summary.varFunc Object
as.matrix.reStruct
Matrices of an reStruct Object
getData.lmList
Extract lmList Object Data
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
pruneLevels
Prune Factor Levels
fitted.gls
Extract gls Fitted Values
Initialize.corStruct
Initialize corStruct Object
recalc.corStruct
Recalculate for corStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
LDEsysMat
Generate system matrix for LDEs
fitted.lmList
Extract lmList Fitted Values
logLik.glsStruct
Log-Likelihood of a glsStruct Object
Initialize.varFunc
Initialize varFunc Object
print.summary.lme
Print a summary.lme Object
Covariate.varFunc
Assign varFunc Covariate
solve.reStruct
Apply Solve to an reStruct Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
residuals.lmeStruct
Calculate lmeStruct Residuals
pdFactor
Square-Root Factor of a Positive-Definite Matrix
MEdecomp
Decompose a mixed-effects model
residuals.lme
Extract lme Residuals
predict.gls
Predictions from a gls Object
coef.reStruct
reStruct Object Coefficients
varWeights
Extract Variance Function Weights
plot.nffGroupedData
Plot an nffGroupedData Object
fixef.lme
Extract lme Fixed Effects
ranef.lme
Extract lme Random Effects
varWeights.lmeStruct
Variance Weights for lmeStruct Object
summary.modelStruct
Summarize a modelStruct Object
logLik.varFunc
Extract varFunc logLik
VarCorr
Extract variance and correlation components
getResponse.gls
Extract gls Object Response
formula.nlme
Extract nlme Object Formula
pdLogChol
General Positive-Definite Matrix
plot.lmList
Plot an lmList Object
getCovariate
Extract Covariate from an Object
coef.lme
Extract lme Coefficients
residuals.lmList
Extract lmList Residuals
varFixed
Fixed Variance Function
random.effects
Extract Random Effects
splitFormula
Split a Formula
varWeights.glsStruct
Variance Weights for glsStruct Object
plot.ranef.lme
Plot a ranef.lme Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
corCompSymm
Compound Symmetry Correlation Structure
corARMA
ARMA(p,q) Correlation Structure
plot.nfnGroupedData
Plot an nfnGroupedData Object
summary.lmList
Summarize an lmList Object
AIC
Akaike Information Criterion
pdConstruct.pdBlocked
Construct pdBlocked Objects
coef.gnls
Extract gnls Coefficients
summary.varFunc
Summarize varFunc Object
Names.pdMat
Names of a pdMat Object
corSpatial
Spatial Correlation Structure
BIC
Bayesian Information Criterion
asTable
Convert groupedData to a matrix
print.anova.lme
Print an anova.lme Object
fixef.lmList
Extract lmList Fixed Effects
formula.modelStruct
Extract modelStruct Object Formula
nlsList.selfStart
nlsList Fit from a selfStart Function
plot.augPred
Plot an augPred Object
plot.Variogram
Plot a Variogram Object
fitted.gnls
Extract gnls Fitted Values
pdClasses
Positive-Definite Matrix Classes
Dim.corSpatial
Dimensions of a corSpatial Object
coef.pdCompSymm
pdCompSymm Object Coefficients
logLik.lme
Log-Likelihood of an lme Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
allCoef
Extract Coefficients from a Set of Objects
recalc.modelStruct
Recalculate for a modelStruct Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
collapse
Collapse According to Groups
gsummary
Summarize by Groups
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
logLik.gnls
Log-Likelihood of a gnls Object
corMatrix.corStruct
Matrix of a corStruct Object
getResponse.lme
Extract lme Object Response
AIC.lme
Akaike Information Criterion
corExp
Exponential Correlation Structure
residuals.gls
Extract gls Residuals
corCAR1
Continuous AR(1) Correlation Structure
getData
Extract Data from an Object
Variogram
Calculate Semi-variogram
fdHess
Finite difference Hessian
intervals.lme
Confidence Intervals on lme Parameters
phenoModel
Model function for the Phenobarb data
fitted.glsStruct
Calculate glsStruct Fitted Values
varPower
Power Variance Function
logDet.reStruct
Extract reStruct Log-Determinants
summary.nlsList
Summarize an nlsList Object
pdConstruct
Construct pdMat Objects
logLik.gls
Log-Likelihood of a gls Object
varFunc
Variance Function Structure
print.lme
Print an lme Object
ACF.lme
Autocorrelation Function for lme Residuals
plot.lme
Plot an lme or nls object
contr.SAS
Contrast Matrices
gnlsStruct
Generalized Nonlinear Least Squares Structure
pairs.lme
Pairs Plot of an lme Object
isInitialized.reStruct
Check if an reStruct Object is Initialized
recalc
Recalculate Condensed Linear Model Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Variogram.default
Calculate Semi-variogram
Dim.pdMat
Dimensions of a pdMat Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
simulate.lme
simulate lme models
Matrix.pdMat
Assign Matrix to a pdMat Object
formula.gnls
Extract gnls Object Formula
groupedData
Construct a groupedData Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
coef.pdIdent
pdIdent Object Coefficients
getData.lme
Extract lme Object Data
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
print.summary.lmList
Print a summary.lmList Object
coef.corStruct
Coefficients of a corStruct Object
pairs.compareFits
Pairs Plot of compareFits Object
reStruct
Random Effects Structure
quinModel
Model function for the Quinidine data
anova.gls
Compare Likelihoods of Fitted Objects
getCovariate.data.frame
Extract Data Frame Covariate
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
glsStruct
Generalized Least Squares Structure
logLik.corStruct
Extract corStruct Log-Likelihood
nlme
Nonlinear Mixed-Effects Models
augPred
Augmented Predictions
varIdent
Constant Variance Function
pooledSD
Extract Pooled Standard Deviation
recalc.reStruct
Recalculate for an reStruct Object
recalc.varFunc
Recalculate for varFunc Object
intervals
Confidence Intervals on Coefficients
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corFactor.corStruct
Factor of a corStruct Object Matrix
pdDiag
Diagonal Positive-Definite Matrix
update.modelStruct
Update a modelStruct Object
Coef
Assign Values to Coefficients
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
print.groupedData
Print a groupedData Object
lmList
List of lm Objects with a Common Model
coef.modelStruct
Extract modelStruct Object Coefficients
corClasses
Correlation Structure Classes
Matrix.reStruct
Assign reStruct Matrices
print.summary.corStruct
Print a summary.corStruct Object
isBalanced
Check a Design for Balance
varClasses
Variance Function Classes
gls
Fit Linear Model Using Generalized Least Squares
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
corSymm
General Correlation Structure
pdIdent
Multiple of the Identity Positive-Definite Matrix
getResponse
Extract Response Variable from an Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
print.summary.pdMat
Print a summary.pdMat Object
coef.varFunc
varFunc Object Coefficients
update.varFunc
Update varFunc Object
logDet
Extract the Logarithm of the Determinant
glsObject
Fitted gls Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
formula.pdMat
Extract pdMat Formula
getGroups.corStruct
Extract corStruct Groups
corNatural
General correlation in natural parameterization
formula.varFunc
Extract varFunc Formula
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
formula.lme
Extract lme Object Formula
getCovariateFormula
Extract Covariates Formula
getData.gls
Extract gls Object Data
formula.reStruct
Extract reStruct Object Formula
gapply
Apply a Function by Groups
formula.pdBlocked
Extract pdBlocked Formula
formula.groupedData
Extract groupedData Formula
getGroups.data.frame
Extract Groups from a Data Frame
getCovariate.corStruct
Extract corStruct Object Covariate
getGroups.gls
Extract gls Object Groups
asOneFormula
Combine Formulas of a Set of Objects
as.matrix.pdMat
Matrix of a pdMat Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
logLik.lmList
Log-Likelihood of an lmList Object
getGroups
Extract Grouping Factors from an Object
getGroupsFormula
Extract Grouping Formula
comparePred
Compare Predictions
getGroups.varFunc
Extract varFunc Groups
getGroups.lme
Extract lme Object Groups
getResponse.lmList
Extract lmList Object Response
nlsList
List of nls Objects with a Common Model
getResponse.data.frame
Extract Response from a Data Frame
compareFits
Compare Fitted Objects
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
as.matrix.corStruct
Matrix of a corStruct Object
nlme.nlsList
NLME fit from nlsList Object
nlmeStruct
Nonlinear Mixed-Effects Structure
coef.gls
Extract gls Coefficients
coef.pdMat
pdMat Object Coefficients
summary.gls
Summarize a gls Object
varComb
Combination of Variance Functions
nlmeObject
Fitted nlme Object
residuals.glsStruct
Calculate glsStruct Residuals
predict.lme
Predictions from an lme Object
predict.lmList
Predictions from an lmList Object
print.modelStruct
Print a modelStruct Object
corRatio
Rational Quadratic Correlation Structure
getVarCov
Extract variance-covariance matrix
print.summary.gls
Print a summary.gls Object
plot.ACF
Plot an ACF Object
lmeScale
Scale for lme Optimization
glsControl
Control Values for gls Fit
pdBlocked
Positive-Definite Block Diagonal Matrix
gnlsObject
Fitted gnls Object
intervals.lmList
Confidence Intervals on lmList Coefficients
lmList.groupedData
lmList Fit from a groupedData Object
formula.gls
Extract gls Object Formula
print.pdMat
Print a pdMat Object
isInitialized
Check if Object is Initialized
lmeControl
Control Values for lme Fit
lmeObject
Fitted lme Object
intervals.gls
Confidence Intervals on gls Parameters
plot.nmGroupedData
Plot an nmGroupedData Object
getResponseFormula
Extract Formula Specifying Response Variable
lme
Linear Mixed-Effects Models
corGaus
Gaussian Correlation Structure
gnls
Fit Nonlinear Model Using Generalized Least Squares
corSpher
Spherical Correlation Structure
getGroups.lmList
Extract lmList Object Groups
print.corStruct
Print a corStruct Object
fitted.lme
Extract lme Fitted Values
getCovariate.varFunc
Extract varFunc Covariate
corLin
Linear Correlation Structure
lme.groupedData
LME fit from groupedData Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
coef.lmList
Extract lmList Coefficients
varConstPower
Constant Plus Power Variance Function
ranef.lmList
Extract lmList Random Effects
coef.pdDiag
pdDiag Object Coefficients
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
corMatrix
Extract Correlation Matrix
collapse.groupedData
Collapse a groupedData Object
balancedGrouped
Create a groupedData object from a matrix
formula.lmList
Extract lmList Object Formula
model.matrix.reStruct
reStruct Model Matrix
logLik.reStruct
Calculate reStruct Log-Likelihood
nlmeControl
Control Values for nlme Fit
nlme-internal
Internal nlme functions
needUpdate
Check if Update is Needed
ergoStool
Ergometrics experiment with stool types
MathAchSchool
School demographic data for MathAchieve
Nitrendipene
Assay of nitrendipene
Wafer
Modeling of Analog MOS Circuits
PBG
Effect of Phenylbiguanide on Blood Pressure
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Orthodont
Growth curve data on an orthdontic measurement
RatPupWeight
The weight of rat pups
Muscle
Contraction of heart muscle sections
Ovary
Counts of Ovarian Follicles
Gun
Methods for firing naval guns
BodyWeight
Rat weight over time for different diets
Oxboys
Heights of Boys in Oxford
MathAchieve
Mathematics achievement scores
Phenobarb
Phenobarbitol Kinetics
Pixel
X-ray pixel intensities over time
Rail
Evaluation of Stress in Railway Rails
Tetracycline2
Pharmacokinetics of tetracycline
Meat
Tenderness of meat
Soybean
Growth of soybean plants
Oxide
Variability in Semiconductor Manufacturing
Earthquake
Earthquake Intensity
Oats
Split-plot Experiment on Varieties of Oats
Cefamandole
Pharmacokinetics of Cefamandole
Wheat2
Wheat Yield Trials
Remifentanil
Pharmacokinetics of remifentanil
Milk
Protein content of cows' milk
Quinidine
Quinidine Kinetics
Tetracycline1
Pharmacokinetics of tetracycline
Fatigue
Cracks caused by metal fatigue
Dialyzer
High-Flux Hemodialyzer
IGF
Radioimmunoassay of IGF-I Protein
Wheat
Yields by growing conditions
Glucose
Glucose levels over time
Relaxin
Assay for Relaxin
bdf
Language scores
Glucose2
Glucose Levels Following Alcohol Ingestion
Spruce
Growth of Spruce Trees
Assay
Bioassay on Cell Culture Plate
Gasoline
Refinery yield of gasoline
Machines
Productivity Scores for Machines and Workers