Rdocumentation
powered by
Learn R Programming
⚠️
There's a newer version (3.1-168) of this package.
Take me there.
nlme (version 3.1-16)
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
149,202
Version
3.1-16
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-16)
Search all functions
corFactor
Factor of a Correlation Matrix
residuals.glsStruct
Calculate glsStruct Residuals
recalc
Recalculate Condensed Linear Model Object
recalc.varFunc
Recalculate for varFunc Object
print.summary.pdMat
Print a summary.pdMat Object
Dim
Extract Dimensions from an Object
BIC
Bayesian Information Criterion
Dim.pdMat
Dimensions of a pdMat Object
coef.pdCompSymm
pdCompSymm Object Coefficients
allCoef
Extract Coefficients from a Set of Objects
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
as.matrix.corStruct
Matrix of a corStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
as.matrix.reStruct
Matrices of an reStruct Object
coef.varFunc
varFunc Object Coefficients
coef.pdIdent
pdIdent Object Coefficients
Dim.corSpatial
Dimensions of a corSpatial Object
coef.pdDiag
pdDiag Object Coefficients
collapse
Collapse According to Groups
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
BIC.logLik
BIC of a logLik Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
MEdims
Calculate dimensions in mixed-effects
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
print.summary.corStruct
Print a summary.corStruct Object
lmeScale
Scale for lme Optimization
varConstPower
Constant Plus Power Variance Function
augPred
Augmented Predictions
varPower
Power Variance Function
varFixed
Fixed Variance Function
Coef
Assign Values to Coefficients
ACF.gls
Autocorrelation Function for gls Residuals
print.anova.lme
Print an anova.lme Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
corGaus
Gaussian Correlation Structure
MEEM
EM iterations for mixed-effects
Covariate
Assign Covariate Values
[.pdMat
Subscript a pdMat Object
AIC.logLik
AIC of a logLik Object
ACF.lme
Autocorrelation Function for lme Residuals
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
coef.pdMat
pdMat Object Coefficients
Variogram
Calculate Semi-variogram
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
corAR1
AR(1) Correlation Structure
corNatural
General correlation in natural parameterization
compareFits
Compare Fitted Objects
corExp
Exponential Correlation Structure
corSpher
Spherical Correlation Structure
residuals.nlmeStruct
Calculate nlmeStruct Residuals
varComb
Combination of Variance Functions
update.modelStruct
Update a modelStruct Object
getGroups.varFunc
Extract varFunc Groups
corMatrix
Extract Correlation Matrix
print.groupedData
Print a groupedData Object
getResponse.lmList
Extract lmList Object Response
summary.corStruct
Summarize a corStruct Object
coef.gnls
Extract gnls Coefficients
varFunc
Variance Function Structure
Covariate.varFunc
Assign varFunc Covariate
update.gls
Update a gls Object
getGroupsFormula
Extract Grouping Formula
print.modelStruct
Print a modelStruct Object
coef.lmList
Extract lmList Coefficients
update.lmList
Update an lmList Object
print.pdMat
Print a pdMat Object
corCompSymm
Compound Symmetry Correlation Structure
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
VarCorr
Extract variance and correlation components
update.groupedData
Update a groupedData Object
print.corStruct
Print a corStruct Object
formula.gls
Extract gls Object Formula
simulate.lme
simulate lme models
logLik.lme
Log-Likelihood of an lme Object
corLin
Linear Correlation Structure
Variogram.default
Calculate Semi-variogram
print.summary.gls
Print a summary.gls Object
logDet.reStruct
Extract reStruct Log-Determinants
lmeStruct
Linear Mixed-Effects Structure
ACF
Autocorrelation Function
varIdent
Constant Variance Function
lmeControl
Control Values for lme Fit
asTable
Convert groupedData to a matrix
logLik.lm
Extract Log-Likelihood from an lm Object
corCAR1
Continuous AR(1) Correlation Structure
Matrix.pdMat
Assign Matrix to a pdMat Object
logLik.reStruct
Calculate reStruct Log-Likelihood
coef.corStruct
Coefficients of a corStruct Object
residuals.lmeStruct
Calculate lmeStruct Residuals
comparePred
Compare Predictions
as.matrix.pdMat
Matrix of a pdMat Object
residuals.gnls
Extract gnls Residuals
nlsList
List of nls Objects with a Common Model
logLik.varFunc
Extract varFunc logLik
anova.lme
Compare Likelihoods of Fitted Objects
formula.nlme
Extract nlme Object Formula
summary.pdMat
Summarize a pdMat Object
getCovariate.data.frame
Extract Data Frame Covariate
random.effects.lmList
Extract lmList Random Effects
getCovariateFormula
Extract Covariates Formula
AIC
Akaike Information Criterion
isInitialized.reStruct
Check if an reStruct Object is Initialized
print.summary.modelStruct
Print a summary.modelStruct Object
pairs.compareFits
Pairs Plot of compareFits Object
update.nlme
Update an nlme Object
update.varFunc
Update varFunc Object
AIC.lme
Akaike Information Criterion
pdIdent
Multiple of the Identity Positive-Definite Matrix
corClasses
Correlation Structure Classes
summary.varFunc
Summarize varFunc Object
update.lme
Update an lme Object
residuals.lmList
Extract lmList Residuals
lmList.groupedData
lmList Fit from a groupedData Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
logDet
Extract the Logarithm of the Determinant
update.nlsList
Update an nlsList Object
recalc.corStruct
Recalculate for corStruct Object
splitFormula
Split a Formula
summary.lme
Summarize an lme Object
plot.lmList
Plot an lmList Object
formula.gnls
Extract gnls Object Formula
fdHess
Finite difference Hessian
logLik.gnls
Log-Likelihood of a gnls Object
coef.gls
Extract gls Coefficients
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
residuals.gls
Extract gls Residuals
fixed.effects.lmList
Extract lmList Fixed Effects
asOneFormula
Combine Formulas of a Set of Objects
coef.modelStruct
Extract modelStruct Object Coefficients
logLik.gls
Log-Likelihood of a gls Object
reStruct
Random Effects Structure
summary.modelStruct
Summarize a modelStruct Object
getResponse.lme
Extract lme Object Response
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
getResponseFormula
Extract Formula Specifying Response Variable
update.gnls
Update a gnls Object
isBalanced
Check a Design for Balance
Dim.corStruct
Dimensions of a corStruct Object
coef.reStruct
reStruct Object Coefficients
anova.gls
Compare Likelihoods of Fitted Objects
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
corARMA
ARMA(p,q) Correlation Structure
coef.lme
Extract lme Coefficients
corFactor.corStruct
Factor of a corStruct Object Matrix
varExp
Exponential Variance Function
fitted.lme
Extract lme Fitted Values
getGroups.lme
Extract lme Object Groups
balancedGrouped
Create a groupedData object from a matrix
gls
Fit Linear Model Using Generalized Least Squares
corSymm
General Correlation Structure
varClasses
Variance Function Classes
varWeights.lmeStruct
Variance Weights for lmeStruct Object
residuals.lme
Extract lme Residuals
summary.nlsList
Summarize an nlsList Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
print.lmList
Print an lmList Object
fitted.gnls
Extract gnls Fitted Values
fixed.effects
Extract Fixed Effects
formula.nlsList
Extract nlsList Object Formula
formula.lme
Extract lme Object Formula
needUpdate
Check if Update is Needed
corRatio
Rational Quadratic Correlation Structure
Names.formula
Extract Names from a formula
getGroups.corStruct
Extract corStruct Groups
fitted.glsStruct
Calculate glsStruct Fitted Values
pdConstruct.pdBlocked
Construct pdBlocked Objects
print.summary.lmList
Print a summary.lmList Object
plot.nffGroupedData
Plot an nffGroupedData Object
fitted.lmList
Extract lmList Fitted Values
formula.lmList
Extract lmList Object Formula
fixed.effects.lme
Extract lme Fixed Effects
lme
Linear Mixed-Effects Models
logLik.corStruct
Extract corStruct Log-Likelihood
fitted.gls
Extract gls Fitted Values
isInitialized
Check if Object is Initialized
getGroups.lmList
Extract lmList Object Groups
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
Matrix.reStruct
Assign reStruct Matrices
varWeights.glsStruct
Variance Weights for glsStruct Object
initialize.lmeStruct
Initialize an lmeStruct Object
contr.SAS
Contrast Matrices
formula.nls
Extract Model Formula from nls Object
pdLogChol
General Positive-Definite Matrix
predict.gls
Predictions from a gls Object
intervals.lme
Confidence Intervals on lme Parameters
gnlsControl
Control Values for gnls Fit
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.Variogram
Plot a Variogram Object
print.gls
Print a gls Object
formula.varFunc
Extract varFunc Formula
pdBlocked
Positive-Definite Block Diagonal Matrix
getData
Extract Data from an Object
pairs.lmList
Pairs Plot of an lmList Object
gsummary
Summarize by Groups
getData.lme
Extract lme Object Data
corSpatial
Spatial Correlation Structure
Matrix
Assign Matrix Values
print.summary.lme
Print a summary.lme Object
formula.reStruct
Extract reStruct Object Formula
logLik.lmList
Log-Likelihood of an lmList Object
gapply
Apply a Function by Groups
getData.lmList
Extract lmList Object Data
MEestimate
Estimate mixed-effects parameters
Names
Names Associated with an Object
MEdecomp
Decompose a mixed-effects model
Names.reStruct
Names of an reStruct Object
pruneLevels
Prune Factor Levels
qqnorm.gls
Normal Plot of Residuals from a gls Object
getData.gls
Extract gls Object Data
Names.pdBlocked
Names of a pdBlocked Object
intervals.gls
Confidence Intervals on gls Parameters
intervals
Confidence Intervals on Coefficients
gnlsStruct
Generalized Nonlinear Least Squares Structure
lme.groupedData
LME fit from groupedData Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdMat
Positive-Definite Matrix
plot.lme
Plot an lme Object
formula.groupedData
Extract groupedData Formula
getGroups.data.frame
Extract Groups from a Data Frame
formula.pdMat
Extract pdMat Formula
initialize
Initialize Object
collapse.groupedData
Collapse a groupedData Object
initialize.varFunc
Initialize varFunc Object
glsStruct
Generalized Least Squares Structure
plot.gls
Plot a gls Object
plot.ranef.lme
Plot a ranef.lme Object
corMatrix.corStruct
Matrix of a corStruct Object
getCovariate.varFunc
Extract varFunc Covariate
random.effects
Extract Random Effects
lme.lmList
LME fit from lmList Object
recalc.reStruct
Recalculate for an reStruct Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
pdSymm
General Positive-Definite Matrix
formula.pdBlocked
Extract pdBlocked Formula
nlme
Nonlinear Mixed-Effects Models
formula.modelStruct
Extract modelStruct Object Formula
gnls
Fit Nonlinear Model Using Generalized Least Squares
print.varFunc
Print a varFunc Object
getResponse.gls
Extract gls Object Response
print.lme
Print an lme Object
plot.nmGroupedData
Plot an nmGroupedData Object
plot.ranef.lmList
Plot a ranef.lmList Object
getCovariate
Extract Covariate from an Object
getResponse.data.frame
Extract Response from a Data Frame
pooledSD
Extract Pooled Standard Deviation
logDet.corStruct
Extract corStruct Log-Determinant
formula.corStruct
Extract corStruct Object Formula
print.reStruct
Print an reStruct Object
getGroups.gls
Extract gls Object Groups
groupedData
Construct a groupedData Object
initialize.corStruct
Initialize corStruct Object
getGroups
Extract Grouping Factors from an Object
nlmeObject
Fitted nlme Object
getCovariate.corStruct
Extract corStruct Object Covariate
nlmeControl
Control Values for nlme Fit
lmList
List of lm Objects with a Common Model
plot.intervals.lmList
Plot lmList Confidence Intervals
initialize.glsStruct
Initialize a glsStruct Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
intervals.lmList
Confidence Intervals on lmList Coefficients
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
plot.ACF
Plot an ACF Object
getResponse
Extract Response Variable from an Object
nlsList.selfStart
nlsList Fit from a selfStart Function
pairs.lme
Pairs Plot of an lme Object
lmeObject
Fitted lme Object
print.summary.varFunc
Print a summary.varFunc Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
varWeights
Extract Variance Function Weights
glsObject
Fitted gls Object
predict.nlme
Predictions from an nlme Object
recalc.modelStruct
Recalculate for a modelStruct Object
Names.pdMat
Names of a pdMat Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
gnlsObject
Fitted gnls Object
pdClasses
Positive-Definite Matrix Classes
nlme.nlsList
NLME fit from nlsList Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
nlmeStruct
Nonlinear Mixed-Effects Structure
plot.nfnGroupedData
Plot an nfnGroupedData Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
glsControl
Control Values for gls Fit
predict.lme
Predictions from an lme Object
predict.gnls
Predictions from a gnls Object
solve.reStruct
Apply Solve to an reStruct Object
predict.lmList
Predictions from an lmList Object
pdConstruct
Construct pdMat Objects
plot.compareFits
Plot a compareFits Object
plot.augPred
Plot an augPred Object
model.matrix.reStruct
reStruct Model Matrix
initialize.reStruct
Initialize reStruct Object
pdDiag
Diagonal Positive-Definite Matrix
random.effects.lme
Extract lme Random Effects
summary.gls
Summarize a gls Object
summary.lmList
Summarize an lmList Object
Assay
Bioassay on Cell Culture Plate
Phenobarb
Phenobarbitol Kinetics
MathAchieve
Mathematics achievement scores
RatPupWeight
The weight of rat pups
IGF
Radioimmunoassay of IGF-I Protein
Fatigue
Cracks caused by metal fatigue
Orthodont
Growth curve data on an orthdontic measurement
Rail
Evaluation of Stress in Railway Rails
Relaxin
Assay for Relaxin
Wheat2
Wheat Yield Trials
Glucose2
Glucose Levels Following Alcohol Ingestion
Oats
Split-plot Experiment on Varieties of Oats
Quinidine
Quinidine Kinetics
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
MathAchSchool
School demographic data for MathAchieve
Dialyzer
High-Flux Hemodialyzer
Glucose
Glucose levels over time
Earthquake
Earthquake Intensity
Pixel
X-ray pixel intensities over time
Remifentanil
Pharmacokinetics of remifentanil
Machines
Productivity Scores for Machines and Workers
Nitrendipene
Assay of nitrendipene
Muscle
Contraction of heart muscle sections
Tetracycline1
Pharmacokinetics of tetracycline
Tetracycline2
Pharmacokinetics of tetracycline
Spruce
Growth of Spruce Trees
BodyWeight
Rat weight over time for different diets
Ovary
Counts of Ovarian Follicles
PBG
Effect of Phenylbiguanide on Blood Pressure
Oxide
Variability in Semiconductor Manufacturing
Wheat
Yields by growing conditions
Soybean
Growth of soybean plants
Gasoline
Refinery yield of gasoline
Wafer
Modeling of Analog MOS Circuits
Cefamandole
Pharmacokinetics of Cefamandole
ergoStool
Ergometrics experiment with stool types
Gun
Methods for firing naval guns
Meat
Tenderness of meat
Milk
Protein content of cows' milk
Oxboys
Heights of Boys in Oxford