Rdocumentation
powered by
Learn R Programming
⚠️
There's a newer version (3.1-168) of this package.
Take me there.
nlme (version 3.1-53)
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
90,510
Version
3.1-53
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-53)
Search all functions
as.matrix.pdMat
Matrix of a pdMat Object
glsStruct
Generalized Least Squares Structure
fitted.lmList
Extract lmList Fitted Values
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
getResponse
Extract Response Variable from an Object
getGroups.lmList
Extract lmList Object Groups
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
gapply
Apply a Function by Groups
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
logLik.lme
Log-Likelihood of an lme Object
pdClasses
Positive-Definite Matrix Classes
[.pdMat
Subscript a pdMat Object
Covariate
Assign Covariate Values
Initialize.glsStruct
Initialize a glsStruct Object
coef.pdMat
pdMat Object Coefficients
lmeStruct
Linear Mixed-Effects Structure
collapse
Collapse According to Groups
varComb
Combination of Variance Functions
nlsList
List of nls Objects with a Common Model
Initialize.corStruct
Initialize corStruct Object
plot.Variogram
Plot a Variogram Object
Initialize
Initialize Object
getCovariate.corStruct
Extract corStruct Object Covariate
recalc
Recalculate Condensed Linear Model Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
phenoModel
Model function for the Phenobarb data
allCoef
Extract Coefficients from a Set of Objects
plot.nfnGroupedData
Plot an nfnGroupedData Object
varFunc
Variance Function Structure
quinModel
Model function for the Quinidine data
getGroups.lme
Extract lme Object Groups
predict.gls
Predictions from a gls Object
BIC.logLik
BIC of a logLik Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
summary.nlsList
Summarize an nlsList Object
print.varFunc
Print a varFunc Object
plot.nmGroupedData
Plot an nmGroupedData Object
logDet.corStruct
Extract corStruct Log-Determinant
glsControl
Control Values for gls Fit
logLik.reStruct
Calculate reStruct Log-Likelihood
lmeObject
Fitted lme Object
intervals.gls
Confidence Intervals on gls Parameters
getData.lmList
Extract lmList Object Data
lmList.groupedData
lmList Fit from a groupedData Object
residuals.glsStruct
Calculate glsStruct Residuals
gnls
Fit Nonlinear Model Using Generalized Least Squares
collapse.groupedData
Collapse a groupedData Object
plot.intervals.lmList
Plot lmList Confidence Intervals
pairs.compareFits
Pairs Plot of compareFits Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
logDet.pdMat
Extract Log-Determinant from a pdMat Object
glsObject
Fitted gls Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
residuals.lmList
Extract lmList Residuals
corGaus
Gaussian Correlation Structure
residuals.gnlsStruct
Calculate gnlsStruct Residuals
plot.gls
Plot a gls Object
nlmeStruct
Nonlinear Mixed-Effects Structure
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
varExp
Exponential Variance Function
pdLogChol
General Positive-Definite Matrix
Dim
Extract Dimensions from an Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
corCAR1
Continuous AR(1) Correlation Structure
pooledSD
Extract Pooled Standard Deviation
getGroups.corStruct
Extract corStruct Groups
summary.gls
Summarize a gls Object
Names.pdBlocked
Names of a pdBlocked Object
Initialize.lmeStruct
Initialize an lmeStruct Object
Dim.corStruct
Dimensions of a corStruct Object
fixed.effects
Extract Fixed Effects
getGroups.varFunc
Extract varFunc Groups
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
BIC
Bayesian Information Criterion
getData.lme
Extract lme Object Data
getData.gls
Extract gls Object Data
fitted.lme
Extract lme Fitted Values
getCovariate.data.frame
Extract Data Frame Covariate
getGroupsFormula
Extract Grouping Formula
Initialize.reStruct
Initialize reStruct Object
getCovariate
Extract Covariate from an Object
Covariate.varFunc
Assign varFunc Covariate
Initialize.varFunc
Initialize varFunc Object
Dim.corSpatial
Dimensions of a corSpatial Object
ACF.lme
Autocorrelation Function for lme Residuals
lme.groupedData
LME fit from groupedData Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logDet.reStruct
Extract reStruct Log-Determinants
lme
Linear Mixed-Effects Models
isBalanced
Check a Design for Balance
nlmeObject
Fitted nlme Object
Coef
Assign Values to Coefficients
nlme.nlsList
NLME fit from nlsList Object
isInitialized
Check if Object is Initialized
getGroups.data.frame
Extract Groups from a Data Frame
gls
Fit Linear Model Using Generalized Least Squares
getCovariate.varFunc
Extract varFunc Covariate
nlmeControl
Control Values for nlme Fit
fixef.lmList
Extract lmList Fixed Effects
groupedData
Construct a groupedData Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
ACF.gls
Autocorrelation Function for gls Residuals
getCovariateFormula
Extract Covariates Formula
intervals.lmList
Confidence Intervals on lmList Coefficients
formula.pdBlocked
Extract pdBlocked Formula
Matrix.reStruct
Assign reStruct Matrices
anova.lme
Compare Likelihoods of Fitted Objects
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
getGroups
Extract Grouping Factors from an Object
gsummary
Summarize by Groups
Variogram.corExp
Calculate Semi-variogram for a corExp Object
as.matrix.reStruct
Matrices of an reStruct Object
getVarCov
Extract variance-covariance matrix
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
intervals.lme
Confidence Intervals on lme Parameters
as.matrix.corStruct
Matrix of a corStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
asTable
Convert groupedData to a matrix
balancedGrouped
Create a groupedData object from a matrix
augPred
Augmented Predictions
coef.varFunc
varFunc Object Coefficients
coef.reStruct
reStruct Object Coefficients
VarCorr
Extract variance and correlation components
Variogram.default
Calculate Semi-variogram
corSymm
General Correlation Structure
corMatrix.corStruct
Matrix of a corStruct Object
corFactor
Factor of a Correlation Matrix
coef.modelStruct
Extract modelStruct Object Coefficients
fdHess
Finite difference Hessian
fitted.glsStruct
Calculate glsStruct Fitted Values
gnlsControl
Control Values for gnls Fit
formula.pdMat
Extract pdMat Formula
compareFits
Compare Fitted Objects
contr.SAS
Contrast Matrices
asOneFormula
Combine Formulas of a Set of Objects
Variogram
Calculate Semi-variogram
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
anova.gls
Compare Likelihoods of Fitted Objects
getData
Extract Data from an Object
Matrix.pdMat
Assign Matrix to a pdMat Object
Matrix
Assign Matrix Values
Names
Names Associated with an Object
LDEsysMat
Generate system matrix for LDEs
ACF
Autocorrelation Function
corNatural
General correlation in natural parameterization
Names.reStruct
Names of an reStruct Object
corAR1
AR(1) Correlation Structure
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
corSpher
Spherical Correlation Structure
comparePred
Compare Predictions
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corExp
Exponential Correlation Structure
corMatrix
Extract Correlation Matrix
corLin
Linear Correlation Structure
formula.reStruct
Extract reStruct Object Formula
corSpatial
Spatial Correlation Structure
getGroups.gls
Extract gls Object Groups
plot.ranef.lmList
Plot a ranef.lmList Object
gnlsObject
Fitted gnls Object
plot.ranef.lme
Plot a ranef.lme Object
corARMA
ARMA(p,q) Correlation Structure
predict.lmList
Predictions from an lmList Object
predict.gnls
Predictions from a gnls Object
predict.lme
Predictions from an lme Object
predict.nlme
Predictions from an nlme Object
print.summary.pdMat
Print a summary.pdMat Object
Names.formula
Extract Names from a formula
Names.pdMat
Names of a pdMat Object
corRatio
Rational Quadratic Correlation Structure
pdMat
Positive-Definite Matrix
coef.lme
Extract lme Coefficients
corClasses
Correlation Structure Classes
corFactor.corStruct
Factor of a corStruct Object Matrix
coef.lmList
Extract lmList Coefficients
getResponseFormula
Extract Formula Specifying Response Variable
coef.gnls
Extract gnls Coefficients
Dim.pdMat
Dimensions of a pdMat Object
lmList
List of lm Objects with a Common Model
coef.corStruct
Coefficients of a corStruct Object
needUpdate
Check if Update is Needed
intervals
Confidence Intervals on Coefficients
lme.lmList
LME fit from lmList Object
pairs.lmList
Pairs Plot of an lmList Object
logDet
Extract the Logarithm of the Determinant
nlme
Nonlinear Mixed-Effects Models
logLik.varFunc
Extract varFunc logLik
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdBlocked
Positive-Definite Block Diagonal Matrix
nlsList.selfStart
nlsList Fit from a selfStart Function
lmeControl
Control Values for lme Fit
pdConstruct.pdBlocked
Construct pdBlocked Objects
model.matrix.reStruct
reStruct Model Matrix
pairs.lme
Pairs Plot of an lme Object
lmeScale
Scale for lme Optimization
logLik.lmList
Log-Likelihood of an lmList Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
pdDiag
Diagonal Positive-Definite Matrix
pdConstruct
Construct pdMat Objects
logLik.corStruct
Extract corStruct Log-Likelihood
logLik.gnls
Log-Likelihood of a gnls Object
solve.reStruct
Apply Solve to an reStruct Object
splitFormula
Split a Formula
residuals.nlmeStruct
Calculate nlmeStruct Residuals
simulate.lme
simulate lme models
summary.modelStruct
Summarize a modelStruct Object
corCompSymm
Compound Symmetry Correlation Structure
summary.lmList
Summarize an lmList Object
summary.lme
Summarize an lme Object
summary.corStruct
Summarize a corStruct Object
update.varFunc
Update varFunc Object
residuals.lmeStruct
Calculate lmeStruct Residuals
varPower
Power Variance Function
varIdent
Constant Variance Function
varWeights.lmeStruct
Variance Weights for lmeStruct Object
recalc.corStruct
Recalculate for corStruct Object
ranef.lme
Extract lme Random Effects
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
residuals.lme
Extract lme Residuals
plot.lmList
Plot an lmList Object
random.effects
Extract Random Effects
pdSymm
General Positive-Definite Matrix
plot.compareFits
Plot a compareFits Object
plot.augPred
Plot an augPred Object
plot.ACF
Plot an ACF Object
plot.lme
Plot an lme or nls object
plot.nffGroupedData
Plot an nffGroupedData Object
recalc.varFunc
Recalculate for varFunc Object
residuals.gls
Extract gls Residuals
recalc.reStruct
Recalculate for an reStruct Object
ranef.lmList
Extract lmList Random Effects
reStruct
Random Effects Structure
recalc.modelStruct
Recalculate for a modelStruct Object
update.modelStruct
Update a modelStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
varClasses
Variance Function Classes
varFixed
Fixed Variance Function
varConstPower
Constant Plus Power Variance Function
summary.varFunc
Summarize varFunc Object
summary.pdMat
Summarize a pdMat Object
varWeights
Extract Variance Function Weights
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Oxide
Variability in Semiconductor Manufacturing
Phenobarb
Phenobarbitol Kinetics
Oats
Split-plot Experiment on Varieties of Oats
Wheat2
Wheat Yield Trials
Rail
Evaluation of Stress in Railway Rails
Gun
Methods for firing naval guns
Remifentanil
Pharmacokinetics of remifentanil
MathAchSchool
School demographic data for MathAchieve
Orthodont
Growth curve data on an orthdontic measurement
Meat
Tenderness of meat
Gasoline
Refinery yield of gasoline
IGF
Radioimmunoassay of IGF-I Protein
Relaxin
Assay for Relaxin
bdf
Language scores
Fatigue
Cracks caused by metal fatigue
Machines
Productivity Scores for Machines and Workers
RatPupWeight
The weight of rat pups
Cefamandole
Pharmacokinetics of Cefamandole
Pixel
X-ray pixel intensities over time
Wheat
Yields by growing conditions
Nitrendipene
Assay of nitrendipene
Ovary
Counts of Ovarian Follicles
Milk
Protein content of cows' milk
Soybean
Growth of soybean plants
ergoStool
Ergometrics experiment with stool types
Wafer
Modeling of Analog MOS Circuits
Oxboys
Heights of Boys in Oxford
Tetracycline2
Pharmacokinetics of tetracycline
MathAchieve
Mathematics achievement scores
Glucose
Glucose levels over time
Dialyzer
High-Flux Hemodialyzer
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Tetracycline1
Pharmacokinetics of tetracycline
Earthquake
Earthquake Intensity
Glucose2
Glucose Levels Following Alcohol Ingestion
Quinidine
Quinidine Kinetics
Spruce
Growth of Spruce Trees
Assay
Bioassay on Cell Culture Plate
BodyWeight
Rat weight over time for different diets
Muscle
Contraction of heart muscle sections
PBG
Effect of Phenylbiguanide on Blood Pressure