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nlme (version 3.1-32)
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
85,005
Version
3.1-32
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-32)
Search all functions
ACF
Autocorrelation Function
Initialize.varFunc
Initialize varFunc Object
BIC
Bayesian Information Criterion
Initialize
Initialize Object
fitted.lmList
Extract lmList Fitted Values
[.pdMat
Subscript a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
Dim
Extract Dimensions from an Object
AIC
Akaike Information Criterion
corSymm
General Correlation Structure
Dim.corSpatial
Dimensions of a corSpatial Object
coef.pdCompSymm
pdCompSymm Object Coefficients
ACF.lme
Autocorrelation Function for lme Residuals
asOneFormula
Combine Formulas of a Set of Objects
Matrix.pdMat
Assign Matrix to a pdMat Object
Matrix
Assign Matrix Values
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Initialize.reStruct
Initialize reStruct Object
coef.gnls
Extract gnls Coefficients
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Covariate.varFunc
Assign varFunc Covariate
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Dim.pdMat
Dimensions of a pdMat Object
MEdecomp
Decompose a mixed-effects model
coef.pdDiag
pdDiag Object Coefficients
corARMA
ARMA(p,q) Correlation Structure
fitted.gls
Extract gls Fitted Values
residuals.lmList
Extract lmList Residuals
contr.SAS
Contrast Matrices
residuals.gnlsStruct
Calculate gnlsStruct Residuals
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
isInitialized
Check if Object is Initialized
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
Covariate
Assign Covariate Values
Initialize.lmeStruct
Initialize an lmeStruct Object
MEEM
EM iterations for mixed-effects
MEestimate
Estimate mixed-effects parameters
ACF.gls
Autocorrelation Function for gls Residuals
BIC.logLik
BIC of a logLik Object
corAR1
AR(1) Correlation Structure
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
as.matrix.reStruct
Matrices of an reStruct Object
coef.varFunc
varFunc Object Coefficients
print.summary.lme
Print a summary.lme Object
balancedGrouped
Create a groupedData object from a matrix
fdHess
Finite difference Hessian
corGaus
Gaussian Correlation Structure
corClasses
Correlation Structure Classes
isInitialized.reStruct
Check if an reStruct Object is Initialized
reStruct
Random Effects Structure
corFactor
Factor of a Correlation Matrix
recalc.corStruct
Recalculate for corStruct Object
varWeights
Extract Variance Function Weights
print.lmList
Print an lmList Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
Initialize.corStruct
Initialize corStruct Object
predict.gls
Predictions from a gls Object
getGroups
Extract Grouping Factors from an Object
plot.lme
Plot an lme or nls object
summary.modelStruct
Summarize a modelStruct Object
pdClasses
Positive-Definite Matrix Classes
Dim.corStruct
Dimensions of a corStruct Object
print.reStruct
Print an reStruct Object
predict.nlme
Predictions from an nlme Object
AIC.lme
Akaike Information Criterion
Names
Names Associated with an Object
corMatrix.corStruct
Matrix of a corStruct Object
solve.reStruct
Apply Solve to an reStruct Object
LDEsysMat
Generate system matrix for LDEs
recalc.reStruct
Recalculate for an reStruct Object
Names.reStruct
Names of an reStruct Object
formula.pdBlocked
Extract pdBlocked Formula
anova.gls
Compare Likelihoods of Fitted Objects
Initialize.glsStruct
Initialize a glsStruct Object
Names.formula
Extract Names from a formula
formula.varFunc
Extract varFunc Formula
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pairs.lme
Pairs Plot of an lme Object
coef.corStruct
Coefficients of a corStruct Object
plot.nmGroupedData
Plot an nmGroupedData Object
asTable
Convert groupedData to a matrix
pairs.compareFits
Pairs Plot of compareFits Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
varConstPower
Constant Plus Power Variance Function
nlsList.selfStart
nlsList Fit from a selfStart Function
comparePred
Compare Predictions
formula.corStruct
Extract corStruct Object Formula
print.pdMat
Print a pdMat Object
VarCorr
Extract variance and correlation components
print.groupedData
Print a groupedData Object
pruneLevels
Prune Factor Levels
allCoef
Extract Coefficients from a Set of Objects
nlmeControl
Control Values for nlme Fit
print.summary.gls
Print a summary.gls Object
print.summary.varFunc
Print a summary.varFunc Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getData.gls
Extract gls Object Data
residuals.glsStruct
Calculate glsStruct Residuals
corNatural
General correlation in natural parameterization
update.varFunc
Update varFunc Object
MEdims
Calculate dimensions in mixed-effects
lmList
List of lm Objects with a Common Model
formula.gls
Extract gls Object Formula
Coef
Assign Values to Coefficients
recalc.varFunc
Recalculate for varFunc Object
summary.pdMat
Summarize a pdMat Object
getGroups.gls
Extract gls Object Groups
varWeights.glsStruct
Variance Weights for glsStruct Object
fitted.gnls
Extract gnls Fitted Values
formula.nlme
Extract nlme Object Formula
print.summary.corStruct
Print a summary.corStruct Object
as.matrix.pdMat
Matrix of a pdMat Object
intervals.lmList
Confidence Intervals on lmList Coefficients
coef.modelStruct
Extract modelStruct Object Coefficients
predict.lme
Predictions from an lme Object
formula.groupedData
Extract groupedData Formula
print.modelStruct
Print a modelStruct Object
varExp
Exponential Variance Function
pooledSD
Extract Pooled Standard Deviation
Variogram
Calculate Semi-variogram
ranef.lmList
Extract lmList Random Effects
logLik.gnls
Log-Likelihood of a gnls Object
lmeStruct
Linear Mixed-Effects Structure
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
lmList.groupedData
lmList Fit from a groupedData Object
corLin
Linear Correlation Structure
anova.lme
Compare Likelihoods of Fitted Objects
pdDiag
Diagonal Positive-Definite Matrix
summary.varFunc
Summarize varFunc Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
gapply
Apply a Function by Groups
Names.pdMat
Names of a pdMat Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
augPred
Augmented Predictions
corCAR1
Continuous AR(1) Correlation Structure
getData.lme
Extract lme Object Data
varPower
Power Variance Function
corCompSymm
Compound Symmetry Correlation Structure
update.modelStruct
Update a modelStruct Object
varClasses
Variance Function Classes
pdSymm
General Positive-Definite Matrix
collapse.groupedData
Collapse a groupedData Object
summary.nlsList
Summarize an nlsList Object
plot.nffGroupedData
Plot an nffGroupedData Object
as.matrix.corStruct
Matrix of a corStruct Object
print.summary.lmList
Print a summary.lmList Object
groupedData
Construct a groupedData Object
fixef.lmList
Extract lmList Fixed Effects
varIdent
Constant Variance Function
nlme-internal
Internal nlme functions
getGroups.varFunc
Extract varFunc Groups
varFunc
Variance Function Structure
logLik.reStruct
Calculate reStruct Log-Likelihood
print.summary.pdMat
Print a summary.pdMat Object
getCovariate.corStruct
Extract corStruct Object Covariate
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
coef.reStruct
reStruct Object Coefficients
formula.lmList
Extract lmList Object Formula
plot.gls
Plot a gls Object
predict.gnls
Predictions from a gnls Object
Matrix.reStruct
Assign reStruct Matrices
splitFormula
Split a Formula
corFactor.corStruct
Factor of a corStruct Object Matrix
compareFits
Compare Fitted Objects
getGroups.lme
Extract lme Object Groups
getCovariateFormula
Extract Covariates Formula
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
getCovariate.data.frame
Extract Data Frame Covariate
fixed.effects
Extract Fixed Effects
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
formula.modelStruct
Extract modelStruct Object Formula
ranef.lme
Extract lme Random Effects
residuals.lmeStruct
Calculate lmeStruct Residuals
getGroups.corStruct
Extract corStruct Groups
nlme.nlsList
NLME fit from nlsList Object
coef.lmList
Extract lmList Coefficients
nlme
Nonlinear Mixed-Effects Models
lme.groupedData
LME fit from groupedData Object
corRatio
Rational Quadratic Correlation Structure
needUpdate
Check if Update is Needed
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
logLik.lmList
Log-Likelihood of an lmList Object
lmeObject
Fitted lme Object
formula.pdMat
Extract pdMat Formula
print.anova.lme
Print an anova.lme Object
summary.gls
Summarize a gls Object
pairs.lmList
Pairs Plot of an lmList Object
print.gls
Print a gls Object
Variogram.default
Calculate Semi-variogram
getVarCov
Extract variance-covariance matrix
model.matrix.reStruct
reStruct Model Matrix
recalc.modelStruct
Recalculate for a modelStruct Object
print.lme
Print an lme Object
residuals.lme
Extract lme Residuals
collapse
Collapse According to Groups
plot.ranef.lmList
Plot a ranef.lmList Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
getGroups.lmList
Extract lmList Object Groups
getGroupsFormula
Extract Grouping Formula
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
isBalanced
Check a Design for Balance
logLik.varFunc
Extract varFunc logLik
getResponse.lmList
Extract lmList Object Response
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
predict.lmList
Predictions from an lmList Object
getGroups.data.frame
Extract Groups from a Data Frame
formula.nlsList
Extract nlsList Object Formula
glsStruct
Generalized Least Squares Structure
fixef.lme
Extract lme Fixed Effects
print.varFunc
Print a varFunc Object
nlmeStruct
Nonlinear Mixed-Effects Structure
coef.pdIdent
pdIdent Object Coefficients
gnlsStruct
Generalized Nonlinear Least Squares Structure
plot.ranef.lme
Plot a ranef.lme Object
logDet
Extract the Logarithm of the Determinant
nlmeObject
Fitted nlme Object
getData
Extract Data from an Object
coef.lme
Extract lme Coefficients
pdConstruct.pdBlocked
Construct pdBlocked Objects
recalc
Recalculate Condensed Linear Model Object
corExp
Exponential Correlation Structure
getResponse.data.frame
Extract Response from a Data Frame
pdConstruct
Construct pdMat Objects
gnlsControl
Control Values for gnls Fit
logLik.lme
Log-Likelihood of an lme Object
corSpher
Spherical Correlation Structure
formula.reStruct
Extract reStruct Object Formula
plot.ACF
Plot an ACF Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
formula.gnls
Extract gnls Object Formula
varComb
Combination of Variance Functions
intervals.lme
Confidence Intervals on lme Parameters
qqnorm.gls
Normal Plot of Residuals from a gls Object
summary.lme
Summarize an lme Object
coef.pdMat
pdMat Object Coefficients
gnlsObject
Fitted gnls Object
getCovariate
Extract Covariate from an Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.lmList
Plot an lmList Object
quinModel
Model function for the Quinidine data
pdMat
Positive-Definite Matrix
getCovariate.varFunc
Extract varFunc Covariate
nlsList
List of nls Objects with a Common Model
plot.Variogram
Plot a Variogram Object
residuals.gls
Extract gls Residuals
intervals.gls
Confidence Intervals on gls Parameters
summary.lmList
Summarize an lmList Object
fitted.glsStruct
Calculate glsStruct Fitted Values
plot.augPred
Plot an augPred Object
glsControl
Control Values for gls Fit
pdBlocked
Positive-Definite Block Diagonal Matrix
glsObject
Fitted gls Object
lme.lmList
LME fit from lmList Object
random.effects
Extract Random Effects
logDet.pdMat
Extract Log-Determinant from a pdMat Object
print.summary.modelStruct
Print a summary.modelStruct Object
plot.intervals.lmList
Plot lmList Confidence Intervals
pdLogChol
General Positive-Definite Matrix
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
summary.corStruct
Summarize a corStruct Object
lme
Linear Mixed-Effects Models
corSpatial
Spatial Correlation Structure
formula.lme
Extract lme Object Formula
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
simulate.lme
simulate lme models
print.corStruct
Print a corStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
phenoModel
Model function for the Phenobarb data
getData.lmList
Extract lmList Object Data
logDet.corStruct
Extract corStruct Log-Determinant
lmeScale
Scale for lme Optimization
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
fitted.lme
Extract lme Fitted Values
pdIdent
Multiple of the Identity Positive-Definite Matrix
corMatrix
Extract Correlation Matrix
coef.gls
Extract gls Coefficients
intervals
Confidence Intervals on Coefficients
lmeControl
Control Values for lme Fit
getResponse
Extract Response Variable from an Object
getResponse.gls
Extract gls Object Response
gnls
Fit Nonlinear Model Using Generalized Least Squares
logLik.gls
Log-Likelihood of a gls Object
gsummary
Summarize by Groups
logDet.reStruct
Extract reStruct Log-Determinants
getResponse.lme
Extract lme Object Response
varFixed
Fixed Variance Function
gls
Fit Linear Model Using Generalized Least Squares
plot.compareFits
Plot a compareFits Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
logLik.glsStruct
Log-Likelihood of a glsStruct Object
getResponseFormula
Extract Formula Specifying Response Variable
logLik.corStruct
Extract corStruct Log-Likelihood
Gun
Methods for firing naval guns
Rail
Evaluation of Stress in Railway Rails
Tetracycline2
Pharmacokinetics of tetracycline
Earthquake
Earthquake Intensity
Orthodont
Growth curve data on an orthdontic measurement
Meat
Tenderness of meat
Muscle
Contraction of heart muscle sections
Nitrendipene
Assay of nitrendipene
Dialyzer
High-Flux Hemodialyzer
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Glucose2
Glucose Levels Following Alcohol Ingestion
Assay
Bioassay on Cell Culture Plate
IGF
Radioimmunoassay of IGF-I Protein
Glucose
Glucose levels over time
Wheat
Yields by growing conditions
Milk
Protein content of cows' milk
Soybean
Growth of soybean plants
BodyWeight
Rat weight over time for different diets
Pixel
X-ray pixel intensities over time
Ovary
Counts of Ovarian Follicles
PBG
Effect of Phenylbiguanide on Blood Pressure
RatPupWeight
The weight of rat pups
Oxide
Variability in Semiconductor Manufacturing
MathAchieve
Mathematics achievement scores
MathAchSchool
School demographic data for MathAchieve
Phenobarb
Phenobarbitol Kinetics
Machines
Productivity Scores for Machines and Workers
Quinidine
Quinidine Kinetics
Oxboys
Heights of Boys in Oxford
Wafer
Modeling of Analog MOS Circuits
Oats
Split-plot Experiment on Varieties of Oats
Cefamandole
Pharmacokinetics of Cefamandole
Fatigue
Cracks caused by metal fatigue
bdf
Language scores
Relaxin
Assay for Relaxin
Gasoline
Refinery yield of gasoline
Tetracycline1
Pharmacokinetics of tetracycline
Spruce
Growth of Spruce Trees
Remifentanil
Pharmacokinetics of remifentanil
Wheat2
Wheat Yield Trials
ergoStool
Ergometrics experiment with stool types