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nlme (version 3.1-17)
Linear and nonlinear mixed effects models
Description
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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3.1-3
3.1-2 (1999/12/23)
3.1-1
Install
install.packages('nlme')
Monthly Downloads
85,005
Version
3.1-17
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-17)
Search all functions
asTable
Convert groupedData to a matrix
corMatrix
Extract Correlation Matrix
Names
Names Associated with an Object
residuals.lmList
Extract lmList Residuals
getData.lme
Extract lme Object Data
VarCorr
Extract variance and correlation components
BIC
Bayesian Information Criterion
Covariate
Assign Covariate Values
comparePred
Compare Predictions
Names.pdMat
Names of a pdMat Object
as.matrix.corStruct
Matrix of a corStruct Object
coef.pdCompSymm
pdCompSymm Object Coefficients
corCompSymm
Compound Symmetry Correlation Structure
coef.pdMat
pdMat Object Coefficients
fitted.lmeStruct
Calculate lmeStruct Fitted Values
allCoef
Extract Coefficients from a Set of Objects
corCAR1
Continuous AR(1) Correlation Structure
corClasses
Correlation Structure Classes
solve.reStruct
Apply Solve to an reStruct Object
AIC.lme
Akaike Information Criterion
corSpher
Spherical Correlation Structure
coef.modelStruct
Extract modelStruct Object Coefficients
contr.SAS
Contrast Matrices
corGaus
Gaussian Correlation Structure
update.nlme
Update an nlme Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corSymm
General Correlation Structure
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Coef
Assign Values to Coefficients
MEEM
EM iterations for mixed-effects
Dim
Extract Dimensions from an Object
Dim.pdMat
Dimensions of a pdMat Object
corFactor
Factor of a Correlation Matrix
Matrix
Assign Matrix Values
logLik.glsStruct
Log-Likelihood of a glsStruct Object
MEdims
Calculate dimensions in mixed-effects
Names.reStruct
Names of an reStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
update.gnls
Update a gnls Object
random.effects.lmList
Extract lmList Random Effects
coef.gls
Extract gls Coefficients
coef.varFunc
varFunc Object Coefficients
update.varFunc
Update varFunc Object
update.nlsList
Update an nlsList Object
varComb
Combination of Variance Functions
corARMA
ARMA(p,q) Correlation Structure
getCovariate.data.frame
Extract Data Frame Covariate
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
fitted.gls
Extract gls Fitted Values
simulate.lme
simulate lme models
coef.corStruct
Coefficients of a corStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
isInitialized
Check if Object is Initialized
update.groupedData
Update a groupedData Object
print.summary.lmList
Print a summary.lmList Object
as.matrix.reStruct
Matrices of an reStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
asOneFormula
Combine Formulas of a Set of Objects
varFixed
Fixed Variance Function
MEdecomp
Decompose a mixed-effects model
summary.modelStruct
Summarize a modelStruct Object
print.lme
Print an lme Object
Covariate.varFunc
Assign varFunc Covariate
plot.augPred
Plot an augPred Object
Variogram
Calculate Semi-variogram
update.gls
Update a gls Object
lme.groupedData
LME fit from groupedData Object
corFactor.corStruct
Factor of a corStruct Object Matrix
fdHess
Finite difference Hessian
ACF.lme
Autocorrelation Function for lme Residuals
compareFits
Compare Fitted Objects
varExp
Exponential Variance Function
plot.compareFits
Plot a compareFits Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Dim.corSpatial
Dimensions of a corSpatial Object
Names.formula
Extract Names from a formula
Matrix.pdMat
Assign Matrix to a pdMat Object
AIC.logLik
AIC of a logLik Object
summary.corStruct
Summarize a corStruct Object
corLin
Linear Correlation Structure
predict.nlme
Predictions from an nlme Object
Names.pdBlocked
Names of a pdBlocked Object
BIC.logLik
BIC of a logLik Object
ACF
Autocorrelation Function
Variogram.corExp
Calculate Semi-variogram for a corExp Object
residuals.lme
Extract lme Residuals
coef.lmList
Extract lmList Coefficients
pdMat
Positive-Definite Matrix
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Matrix.reStruct
Assign reStruct Matrices
lme.lmList
LME fit from lmList Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
AIC
Akaike Information Criterion
getGroups.corStruct
Extract corStruct Groups
summary.lme
Summarize an lme Object
residuals.gls
Extract gls Residuals
recalc.corStruct
Recalculate for corStruct Object
print.summary.modelStruct
Print a summary.modelStruct Object
ACF.gls
Autocorrelation Function for gls Residuals
[.pdMat
Subscript a pdMat Object
augPred
Augmented Predictions
varPower
Power Variance Function
random.effects
Extract Random Effects
formula.varFunc
Extract varFunc Formula
plot.ranef.lme
Plot a ranef.lme Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
fitted.glsStruct
Calculate glsStruct Fitted Values
print.summary.gls
Print a summary.gls Object
anova.gls
Compare Likelihoods of Fitted Objects
formula.nlme
Extract nlme Object Formula
MEestimate
Estimate mixed-effects parameters
fitted.lmList
Extract lmList Fitted Values
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
summary.pdMat
Summarize a pdMat Object
varConstPower
Constant Plus Power Variance Function
update.modelStruct
Update a modelStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
corNatural
General correlation in natural parameterization
predict.lme
Predictions from an lme Object
corRatio
Rational Quadratic Correlation Structure
qqnorm.gls
Normal Plot of Residuals from a gls Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
print.reStruct
Print an reStruct Object
predict.gnls
Predictions from a gnls Object
plot.ranef.lmList
Plot a ranef.lmList Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
initialize.reStruct
Initialize reStruct Object
print.summary.varFunc
Print a summary.varFunc Object
getGroups.lmList
Extract lmList Object Groups
logDet.reStruct
Extract reStruct Log-Determinants
Dim.corStruct
Dimensions of a corStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
coef.pdIdent
pdIdent Object Coefficients
glsObject
Fitted gls Object
print.corStruct
Print a corStruct Object
logLik.lme
Log-Likelihood of an lme Object
getCovariate.varFunc
Extract varFunc Covariate
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
fitted.gnls
Extract gnls Fitted Values
print.pdMat
Print a pdMat Object
corMatrix.corStruct
Matrix of a corStruct Object
glsStruct
Generalized Least Squares Structure
print.modelStruct
Print a modelStruct Object
collapse.groupedData
Collapse a groupedData Object
formula.lmList
Extract lmList Object Formula
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
print.groupedData
Print a groupedData Object
print.lmList
Print an lmList Object
varWeights.glsStruct
Variance Weights for glsStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
pooledSD
Extract Pooled Standard Deviation
reStruct
Random Effects Structure
residuals.lmeStruct
Calculate lmeStruct Residuals
coef.reStruct
reStruct Object Coefficients
initialize.varFunc
Initialize varFunc Object
balancedGrouped
Create a groupedData object from a matrix
summary.varFunc
Summarize varFunc Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
varClasses
Variance Function Classes
corAR1
AR(1) Correlation Structure
splitFormula
Split a Formula
summary.gls
Summarize a gls Object
recalc.modelStruct
Recalculate for a modelStruct Object
as.matrix.pdMat
Matrix of a pdMat Object
coef.gnls
Extract gnls Coefficients
getGroups.gls
Extract gls Object Groups
corExp
Exponential Correlation Structure
residuals.nlmeStruct
Calculate nlmeStruct Residuals
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
initialize
Initialize Object
plot.ACF
Plot an ACF Object
print.summary.lme
Print a summary.lme Object
random.effects.lme
Extract lme Random Effects
getData
Extract Data from an Object
Variogram.default
Calculate Semi-variogram
fixed.effects.lme
Extract lme Fixed Effects
pdConstruct
Construct pdMat Objects
predict.lmList
Predictions from an lmList Object
intervals.lme
Confidence Intervals on lme Parameters
formula.pdBlocked
Extract pdBlocked Formula
formula.pdMat
Extract pdMat Formula
pdSymm
General Positive-Definite Matrix
print.summary.pdMat
Print a summary.pdMat Object
fixed.effects
Extract Fixed Effects
getCovariate
Extract Covariate from an Object
nlsList.selfStart
nlsList Fit from a selfStart Function
plot.nffGroupedData
Plot an nffGroupedData Object
formula.nlsList
Extract nlsList Object Formula
plot.nmGroupedData
Plot an nmGroupedData Object
varFunc
Variance Function Structure
collapse
Collapse According to Groups
summary.lmList
Summarize an lmList Object
intervals
Confidence Intervals on Coefficients
recalc.reStruct
Recalculate for an reStruct Object
coef.pdDiag
pdDiag Object Coefficients
nlmeObject
Fitted nlme Object
update.lmList
Update an lmList Object
nlmeControl
Control Values for nlme Fit
varIdent
Constant Variance Function
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
recalc
Recalculate Condensed Linear Model Object
pairs.compareFits
Pairs Plot of compareFits Object
nlme.nlsList
NLME fit from nlsList Object
residuals.gnls
Extract gnls Residuals
pdDiag
Diagonal Positive-Definite Matrix
summary.nlsList
Summarize an nlsList Object
corSpatial
Spatial Correlation Structure
varWeights
Extract Variance Function Weights
logDet.pdMat
Extract Log-Determinant from a pdMat Object
coef.lme
Extract lme Coefficients
logLik.varFunc
Extract varFunc logLik
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
fixed.effects.lmList
Extract lmList Fixed Effects
needUpdate
Check if Update is Needed
formula.modelStruct
Extract modelStruct Object Formula
logLik.reStruct
Calculate reStruct Log-Likelihood
getCovariate.corStruct
Extract corStruct Object Covariate
model.matrix.reStruct
reStruct Model Matrix
formula.corStruct
Extract corStruct Object Formula
pairs.lme
Pairs Plot of an lme Object
print.summary.corStruct
Print a summary.corStruct Object
formula.groupedData
Extract groupedData Formula
pdClasses
Positive-Definite Matrix Classes
initialize.lmeStruct
Initialize an lmeStruct Object
nlsList
List of nls Objects with a Common Model
formula.gnls
Extract gnls Object Formula
formula.nls
Extract Model Formula from nls Object
logLik.gnls
Log-Likelihood of a gnls Object
lmeScale
Scale for lme Optimization
print.varFunc
Print a varFunc Object
getResponse.lmList
Extract lmList Object Response
plot.lmList
Plot an lmList Object
gapply
Apply a Function by Groups
predict.gls
Predictions from a gls Object
initialize.glsStruct
Initialize a glsStruct Object
plot.Variogram
Plot a Variogram Object
update.lme
Update an lme Object
recalc.varFunc
Recalculate for varFunc Object
gsummary
Summarize by Groups
getResponse.data.frame
Extract Response from a Data Frame
print.gls
Print a gls Object
fitted.lme
Extract lme Fitted Values
lmeStruct
Linear Mixed-Effects Structure
getResponse.gls
Extract gls Object Response
getResponseFormula
Extract Formula Specifying Response Variable
logLik.gls
Log-Likelihood of a gls Object
logDet.corStruct
Extract corStruct Log-Determinant
getData.gls
Extract gls Object Data
print.anova.lme
Print an anova.lme Object
initialize.corStruct
Initialize corStruct Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
logDet
Extract the Logarithm of the Determinant
getData.lmList
Extract lmList Object Data
gnlsControl
Control Values for gnls Fit
formula.gls
Extract gls Object Formula
intervals.lmList
Confidence Intervals on lmList Coefficients
pdBlocked
Positive-Definite Block Diagonal Matrix
groupedData
Construct a groupedData Object
logLik.lm
Extract Log-Likelihood from an lm Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
intervals.gls
Confidence Intervals on gls Parameters
plot.intervals.lmList
Plot lmList Confidence Intervals
getGroups.lme
Extract lme Object Groups
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pdIdent
Multiple of the Identity Positive-Definite Matrix
nlme
Nonlinear Mixed-Effects Models
gnls
Fit Nonlinear Model Using Generalized Least Squares
logLik.corStruct
Extract corStruct Log-Likelihood
lmeControl
Control Values for lme Fit
isInitialized.reStruct
Check if an reStruct Object is Initialized
lmeObject
Fitted lme Object
getResponse
Extract Response Variable from an Object
pruneLevels
Prune Factor Levels
varWeights.lmeStruct
Variance Weights for lmeStruct Object
pdLogChol
General Positive-Definite Matrix
isBalanced
Check a Design for Balance
getGroupsFormula
Extract Grouping Formula
glsControl
Control Values for gls Fit
getGroups.varFunc
Extract varFunc Groups
lmList
List of lm Objects with a Common Model
lmList.groupedData
lmList Fit from a groupedData Object
getCovariateFormula
Extract Covariates Formula
getGroups
Extract Grouping Factors from an Object
getResponse.lme
Extract lme Object Response
gls
Fit Linear Model Using Generalized Least Squares
gnlsObject
Fitted gnls Object
lme
Linear Mixed-Effects Models
getGroups.data.frame
Extract Groups from a Data Frame
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
formula.reStruct
Extract reStruct Object Formula
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pairs.lmList
Pairs Plot of an lmList Object
formula.lme
Extract lme Object Formula
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
nlmeStruct
Nonlinear Mixed-Effects Structure
plot.lme
Plot an lme Object
plot.gls
Plot a gls Object
Assay
Bioassay on Cell Culture Plate
Soybean
Growth of soybean plants
Oats
Split-plot Experiment on Varieties of Oats
Machines
Productivity Scores for Machines and Workers
Tetracycline2
Pharmacokinetics of tetracycline
Quinidine
Quinidine Kinetics
IGF
Radioimmunoassay of IGF-I Protein
Nitrendipene
Assay of nitrendipene
Oxide
Variability in Semiconductor Manufacturing
Wafer
Modeling of Analog MOS Circuits
Milk
Protein content of cows' milk
Pixel
X-ray pixel intensities over time
Phenobarb
Phenobarbitol Kinetics
Meat
Tenderness of meat
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Tetracycline1
Pharmacokinetics of tetracycline
Spruce
Growth of Spruce Trees
Glucose2
Glucose Levels Following Alcohol Ingestion
PBG
Effect of Phenylbiguanide on Blood Pressure
Rail
Evaluation of Stress in Railway Rails
Oxboys
Heights of Boys in Oxford
Gun
Methods for firing naval guns
RatPupWeight
The weight of rat pups
Glucose
Glucose levels over time
Earthquake
Earthquake Intensity
Remifentanil
Pharmacokinetics of remifentanil
Muscle
Contraction of heart muscle sections
Wheat
Yields by growing conditions
Gasoline
Refinery yield of gasoline
Dialyzer
High-Flux Hemodialyzer
MathAchSchool
School demographic data for MathAchieve
MathAchieve
Mathematics achievement scores
Ovary
Counts of Ovarian Follicles
Cefamandole
Pharmacokinetics of Cefamandole
BodyWeight
Rat weight over time for different diets
Fatigue
Cracks caused by metal fatigue
Relaxin
Assay for Relaxin
Wheat2
Wheat Yield Trials
Orthodont
Growth curve data on an orthdontic measurement
ergoStool
Ergometrics experiment with stool types