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nlme (version 3.1-27)
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
100,391
Version
3.1-27
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-27)
Search all functions
coef.pdIdent
pdIdent Object Coefficients
random.effects
Extract Random Effects
ACF.lme
Autocorrelation Function for lme Residuals
Dim.corSpatial
Dimensions of a corSpatial Object
MEEM
EM iterations for mixed-effects
corMatrix
Extract Correlation Matrix
formula.modelStruct
Extract modelStruct Object Formula
[.pdMat
Subscript a pdMat Object
ACF
Autocorrelation Function
Dim.pdMat
Dimensions of a pdMat Object
MEestimate
Estimate mixed-effects parameters
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Dim.corStruct
Dimensions of a corStruct Object
Covariate.varFunc
Assign varFunc Covariate
BIC.logLik
BIC of a logLik Object
BIC
Bayesian Information Criterion
Dim
Extract Dimensions from an Object
allCoef
Extract Coefficients from a Set of Objects
asOneFormula
Combine Formulas of a Set of Objects
Variogram
Calculate Semi-variogram
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
formula.gls
Extract gls Object Formula
formula.gnls
Extract gnls Object Formula
VarCorr
Extract variance and correlation components
corFactor
Factor of a Correlation Matrix
AIC.lme
Akaike Information Criterion
summary.corStruct
Summarize a corStruct Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
fdHess
Finite difference Hessian
varFunc
Variance Function Structure
update.varFunc
Update varFunc Object
corExp
Exponential Correlation Structure
pdClasses
Positive-Definite Matrix Classes
residuals.nlmeStruct
Calculate nlmeStruct Residuals
collapse.groupedData
Collapse a groupedData Object
coef.pdMat
pdMat Object Coefficients
formula.lme
Extract lme Object Formula
varClasses
Variance Function Classes
print.summary.varFunc
Print a summary.varFunc Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
formula.lmList
Extract lmList Object Formula
coef.lme
Extract lme Coefficients
coef.gls
Extract gls Coefficients
Covariate
Assign Covariate Values
corARMA
ARMA(p,q) Correlation Structure
as.matrix.corStruct
Matrix of a corStruct Object
augPred
Augmented Predictions
as.matrix.pdMat
Matrix of a pdMat Object
fixef.lmList
Extract lmList Fixed Effects
collapse
Collapse According to Groups
coef.lmList
Extract lmList Coefficients
as.matrix.reStruct
Matrices of an reStruct Object
AIC
Akaike Information Criterion
ACF.gls
Autocorrelation Function for gls Residuals
coef.pdCompSymm
pdCompSymm Object Coefficients
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
pruneLevels
Prune Factor Levels
balancedGrouped
Create a groupedData object from a matrix
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
coef.modelStruct
Extract modelStruct Object Coefficients
summary.lmList
Summarize an lmList Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
corClasses
Correlation Structure Classes
varIdent
Constant Variance Function
Variogram.corExp
Calculate Semi-variogram for a corExp Object
varFixed
Fixed Variance Function
corRatio
Rational Quadratic Correlation Structure
varWeights.glsStruct
Variance Weights for glsStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
MEdims
Calculate dimensions in mixed-effects
contr.SAS
Contrast Matrices
formula.reStruct
Extract reStruct Object Formula
pdConstruct.pdBlocked
Construct pdBlocked Objects
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.glsStruct
Calculate glsStruct Fitted Values
print.summary.corStruct
Print a summary.corStruct Object
coef.reStruct
reStruct Object Coefficients
formula.groupedData
Extract groupedData Formula
phenoModel
Model function for the Phenobarb data
summary.gls
Summarize a gls Object
print.varFunc
Print a varFunc Object
varWeights
Extract Variance Function Weights
fitted.lmList
Extract lmList Fitted Values
formula.pdMat
Extract pdMat Formula
plot.Variogram
Plot a Variogram Object
fitted.gnls
Extract gnls Fitted Values
asTable
Convert groupedData to a matrix
simulate.lme
simulate lme models
getData
Extract Data from an Object
corCAR1
Continuous AR(1) Correlation Structure
varPower
Power Variance Function
pooledSD
Extract Pooled Standard Deviation
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
Coef
Assign Values to Coefficients
summary.lme
Summarize an lme Object
coef.varFunc
varFunc Object Coefficients
lmeControl
Control Values for lme Fit
varConstPower
Constant Plus Power Variance Function
print.pdMat
Print a pdMat Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
compareFits
Compare Fitted Objects
coef.pdDiag
pdDiag Object Coefficients
plot.lme
Plot an lme or nls object
summary.pdMat
Summarize a pdMat Object
quinModel
Model function for the Quinidine data
plot.ranef.lme
Plot a ranef.lme Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
recalc
Recalculate Condensed Linear Model Object
print.summary.lmList
Print a summary.lmList Object
varExp
Exponential Variance Function
anova.gls
Compare Likelihoods of Fitted Objects
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
print.reStruct
Print an reStruct Object
print.summary.pdMat
Print a summary.pdMat Object
residuals.lmList
Extract lmList Residuals
glsObject
Fitted gls Object
residuals.lme
Extract lme Residuals
Variogram.default
Calculate Semi-variogram
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
fitted.lme
Extract lme Fitted Values
corLin
Linear Correlation Structure
formula.nlsList
Extract nlsList Object Formula
corAR1
AR(1) Correlation Structure
update.modelStruct
Update a modelStruct Object
lmeStruct
Linear Mixed-Effects Structure
plot.ACF
Plot an ACF Object
getGroups.data.frame
Extract Groups from a Data Frame
varWeights.lmeStruct
Variance Weights for lmeStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
getGroupsFormula
Extract Grouping Formula
print.summary.gls
Print a summary.gls Object
residuals.lmeStruct
Calculate lmeStruct Residuals
getGroups.varFunc
Extract varFunc Groups
getGroups.gls
Extract gls Object Groups
getCovariateFormula
Extract Covariates Formula
getResponse.gls
Extract gls Object Response
getGroups.lme
Extract lme Object Groups
formula.nlme
Extract nlme Object Formula
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
getResponse.data.frame
Extract Response from a Data Frame
pdConstruct
Construct pdMat Objects
glsControl
Control Values for gls Fit
comparePred
Compare Predictions
getResponse.lme
Extract lme Object Response
summary.nlsList
Summarize an nlsList Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
initialize.reStruct
Initialize reStruct Object
recalc.varFunc
Recalculate for varFunc Object
predict.nlme
Predictions from an nlme Object
corSymm
General Correlation Structure
pdLogChol
General Positive-Definite Matrix
predict.lmList
Predictions from an lmList Object
Names.reStruct
Names of an reStruct Object
residuals.gls
Extract gls Residuals
getResponseFormula
Extract Formula Specifying Response Variable
ranef.lmList
Extract lmList Random Effects
lmList
List of lm Objects with a Common Model
corMatrix.corStruct
Matrix of a corStruct Object
predict.gnls
Predictions from a gnls Object
coef.corStruct
Coefficients of a corStruct Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
corGaus
Gaussian Correlation Structure
fitted.gls
Extract gls Fitted Values
logDet
Extract the Logarithm of the Determinant
ranef.lme
Extract lme Random Effects
coef.gnls
Extract gnls Coefficients
varComb
Combination of Variance Functions
Matrix
Assign Matrix Values
nlme
Nonlinear Mixed-Effects Models
corNatural
General correlation in natural parameterization
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
anova.lme
Compare Likelihoods of Fitted Objects
Matrix.pdMat
Assign Matrix to a pdMat Object
MEdecomp
Decompose a mixed-effects model
corSpher
Spherical Correlation Structure
Names.pdBlocked
Names of a pdBlocked Object
print.summary.lme
Print a summary.lme Object
lmeScale
Scale for lme Optimization
plot.intervals.lmList
Plot lmList Confidence Intervals
getVarCov
Extract variance-covariance matrix
splitFormula
Split a Formula
plot.nfnGroupedData
Plot an nfnGroupedData Object
getResponse
Extract Response Variable from an Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
initialize.varFunc
Initialize varFunc Object
LDEsysMat
Generate system matrix for LDEs
fitted.lmeStruct
Calculate lmeStruct Fitted Values
summary.modelStruct
Summarize a modelStruct Object
plot.compareFits
Plot a compareFits Object
initialize.corStruct
Initialize corStruct Object
pdSymm
General Positive-Definite Matrix
predict.gls
Predictions from a gls Object
print.groupedData
Print a groupedData Object
print.summary.modelStruct
Print a summary.modelStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
intervals
Confidence Intervals on Coefficients
Matrix.reStruct
Assign reStruct Matrices
plot.nmGroupedData
Plot an nmGroupedData Object
summary.varFunc
Summarize varFunc Object
solve.reStruct
Apply Solve to an reStruct Object
pdDiag
Diagonal Positive-Definite Matrix
needUpdate
Check if Update is Needed
intervals.lmList
Confidence Intervals on lmList Coefficients
formula.corStruct
Extract corStruct Object Formula
lme.groupedData
LME fit from groupedData Object
gls
Fit Linear Model Using Generalized Least Squares
reStruct
Random Effects Structure
lme
Linear Mixed-Effects Models
Names.formula
Extract Names from a formula
nlme.nlsList
NLME fit from nlsList Object
recalc.corStruct
Recalculate for corStruct Object
print.modelStruct
Print a modelStruct Object
pdMat
Positive-Definite Matrix
recalc.reStruct
Recalculate for an reStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
isBalanced
Check a Design for Balance
pairs.compareFits
Pairs Plot of compareFits Object
Names.pdMat
Names of a pdMat Object
getGroups.lmList
Extract lmList Object Groups
nlmeControl
Control Values for nlme Fit
nlmeObject
Fitted nlme Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logDet.corStruct
Extract corStruct Log-Determinant
gsummary
Summarize by Groups
corFactor.corStruct
Factor of a corStruct Object Matrix
nlme-internal
Internal nlme functions
isInitialized.reStruct
Check if an reStruct Object is Initialized
print.lmList
Print an lmList Object
lme.lmList
LME fit from lmList Object
plot.ranef.lmList
Plot a ranef.lmList Object
print.corStruct
Print a corStruct Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
print.anova.lme
Print an anova.lme Object
Names
Names Associated with an Object
nlsList.selfStart
nlsList Fit from a selfStart Function
pairs.lme
Pairs Plot of an lme Object
print.gls
Print a gls Object
getCovariate.varFunc
Extract varFunc Covariate
getData.gls
Extract gls Object Data
intervals.lme
Confidence Intervals on lme Parameters
plot.gls
Plot a gls Object
getGroups
Extract Grouping Factors from an Object
formula.pdBlocked
Extract pdBlocked Formula
gapply
Apply a Function by Groups
predict.lme
Predictions from an lme Object
pdBlocked
Positive-Definite Block Diagonal Matrix
getData.lme
Extract lme Object Data
lmList.groupedData
lmList Fit from a groupedData Object
fixed.effects
Extract Fixed Effects
formula.varFunc
Extract varFunc Formula
pdNatural
General Positive-Definite Matrix in Natural Parametrization
isInitialized
Check if Object is Initialized
plot.augPred
Plot an augPred Object
initialize
Initialize Object
getResponse.lmList
Extract lmList Object Response
getData.lmList
Extract lmList Object Data
getCovariate.corStruct
Extract corStruct Object Covariate
intervals.gls
Confidence Intervals on gls Parameters
getGroups.corStruct
Extract corStruct Groups
getCovariate.data.frame
Extract Data Frame Covariate
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
getCovariate
Extract Covariate from an Object
initialize.lmeStruct
Initialize an lmeStruct Object
plot.lmList
Plot an lmList Object
nlmeStruct
Nonlinear Mixed-Effects Structure
groupedData
Construct a groupedData Object
initialize.glsStruct
Initialize a glsStruct Object
print.lme
Print an lme Object
corSpatial
Spatial Correlation Structure
glsStruct
Generalized Least Squares Structure
corCompSymm
Compound Symmetry Correlation Structure
gnlsObject
Fitted gnls Object
gnlsControl
Control Values for gnls Fit
gnlsStruct
Generalized Nonlinear Least Squares Structure
logLik.gls
Log-Likelihood of a gls Object
logLik.reStruct
Calculate reStruct Log-Likelihood
logLik.gnls
Log-Likelihood of a gnls Object
logLik.corStruct
Extract corStruct Log-Likelihood
logLik.lmList
Log-Likelihood of an lmList Object
logLik.varFunc
Extract varFunc logLik
nlsList
List of nls Objects with a Common Model
pairs.lmList
Pairs Plot of an lmList Object
logLik.lme
Log-Likelihood of an lme Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
fixef.lme
Extract lme Fixed Effects
logDet.pdMat
Extract Log-Determinant from a pdMat Object
lmeObject
Fitted lme Object
model.matrix.reStruct
reStruct Model Matrix
logDet.reStruct
Extract reStruct Log-Determinants
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Phenobarb
Phenobarbitol Kinetics
Ovary
Counts of Ovarian Follicles
Tetracycline1
Pharmacokinetics of tetracycline
bdf
Language scores
Gasoline
Refinery yield of gasoline
Meat
Tenderness of meat
Machines
Productivity Scores for Machines and Workers
Oats
Split-plot Experiment on Varieties of Oats
Spruce
Growth of Spruce Trees
Remifentanil
Pharmacokinetics of remifentanil
IGF
Radioimmunoassay of IGF-I Protein
Muscle
Contraction of heart muscle sections
ergoStool
Ergometrics experiment with stool types
Nitrendipene
Assay of nitrendipene
Wheat2
Wheat Yield Trials
Quinidine
Quinidine Kinetics
Relaxin
Assay for Relaxin
Earthquake
Earthquake Intensity
Gun
Methods for firing naval guns
Wafer
Modeling of Analog MOS Circuits
Assay
Bioassay on Cell Culture Plate
BodyWeight
Rat weight over time for different diets
Oxboys
Heights of Boys in Oxford
Soybean
Growth of soybean plants
Dialyzer
High-Flux Hemodialyzer
Fatigue
Cracks caused by metal fatigue
MathAchSchool
School demographic data for MathAchieve
RatPupWeight
The weight of rat pups
Rail
Evaluation of Stress in Railway Rails
MathAchieve
Mathematics achievement scores
Milk
Protein content of cows' milk
Pixel
X-ray pixel intensities over time
Wheat
Yields by growing conditions
Tetracycline2
Pharmacokinetics of tetracycline
Glucose
Glucose levels over time
Cefamandole
Pharmacokinetics of Cefamandole
Oxide
Variability in Semiconductor Manufacturing
Glucose2
Glucose Levels Following Alcohol Ingestion
PBG
Effect of Phenylbiguanide on Blood Pressure
Orthodont
Growth curve data on an orthdontic measurement