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nlme (version 3.1-29)
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
100,391
Version
3.1-29
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-29)
Search all functions
AIC
Akaike Information Criterion
ACF.lme
Autocorrelation Function for lme Residuals
Initialize.glsStruct
Initialize a glsStruct Object
Initialize
Initialize Object
Covariate
Assign Covariate Values
Initialize.reStruct
Initialize reStruct Object
BIC
Bayesian Information Criterion
Initialize.varFunc
Initialize varFunc Object
Coef
Assign Values to Coefficients
Dim.corStruct
Dimensions of a corStruct Object
Matrix.reStruct
Assign reStruct Matrices
MEEM
EM iterations for mixed-effects
BIC.logLik
BIC of a logLik Object
Matrix
Assign Matrix Values
Names.reStruct
Names of an reStruct Object
Matrix.pdMat
Assign Matrix to a pdMat Object
MEdims
Calculate dimensions in mixed-effects
Dim.corSpatial
Dimensions of a corSpatial Object
ACF.gls
Autocorrelation Function for gls Residuals
corMatrix
Extract Correlation Matrix
asTable
Convert groupedData to a matrix
recalc.reStruct
Recalculate for an reStruct Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Dim
Extract Dimensions from an Object
Dim.pdMat
Dimensions of a pdMat Object
Variogram.default
Calculate Semi-variogram
fitted.lme
Extract lme Fitted Values
print.summary.gls
Print a summary.gls Object
LDEsysMat
Generate system matrix for LDEs
residuals.lmeStruct
Calculate lmeStruct Residuals
corNatural
General correlation in natural parameterization
Names
Names Associated with an Object
print.summary.modelStruct
Print a summary.modelStruct Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
VarCorr
Extract variance and correlation components
as.matrix.reStruct
Matrices of an reStruct Object
MEdecomp
Decompose a mixed-effects model
ranef.lmList
Extract lmList Random Effects
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
splitFormula
Split a Formula
Names.formula
Extract Names from a formula
MEestimate
Estimate mixed-effects parameters
Names.pdBlocked
Names of a pdBlocked Object
summary.gls
Summarize a gls Object
print.gls
Print a gls Object
ACF
Autocorrelation Function
Initialize.lmeStruct
Initialize an lmeStruct Object
summary.varFunc
Summarize varFunc Object
anova.lme
Compare Likelihoods of Fitted Objects
residuals.lmList
Extract lmList Residuals
lme.groupedData
LME fit from groupedData Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
recalc.modelStruct
Recalculate for a modelStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
varIdent
Constant Variance Function
getData.lme
Extract lme Object Data
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
model.matrix.reStruct
reStruct Model Matrix
print.summary.lme
Print a summary.lme Object
print.modelStruct
Print a modelStruct Object
print.summary.pdMat
Print a summary.pdMat Object
reStruct
Random Effects Structure
print.lmList
Print an lmList Object
isInitialized
Check if Object is Initialized
logLik.lme
Log-Likelihood of an lme Object
fixef.lmList
Extract lmList Fixed Effects
random.effects
Extract Random Effects
logDet
Extract the Logarithm of the Determinant
logLik.gnls
Log-Likelihood of a gnls Object
coef.pdMat
pdMat Object Coefficients
corSpatial
Spatial Correlation Structure
coef.modelStruct
Extract modelStruct Object Coefficients
recalc.varFunc
Recalculate for varFunc Object
simulate.lme
simulate lme models
residuals.gnlsStruct
Calculate gnlsStruct Residuals
quinModel
Model function for the Quinidine data
corRatio
Rational Quadratic Correlation Structure
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.gnls
Extract gnls Fitted Values
isInitialized.reStruct
Check if an reStruct Object is Initialized
compareFits
Compare Fitted Objects
recalc.corStruct
Recalculate for corStruct Object
corCAR1
Continuous AR(1) Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
varComb
Combination of Variance Functions
logLik.lmList
Log-Likelihood of an lmList Object
glsStruct
Generalized Least Squares Structure
getCovariate.corStruct
Extract corStruct Object Covariate
getGroups.gls
Extract gls Object Groups
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
varFixed
Fixed Variance Function
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
glsObject
Fitted gls Object
getResponse.gls
Extract gls Object Response
getGroups
Extract Grouping Factors from an Object
getResponseFormula
Extract Formula Specifying Response Variable
intervals.gls
Confidence Intervals on gls Parameters
pairs.compareFits
Pairs Plot of compareFits Object
getGroups.varFunc
Extract varFunc Groups
corSymm
General Correlation Structure
Initialize.corStruct
Initialize corStruct Object
corMatrix.corStruct
Matrix of a corStruct Object
print.lme
Print an lme Object
pairs.lme
Pairs Plot of an lme Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Covariate.varFunc
Assign varFunc Covariate
corCompSymm
Compound Symmetry Correlation Structure
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
print.anova.lme
Print an anova.lme Object
recalc
Recalculate Condensed Linear Model Object
as.matrix.pdMat
Matrix of a pdMat Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
nlsList
List of nls Objects with a Common Model
pairs.lmList
Pairs Plot of an lmList Object
gls
Fit Linear Model Using Generalized Least Squares
varConstPower
Constant Plus Power Variance Function
varExp
Exponential Variance Function
getResponse
Extract Response Variable from an Object
plot.lmList
Plot an lmList Object
residuals.gls
Extract gls Residuals
predict.gls
Predictions from a gls Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
pruneLevels
Prune Factor Levels
residuals.glsStruct
Calculate glsStruct Residuals
nlme-internal
Internal nlme functions
phenoModel
Model function for the Phenobarb data
varWeights.lmeStruct
Variance Weights for lmeStruct Object
print.summary.lmList
Print a summary.lmList Object
update.varFunc
Update varFunc Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pdClasses
Positive-Definite Matrix Classes
varClasses
Variance Function Classes
pdFactor
Square-Root Factor of a Positive-Definite Matrix
coef.pdDiag
pdDiag Object Coefficients
varPower
Power Variance Function
getGroups.lmList
Extract lmList Object Groups
predict.gnls
Predictions from a gnls Object
glsControl
Control Values for gls Fit
summary.corStruct
Summarize a corStruct Object
solve.reStruct
Apply Solve to an reStruct Object
getGroups.corStruct
Extract corStruct Groups
nlmeStruct
Nonlinear Mixed-Effects Structure
print.corStruct
Print a corStruct Object
allCoef
Extract Coefficients from a Set of Objects
coef.varFunc
varFunc Object Coefficients
print.summary.corStruct
Print a summary.corStruct Object
coef.reStruct
reStruct Object Coefficients
predict.lmList
Predictions from an lmList Object
[.pdMat
Subscript a pdMat Object
print.pdMat
Print a pdMat Object
formula.modelStruct
Extract modelStruct Object Formula
qqnorm.gls
Normal Plot of Residuals from a gls Object
pdLogChol
General Positive-Definite Matrix
getResponse.lme
Extract lme Object Response
pdConstruct
Construct pdMat Objects
residuals.lme
Extract lme Residuals
fdHess
Finite difference Hessian
Names.pdMat
Names of a pdMat Object
getGroupsFormula
Extract Grouping Formula
groupedData
Construct a groupedData Object
plot.augPred
Plot an augPred Object
gapply
Apply a Function by Groups
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
fitted.gls
Extract gls Fitted Values
lme.lmList
LME fit from lmList Object
print.groupedData
Print a groupedData Object
getCovariate
Extract Covariate from an Object
nlme
Nonlinear Mixed-Effects Models
getResponse.data.frame
Extract Response from a Data Frame
pdSymm
General Positive-Definite Matrix
lme
Linear Mixed-Effects Models
plot.ranef.lme
Plot a ranef.lme Object
print.reStruct
Print an reStruct Object
nlmeControl
Control Values for nlme Fit
nlsList.selfStart
nlsList Fit from a selfStart Function
corARMA
ARMA(p,q) Correlation Structure
plot.gls
Plot a gls Object
nlme.nlsList
NLME fit from nlsList Object
varWeights.glsStruct
Variance Weights for glsStruct Object
balancedGrouped
Create a groupedData object from a matrix
logLik.varFunc
Extract varFunc logLik
lmeStruct
Linear Mixed-Effects Structure
plot.Variogram
Plot a Variogram Object
plot.nmGroupedData
Plot an nmGroupedData Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdDiag
Diagonal Positive-Definite Matrix
getGroups.data.frame
Extract Groups from a Data Frame
formula.nlme
Extract nlme Object Formula
coef.gls
Extract gls Coefficients
getResponse.lmList
Extract lmList Object Response
AIC.lme
Akaike Information Criterion
getVarCov
Extract variance-covariance matrix
corExp
Exponential Correlation Structure
pdBlocked
Positive-Definite Block Diagonal Matrix
nlmeObject
Fitted nlme Object
needUpdate
Check if Update is Needed
plot.ranef.lmList
Plot a ranef.lmList Object
corFactor
Factor of a Correlation Matrix
augPred
Augmented Predictions
summary.lme
Summarize an lme Object
summary.modelStruct
Summarize a modelStruct Object
varFunc
Variance Function Structure
gnlsControl
Control Values for gnls Fit
logLik.gls
Log-Likelihood of a gls Object
corGaus
Gaussian Correlation Structure
predict.lme
Predictions from an lme Object
gsummary
Summarize by Groups
gnls
Fit Nonlinear Model Using Generalized Least Squares
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.nffGroupedData
Plot an nffGroupedData Object
update.modelStruct
Update a modelStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
coef.lme
Extract lme Coefficients
plot.ACF
Plot an ACF Object
comparePred
Compare Predictions
gnlsObject
Fitted gnls Object
predict.nlme
Predictions from an nlme Object
corLin
Linear Correlation Structure
print.varFunc
Print a varFunc Object
collapse
Collapse According to Groups
varWeights
Extract Variance Function Weights
contr.SAS
Contrast Matrices
logLik.reStruct
Calculate reStruct Log-Likelihood
formula.gnls
Extract gnls Object Formula
logLik.glsStruct
Log-Likelihood of a glsStruct Object
summary.pdMat
Summarize a pdMat Object
getGroups.lme
Extract lme Object Groups
formula.lme
Extract lme Object Formula
formula.varFunc
Extract varFunc Formula
pdMat
Positive-Definite Matrix
fitted.lmList
Extract lmList Fitted Values
collapse.groupedData
Collapse a groupedData Object
ranef.lme
Extract lme Random Effects
corSpher
Spherical Correlation Structure
logDet.reStruct
Extract reStruct Log-Determinants
intervals
Confidence Intervals on Coefficients
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
coef.lmList
Extract lmList Coefficients
logDet.pdMat
Extract Log-Determinant from a pdMat Object
anova.gls
Compare Likelihoods of Fitted Objects
corClasses
Correlation Structure Classes
getCovariate.varFunc
Extract varFunc Covariate
lmList
List of lm Objects with a Common Model
lmeControl
Control Values for lme Fit
getData
Extract Data from an Object
lmeScale
Scale for lme Optimization
formula.pdBlocked
Extract pdBlocked Formula
corAR1
AR(1) Correlation Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
getCovariate.data.frame
Extract Data Frame Covariate
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.corStruct
Extract corStruct Log-Likelihood
getData.gls
Extract gls Object Data
gnlsStruct
Generalized Nonlinear Least Squares Structure
formula.pdMat
Extract pdMat Formula
logDet.corStruct
Extract corStruct Log-Determinant
fixef.lme
Extract lme Fixed Effects
coef.gnls
Extract gnls Coefficients
fitted.lmeStruct
Calculate lmeStruct Fitted Values
formula.groupedData
Extract groupedData Formula
lmList.groupedData
lmList Fit from a groupedData Object
lmeObject
Fitted lme Object
formula.gls
Extract gls Object Formula
fixed.effects
Extract Fixed Effects
getCovariateFormula
Extract Covariates Formula
getData.lmList
Extract lmList Object Data
isBalanced
Check a Design for Balance
Variogram
Calculate Semi-variogram
coef.pdIdent
pdIdent Object Coefficients
formula.reStruct
Extract reStruct Object Formula
intervals.lmList
Confidence Intervals on lmList Coefficients
coef.corStruct
Coefficients of a corStruct Object
asOneFormula
Combine Formulas of a Set of Objects
formula.lmList
Extract lmList Object Formula
Variogram.corLin
Calculate Semi-variogram for a corLin Object
intervals.lme
Confidence Intervals on lme Parameters
summary.lmList
Summarize an lmList Object
coef.pdCompSymm
pdCompSymm Object Coefficients
formula.nlsList
Extract nlsList Object Formula
formula.corStruct
Extract corStruct Object Formula
pooledSD
Extract Pooled Standard Deviation
summary.nlsList
Summarize an nlsList Object
print.summary.varFunc
Print a summary.varFunc Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.compareFits
Plot a compareFits Object
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.lme
Plot an lme or nls object
Cefamandole
Pharmacokinetics of Cefamandole
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Milk
Protein content of cows' milk
Assay
Bioassay on Cell Culture Plate
IGF
Radioimmunoassay of IGF-I Protein
Oats
Split-plot Experiment on Varieties of Oats
Oxide
Variability in Semiconductor Manufacturing
Wafer
Modeling of Analog MOS Circuits
Wheat
Yields by growing conditions
Gasoline
Refinery yield of gasoline
Wheat2
Wheat Yield Trials
Nitrendipene
Assay of nitrendipene
Orthodont
Growth curve data on an orthdontic measurement
Meat
Tenderness of meat
Tetracycline1
Pharmacokinetics of tetracycline
Tetracycline2
Pharmacokinetics of tetracycline
Ovary
Counts of Ovarian Follicles
Machines
Productivity Scores for Machines and Workers
Soybean
Growth of soybean plants
Phenobarb
Phenobarbitol Kinetics
Earthquake
Earthquake Intensity
Muscle
Contraction of heart muscle sections
Fatigue
Cracks caused by metal fatigue
Pixel
X-ray pixel intensities over time
Gun
Methods for firing naval guns
Quinidine
Quinidine Kinetics
bdf
Language scores
Relaxin
Assay for Relaxin
ergoStool
Ergometrics experiment with stool types
MathAchieve
Mathematics achievement scores
Glucose2
Glucose Levels Following Alcohol Ingestion
Oxboys
Heights of Boys in Oxford
Glucose
Glucose levels over time
RatPupWeight
The weight of rat pups
Dialyzer
High-Flux Hemodialyzer
MathAchSchool
School demographic data for MathAchieve
BodyWeight
Rat weight over time for different diets
Rail
Evaluation of Stress in Railway Rails
PBG
Effect of Phenylbiguanide on Blood Pressure
Remifentanil
Pharmacokinetics of remifentanil
Spruce
Growth of Spruce Trees