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nlme (version 3.1-13)
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
90,510
Version
3.1-13
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-13)
Search all functions
ACF.gls
Autocorrelation Function for gls Residuals
ACF.lme
Autocorrelation Function for lme Residuals
Covariate
Assign Covariate Values
corRatio
Rational Quadratic Correlation Structure
Variogram.corExp
Calculate Semi-variogram for a corExp Object
formula.lmList
Extract lmList Object Formula
Names.reStruct
Names of an reStruct Object
intervals.lme
Confidence Intervals on lme Parameters
getResponse.lmList
Extract lmList Object Response
getGroupsFormula
Extract Grouping Formula
ACF
Autocorrelation Function
BIC.logLik
BIC of a logLik Object
formula.nls
Extract Model Formula from nls Object
Covariate.varFunc
Assign varFunc Covariate
as.matrix.reStruct
Matrices of an reStruct Object
coef.varFunc
varFunc Object Coefficients
fitted.lme
Extract lme Fitted Values
MEdecomp
Decompose a mixed-effects model
model.matrix.reStruct
reStruct Model Matrix
Dim.corSpatial
Dimensions of a corSpatial Object
VarCorr
Extract variance and correlation components
as.matrix.corStruct
Matrix of a corStruct Object
Dim.pdMat
Dimensions of a pdMat Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
AIC
Akaike Information Criterion
formula.nlsList
Extract nlsList Object Formula
pairs.lme
Pairs Plot of an lme Object
Dim
Extract Dimensions from an Object
lmeScale
Scale for lme Optimization
[.pdMat
Subscript a pdMat Object
corARMA
ARMA(p,q) Correlation Structure
AIC.logLik
AIC of a logLik Object
Matrix
Assign Matrix Values
anova.lme
Compare Likelihoods of Fitted Objects
plot.nffGroupedData
Plot an nffGroupedData Object
plot.compareFits
Plot a compareFits Object
Matrix.pdMat
Assign Matrix to a pdMat Object
contr.SAS
Contrast Matrices
corFactor
Factor of a Correlation Matrix
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Dim.corStruct
Dimensions of a corStruct Object
MEdims
Calculate dimensions in mixed-effects
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Matrix.reStruct
Assign reStruct Matrices
Names.pdBlocked
Names of a pdBlocked Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getGroups.corStruct
Extract corStruct Groups
predict.lme
Predictions from an lme Object
corCompSymm
Compound Symmetry Correlation Structure
coef.corStruct
Coefficients of a corStruct Object
corExp
Exponential Correlation Structure
Variogram.default
Calculate Semi-variogram
formula.reStruct
Extract reStruct Object Formula
anova.gls
Compare Likelihoods of Fitted Objects
getData.lmList
Extract lmList Object Data
fitted.lmList
Extract lmList Fitted Values
print.intervals.gls
Print an intervals.gls Object
MEEM
EM iterations for mixed-effects
augPred
Augmented Predictions
coef.lme
Extract lme Coefficients
getResponse.lme
Extract lme Object Response
corMatrix.corStruct
Matrix of a corStruct Object
fixed.effects
Extract Fixed Effects
Names.formula
Extract Names from a formula
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
formula.nlme
Extract nlme Object Formula
print.lme
Print an lme Object
Names
Names Associated with an Object
asOneFormula
Combine Formulas of a Set of Objects
formula.modelStruct
Extract modelStruct Object Formula
glsControl
Control Values for gls Fit
asTable
Convert groupedData to a matrix
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
isBalanced
Check a Design for Balance
balancedGrouped
Create a groupedData object from a matrix
allCoef
Extract Coefficients from a Set of Objects
plot.ACF
Plot an ACF Object
coef.pdIdent
pdIdent Object Coefficients
pruneLevels
Prune Factor Levels
corCAR1
Continuous AR(1) Correlation Structure
compareFits
Compare Fitted Objects
formula.lme
Extract lme Object Formula
getGroups.lmList
Extract lmList Object Groups
initialize.lmeStruct
Initialize an lmeStruct Object
coef.pdMat
pdMat Object Coefficients
coef.gls
Extract gls Coefficients
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
collapse.groupedData
Collapse a groupedData Object
collapse
Collapse According to Groups
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
varExp
Exponential Variance Function
getCovariate
Extract Covariate from an Object
getResponseFormula
Extract Formula Specifying Response Variable
fdHess
Finite difference Hessian
logLik.lmList
Log-Likelihood of an lmList Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
lmList
List of lm Objects with a Common Model
coef.pdDiag
pdDiag Object Coefficients
logLik.reStruct
Calculate reStruct Log-Likelihood
isInitialized.reStruct
Check if an reStruct Object is Initialized
corAR1
AR(1) Correlation Structure
logDet.corStruct
Extract corStruct Log-Determinant
formula.varFunc
Extract varFunc Formula
update.lmList
Update an lmList Object
coef.lmList
Extract lmList Coefficients
corFactor.corStruct
Factor of a corStruct Object Matrix
coef.gnls
Extract gnls Coefficients
getResponse
Extract Response Variable from an Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
nlme.nlsList
NLME fit from nlsList Object
fixed.effects.lmList
Extract lmList Fixed Effects
getGroupsFormula.lmList
Extract lmList Object Grouping Formula
gapply
Apply a Function by Groups
getGroups
Extract Grouping Factors from an Object
logLik.gnls
Log-Likelihood of a gnls Object
logDet
Extract the Logarithm of the Determinant
formula.corStruct
Extract corStruct Object Formula
logDet.reStruct
Extract reStruct Log-Determinants
getCovariate.data.frame
Extract Data Frame Covariate
nlme
Nonlinear Mixed-Effects Models
fixed.effects.lme
Extract lme Fixed Effects
MEestimate
Estimate mixed-effects parameters
varPower
Power Variance Function
Variogram
Calculate Semi-variogram
lmeObject
Fitted lme Object
coef.reStruct
reStruct Object Coefficients
logLik.lme
Log-Likelihood of an lme Object
isInitialized
Check if Object is Initialized
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
plot.ranef.lmList
Plot a ranef.lmList Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
getCovariateFormula
Extract Covariates Formula
getCovariate.corStruct
Extract corStruct Object Covariate
Names.pdMat
Names of a pdMat Object
getData.lme
Extract lme Object Data
pdDiag
Diagonal Positive-Definite Matrix
lmeStruct
Linear Mixed-Effects Structure
comparePred
Compare Predictions
residuals.lme
Extract lme Residuals
print.summary.varFunc
Print a summary.varFunc Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
getGroups.gls
Extract gls Object Groups
pdFactor
Square-Root Factor of a Positive-Definite Matrix
predict.gnls
Predictions from a gnls Object
groupedData
Construct a groupedData Object
corClasses
Correlation Structure Classes
corLin
Linear Correlation Structure
corMatrix
Extract Correlation Matrix
gnlsControl
Control Values for gnls Fit
plot.Variogram
Plot a Variogram Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
coef.modelStruct
Extract modelStruct Object Coefficients
Coef
Assign Values to Coefficients
Variogram.corLin
Calculate Semi-variogram for a corLin Object
recalc.corStruct
Recalculate for corStruct Object
BIC
Bayesian Information Criterion
gnlsStruct
Generalized Nonlinear Least Squares Structure
fitted.gnls
Extract gnls Fitted Values
solve.reStruct
Apply Solve to an reStruct Object
corSpatial
Spatial Correlation Structure
initialize.reStruct
Initialize reStruct Object
getGroupsFormula.gls
Extract gls Object Grouping Formula
lme.lmList
LME fit from lmList Object
print.pdMat
Print a pdMat Object
getResponse.gls
Extract gls Object Response
nlmeControl
Control Values for nlme Fit
nlmeObject
Fitted nlme Object
formula.pdBlocked
Extract pdBlocked Formula
formula.gnls
Extract gnls Object Formula
corSpher
Spherical Correlation Structure
getCovariate.varFunc
Extract varFunc Covariate
fitted.glsStruct
Calculate glsStruct Fitted Values
glsObject
Fitted gls Object
gls
Fit Linear Model Using Generalized Least Squares
initialize.corStruct
Initialize corStruct Object
gnlsObject
Fitted gnls Object
nlmeStruct
Nonlinear Mixed-Effects Structure
plot.nfnGroupedData
Plot an nfnGroupedData Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.lmList
Plot an lmList Object
pdClasses
Positive-Definite Matrix Classes
formula.gls
Extract gls Object Formula
getGroups.data.frame
Extract Groups from a Data Frame
plot.nmGroupedData
Plot an nmGroupedData Object
logLik.corStruct
Extract corStruct Log-Likelihood
corGaus
Gaussian Correlation Structure
lme
Linear Mixed-Effects Models
random.effects.lme
Extract lme Random Effects
random.effects.lmList
Extract lmList Random Effects
as.matrix.pdMat
Matrix of a pdMat Object
logLik.lm
Extract Log-Likelihood from an lm Object
corSymm
General Correlation Structure
update.gls
Update a gls Object
predict.nlme
Predictions from an nlme Object
print.summary.lmList
Print a summary.lmList Object
print.lmList
Print an lmList Object
residuals.lmList
Extract lmList Residuals
intervals.lmList
Confidence Intervals on lmList Coefficients
fitted.gls
Extract gls Fitted Values
gsummary
Summarize by Groups
logLik.gls
Log-Likelihood of a gls Object
print.corStruct
Print a corStruct Object
lme.groupedData
LME fit from groupedData Object
needUpdate
Check if Update is Needed
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
getGroupsFormula.reStruct
Extract reStruct Grouping Formula
logLik.varFunc
Extract varFunc logLik
getData.gls
Extract gls Object Data
gnls
Fit Nonlinear Model Using Generalized Least Squares
print.anova.lme
Print an anova.lme Object
initialize.varFunc
Initialize varFunc Object
nlsList.selfStart
nlsList Fit from a selfStart Function
summary.lme
Summarize an lme Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
coef.pdCompSymm
pdCompSymm Object Coefficients
print.reStruct
Print an reStruct Object
getGroups.varFunc
Extract varFunc Groups
pdBlocked
Positive-Definite Block Diagonal Matrix
intervals.gls
Confidence Intervals on gls Parameters
summary.varFunc
Summarize varFunc Object
formula.pdMat
Extract pdMat Formula
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
getResponse.data.frame
Extract Response from a Data Frame
varConstPower
Constant Plus Power Variance Function
summary.pdMat
Summarize a pdMat Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
plot.lme
Plot an lme Object
pdMat
Positive-Definite Matrix
glsStruct
Generalized Least Squares Structure
pairs.compareFits
Pairs Plot of compareFits Object
pairs.lmList
Pairs Plot of an lmList Object
getGroupsFormula.lme
Extract lme Object Grouping Formula
summary.modelStruct
Summarize a modelStruct Object
pdConstruct
Construct pdMat Objects
plot.augPred
Plot an augPred Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
reStruct
Random Effects Structure
print.summary.corStruct
Print a summary.corStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
getGroups.lme
Extract lme Object Groups
print.summary.modelStruct
Print a summary.modelStruct Object
nlsList
List of nls Objects with a Common Model
lmList.groupedData
lmList Fit from a groupedData Object
recalc
Recalculate Condensed Linear Model Object
initialize
Initialize Object
initialize.glsStruct
Initialize a glsStruct Object
intervals
Confidence Intervals on Coefficients
print.varFunc
Print a varFunc Object
recalc.modelStruct
Recalculate for a modelStruct Object
plot.intervals.lmList
Plot lmList Confidence Intervals
random.effects
Extract Random Effects
lmeControl
Control Values for lme Fit
pdSymm
General Positive-Definite Matrix
print.modelStruct
Print a modelStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
print.summary.lme
Print a summary.lme Object
residuals.glsStruct
Calculate glsStruct Residuals
pooledSD
Extract Pooled Standard Deviation
plot.ranef.lme
Plot a ranef.lme Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
residuals.gls
Extract gls Residuals
varIdent
Constant Variance Function
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
plot.gls
Plot a gls Object
predict.lmList
Predictions from an lmList Object
summary.lmList
Summarize an lmList Object
print.gls
Print a gls Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
summary.gls
Summarize a gls Object
predict.gls
Predictions from a gls Object
recalc.reStruct
Recalculate for an reStruct Object
print.summary.pdMat
Print a summary.pdMat Object
print.groupedData
Print a groupedData Object
simulate.lme
simulate lme models
residuals.gnls
Extract gnls Residuals
varComb
Combination of Variance Functions
varFixed
Fixed Variance Function
residuals.lmeStruct
Calculate lmeStruct Residuals
update.modelStruct
Update a modelStruct Object
varFunc
Variance Function Structure
getData
Extract Data from an Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
summary.nlsList
Summarize an nlsList Object
print.intervals.lme
Print an intervals.lme Object
summary.corStruct
Summarize a corStruct Object
update.lme
Update an lme Object
recalc.varFunc
Recalculate for varFunc Object
splitFormula
Split a Formula
residuals.gnlsStruct
Calculate gnlsStruct Residuals
pdIdent
Multiple of the Identity Positive-Definite Matrix
update.nlme
Update an nlme Object
print.summary.gls
Print a summary.gls Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
update.groupedData
Update a groupedData Object
update.varFunc
Update varFunc Object
update.nlsList
Update an nlsList Object
varClasses
Variance Function Classes
update.gnls
Update a gnls Object
varWeights
Extract Variance Function Weights
formula.groupedData
Extract groupedData Formula
Milk
Protein content of cows' milk
PBG
Effect of Phenylbiguanide on Blood Pressure
Ovary
Counts of Ovarian Follicles
Rail
Evaluation of Stress in Railway Rails
Glucose2
Glucose Levels Following Alcohol Ingestion
MathAchieve
Mathematics achievement scores
Assay
Bioassay on Cell Culture Plate
Phenobarb
Phenobarbitol Kinetics
MathAchSchool
School demographic data for MathAchieve
Muscle
Contraction of heart muscle sections
Relaxin
Assay for Relaxin
Machines
Productivity Scores for Machines and Workers
Tetracycline2
Pharmacokinetics of tetracycline
Pixel
X-ray pixel intensities over time
Spruce
Growth of Spruce Trees
Fatigue
Cracks caused by metal fatigue
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Cefamandole
Pharmacokinetics of Cefamandole
RatPupWeight
The weight of rat pups
ergoStool
Ergometrics experiment with stool types
Meat
Tenderness of meat
Earthquake
Earthquake Intensity
Tetracycline1
Pharmacokinetics of tetracycline
Gun
Methods for firing naval guns
Oats
Split-plot Experiment on Varieties of Oats
Oxide
Variability in Semiconductor Manufacturing
Wafer
Modeling of Analog MOS Circuits
Oxboys
Heights of Boys in Oxford
Gasoline
Refinery yield of gasoline
IGF
Radioimmunoassay of IGF-I Protein
Glucose
Glucose levels over time
Orthodont
Growth curve data on an orthdontic measurement
Remifentanil
Pharmacokinetics of remifentanil
Soybean
Growth of soybean plants
Nitrendipene
Assay of nitrendipene
Quinidine
Quinidine Kinetics
Wheat
Yields by growing conditions
Dialyzer
High-Flux Hemodialyzer
BodyWeight
Rat weight over time for different diets
Wheat2
Wheat Yield Trials