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nlme (version 3.1-31)
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
149,202
Version
3.1-31
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-31)
Search all functions
Initialize.reStruct
Initialize reStruct Object
fitted.gnls
Extract gnls Fitted Values
ACF.lme
Autocorrelation Function for lme Residuals
Coef
Assign Values to Coefficients
[.pdMat
Subscript a pdMat Object
augPred
Augmented Predictions
corRatio
Rational Quadratic Correlation Structure
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
residuals.lmeStruct
Calculate lmeStruct Residuals
varExp
Exponential Variance Function
splitFormula
Split a Formula
Matrix.pdMat
Assign Matrix to a pdMat Object
Initialize
Initialize Object
AIC.lme
Akaike Information Criterion
Matrix
Assign Matrix Values
getResponse.lmList
Extract lmList Object Response
residuals.nlmeStruct
Calculate nlmeStruct Residuals
print.summary.gls
Print a summary.gls Object
corFactor
Factor of a Correlation Matrix
Dim.pdMat
Dimensions of a pdMat Object
varWeights.glsStruct
Variance Weights for glsStruct Object
formula.modelStruct
Extract modelStruct Object Formula
getCovariate.corStruct
Extract corStruct Object Covariate
corFactor.corStruct
Factor of a corStruct Object Matrix
contr.SAS
Contrast Matrices
corMatrix
Extract Correlation Matrix
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
allCoef
Extract Coefficients from a Set of Objects
varClasses
Variance Function Classes
Initialize.corStruct
Initialize corStruct Object
needUpdate
Check if Update is Needed
balancedGrouped
Create a groupedData object from a matrix
ACF.gls
Autocorrelation Function for gls Residuals
MEdecomp
Decompose a mixed-effects model
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Names.pdBlocked
Names of a pdBlocked Object
AIC
Akaike Information Criterion
coef.lmList
Extract lmList Coefficients
Names.pdMat
Names of a pdMat Object
print.varFunc
Print a varFunc Object
MEEM
EM iterations for mixed-effects
Matrix.reStruct
Assign reStruct Matrices
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
print.summary.lmList
Print a summary.lmList Object
as.matrix.reStruct
Matrices of an reStruct Object
Dim.corStruct
Dimensions of a corStruct Object
Initialize.glsStruct
Initialize a glsStruct Object
glsObject
Fitted gls Object
formula.reStruct
Extract reStruct Object Formula
residuals.lmList
Extract lmList Residuals
formula.lme
Extract lme Object Formula
fitted.lme
Extract lme Fitted Values
pruneLevels
Prune Factor Levels
lmeStruct
Linear Mixed-Effects Structure
simulate.lme
simulate lme models
pdMat
Positive-Definite Matrix
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
corCompSymm
Compound Symmetry Correlation Structure
coef.gls
Extract gls Coefficients
intervals.lme
Confidence Intervals on lme Parameters
asTable
Convert groupedData to a matrix
asOneFormula
Combine Formulas of a Set of Objects
corGaus
Gaussian Correlation Structure
summary.corStruct
Summarize a corStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
corExp
Exponential Correlation Structure
coef.pdDiag
pdDiag Object Coefficients
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
corMatrix.corStruct
Matrix of a corStruct Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
ACF
Autocorrelation Function
print.summary.varFunc
Print a summary.varFunc Object
print.groupedData
Print a groupedData Object
pdBlocked
Positive-Definite Block Diagonal Matrix
MEdims
Calculate dimensions in mixed-effects
getData.gls
Extract gls Object Data
Names.formula
Extract Names from a formula
coef.varFunc
varFunc Object Coefficients
qqnorm.gls
Normal Plot of Residuals from a gls Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
lme.lmList
LME fit from lmList Object
gnlsControl
Control Values for gnls Fit
logLik.glsStruct
Log-Likelihood of a glsStruct Object
pdClasses
Positive-Definite Matrix Classes
print.gls
Print a gls Object
Variogram
Calculate Semi-variogram
compareFits
Compare Fitted Objects
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
summary.pdMat
Summarize a pdMat Object
quinModel
Model function for the Quinidine data
random.effects
Extract Random Effects
Initialize.lmeStruct
Initialize an lmeStruct Object
print.modelStruct
Print a modelStruct Object
isInitialized
Check if Object is Initialized
varComb
Combination of Variance Functions
recalc
Recalculate Condensed Linear Model Object
predict.lme
Predictions from an lme Object
Dim.corSpatial
Dimensions of a corSpatial Object
print.summary.pdMat
Print a summary.pdMat Object
predict.lmList
Predictions from an lmList Object
logDet.reStruct
Extract reStruct Log-Determinants
corAR1
AR(1) Correlation Structure
varWeights.lmeStruct
Variance Weights for lmeStruct Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Dim
Extract Dimensions from an Object
lmList.groupedData
lmList Fit from a groupedData Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
coef.gnls
Extract gnls Coefficients
Covariate
Assign Covariate Values
recalc.varFunc
Recalculate for varFunc Object
intervals
Confidence Intervals on Coefficients
plot.nfnGroupedData
Plot an nfnGroupedData Object
pdDiag
Diagonal Positive-Definite Matrix
plot.Variogram
Plot a Variogram Object
getGroups.data.frame
Extract Groups from a Data Frame
logDet.corStruct
Extract corStruct Log-Determinant
MEestimate
Estimate mixed-effects parameters
reStruct
Random Effects Structure
as.matrix.pdMat
Matrix of a pdMat Object
BIC
Bayesian Information Criterion
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
summary.varFunc
Summarize varFunc Object
getCovariateFormula
Extract Covariates Formula
varFixed
Fixed Variance Function
plot.nffGroupedData
Plot an nffGroupedData Object
collapse
Collapse According to Groups
logLik.gnls
Log-Likelihood of a gnls Object
fixed.effects
Extract Fixed Effects
plot.ACF
Plot an ACF Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
lme
Linear Mixed-Effects Models
VarCorr
Extract variance and correlation components
predict.gls
Predictions from a gls Object
model.matrix.reStruct
reStruct Model Matrix
pdLogChol
General Positive-Definite Matrix
logLik.corStruct
Extract corStruct Log-Likelihood
corARMA
ARMA(p,q) Correlation Structure
as.matrix.corStruct
Matrix of a corStruct Object
getGroupsFormula
Extract Grouping Formula
recalc.corStruct
Recalculate for corStruct Object
comparePred
Compare Predictions
getCovariate.data.frame
Extract Data Frame Covariate
lmeObject
Fitted lme Object
predict.gnls
Predictions from a gnls Object
pdConstruct
Construct pdMat Objects
summary.lme
Summarize an lme Object
coef.pdCompSymm
pdCompSymm Object Coefficients
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
formula.gls
Extract gls Object Formula
recalc.reStruct
Recalculate for an reStruct Object
Covariate.varFunc
Assign varFunc Covariate
residuals.lme
Extract lme Residuals
print.corStruct
Print a corStruct Object
print.lmList
Print an lmList Object
varFunc
Variance Function Structure
gsummary
Summarize by Groups
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
corClasses
Correlation Structure Classes
formula.lmList
Extract lmList Object Formula
print.summary.modelStruct
Print a summary.modelStruct Object
print.summary.lme
Print a summary.lme Object
logLik.varFunc
Extract varFunc logLik
glsControl
Control Values for gls Fit
BIC.logLik
BIC of a logLik Object
logLik.lme
Log-Likelihood of an lme Object
lmeScale
Scale for lme Optimization
corSpher
Spherical Correlation Structure
coef.modelStruct
Extract modelStruct Object Coefficients
varIdent
Constant Variance Function
anova.lme
Compare Likelihoods of Fitted Objects
fixef.lmList
Extract lmList Fixed Effects
solve.reStruct
Apply Solve to an reStruct Object
varWeights
Extract Variance Function Weights
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
corSpatial
Spatial Correlation Structure
plot.ranef.lme
Plot a ranef.lme Object
getResponse.gls
Extract gls Object Response
getResponse.lme
Extract lme Object Response
lme.groupedData
LME fit from groupedData Object
coef.corStruct
Coefficients of a corStruct Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
phenoModel
Model function for the Phenobarb data
fixef.lme
Extract lme Fixed Effects
isBalanced
Check a Design for Balance
getVarCov
Extract variance-covariance matrix
plot.augPred
Plot an augPred Object
Names
Names Associated with an Object
Initialize.varFunc
Initialize varFunc Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
update.varFunc
Update varFunc Object
Variogram.default
Calculate Semi-variogram
summary.gls
Summarize a gls Object
anova.gls
Compare Likelihoods of Fitted Objects
Variogram.corExp
Calculate Semi-variogram for a corExp Object
summary.lmList
Summarize an lmList Object
residuals.gls
Extract gls Residuals
fitted.lmeStruct
Calculate lmeStruct Fitted Values
ranef.lmList
Extract lmList Random Effects
varPower
Power Variance Function
coef.pdIdent
pdIdent Object Coefficients
coef.pdMat
pdMat Object Coefficients
ranef.lme
Extract lme Random Effects
lmList
List of lm Objects with a Common Model
gnls
Fit Nonlinear Model Using Generalized Least Squares
residuals.glsStruct
Calculate glsStruct Residuals
print.reStruct
Print an reStruct Object
print.anova.lme
Print an anova.lme Object
pairs.lme
Pairs Plot of an lme Object
print.pdMat
Print a pdMat Object
predict.nlme
Predictions from an nlme Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
recalc.modelStruct
Recalculate for a modelStruct Object
print.lme
Print an lme Object
groupedData
Construct a groupedData Object
LDEsysMat
Generate system matrix for LDEs
formula.nlsList
Extract nlsList Object Formula
formula.nlme
Extract nlme Object Formula
gapply
Apply a Function by Groups
formula.groupedData
Extract groupedData Formula
getCovariate.varFunc
Extract varFunc Covariate
formula.pdMat
Extract pdMat Formula
getData.lme
Extract lme Object Data
fitted.glsStruct
Calculate glsStruct Fitted Values
formula.gnls
Extract gnls Object Formula
getGroups.lmList
Extract lmList Object Groups
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
getData.lmList
Extract lmList Object Data
isInitialized.reStruct
Check if an reStruct Object is Initialized
collapse.groupedData
Collapse a groupedData Object
getGroups.lme
Extract lme Object Groups
gls
Fit Linear Model Using Generalized Least Squares
corNatural
General correlation in natural parameterization
getGroups
Extract Grouping Factors from an Object
nlme-internal
Internal nlme functions
getData
Extract Data from an Object
formula.corStruct
Extract corStruct Object Formula
getGroups.corStruct
Extract corStruct Groups
gnlsStruct
Generalized Nonlinear Least Squares Structure
pdFactor
Square-Root Factor of a Positive-Definite Matrix
summary.modelStruct
Summarize a modelStruct Object
glsStruct
Generalized Least Squares Structure
logDet
Extract the Logarithm of the Determinant
print.summary.corStruct
Print a summary.corStruct Object
corSymm
General Correlation Structure
plot.gls
Plot a gls Object
nlme
Nonlinear Mixed-Effects Models
intervals.gls
Confidence Intervals on gls Parameters
corLin
Linear Correlation Structure
fitted.lmList
Extract lmList Fitted Values
corCAR1
Continuous AR(1) Correlation Structure
lmeControl
Control Values for lme Fit
pairs.compareFits
Pairs Plot of compareFits Object
logLik.gls
Log-Likelihood of a gls Object
nlme.nlsList
NLME fit from nlsList Object
plot.compareFits
Plot a compareFits Object
getGroups.gls
Extract gls Object Groups
nlmeStruct
Nonlinear Mixed-Effects Structure
nlsList.selfStart
nlsList Fit from a selfStart Function
pairs.lmList
Pairs Plot of an lmList Object
fdHess
Finite difference Hessian
logLik.lmList
Log-Likelihood of an lmList Object
gnlsObject
Fitted gnls Object
update.modelStruct
Update a modelStruct Object
fitted.gls
Extract gls Fitted Values
summary.nlsList
Summarize an nlsList Object
nlmeObject
Fitted nlme Object
varConstPower
Constant Plus Power Variance Function
getResponseFormula
Extract Formula Specifying Response Variable
coef.lme
Extract lme Coefficients
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
plot.lme
Plot an lme or nls object
plot.nmGroupedData
Plot an nmGroupedData Object
nlmeControl
Control Values for nlme Fit
plot.lmList
Plot an lmList Object
formula.varFunc
Extract varFunc Formula
formula.pdBlocked
Extract pdBlocked Formula
Names.reStruct
Names of an reStruct Object
pdSymm
General Positive-Definite Matrix
nlsList
List of nls Objects with a Common Model
plot.intervals.lmList
Plot lmList Confidence Intervals
intervals.lmList
Confidence Intervals on lmList Coefficients
pooledSD
Extract Pooled Standard Deviation
getResponse.data.frame
Extract Response from a Data Frame
getResponse
Extract Response Variable from an Object
getGroups.varFunc
Extract varFunc Groups
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.reStruct
Calculate reStruct Log-Likelihood
coef.reStruct
reStruct Object Coefficients
plot.ranef.lmList
Plot a ranef.lmList Object
getCovariate
Extract Covariate from an Object
IGF
Radioimmunoassay of IGF-I Protein
Assay
Bioassay on Cell Culture Plate
Quinidine
Quinidine Kinetics
Gun
Methods for firing naval guns
PBG
Effect of Phenylbiguanide on Blood Pressure
Tetracycline1
Pharmacokinetics of tetracycline
Glucose2
Glucose Levels Following Alcohol Ingestion
MathAchSchool
School demographic data for MathAchieve
Glucose
Glucose levels over time
Milk
Protein content of cows' milk
Meat
Tenderness of meat
Cefamandole
Pharmacokinetics of Cefamandole
Soybean
Growth of soybean plants
Oats
Split-plot Experiment on Varieties of Oats
Nitrendipene
Assay of nitrendipene
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Remifentanil
Pharmacokinetics of remifentanil
RatPupWeight
The weight of rat pups
bdf
Language scores
Fatigue
Cracks caused by metal fatigue
Pixel
X-ray pixel intensities over time
Wheat
Yields by growing conditions
BodyWeight
Rat weight over time for different diets
Gasoline
Refinery yield of gasoline
Dialyzer
High-Flux Hemodialyzer
MathAchieve
Mathematics achievement scores
ergoStool
Ergometrics experiment with stool types
Spruce
Growth of Spruce Trees
Muscle
Contraction of heart muscle sections
Wafer
Modeling of Analog MOS Circuits
Oxide
Variability in Semiconductor Manufacturing
Ovary
Counts of Ovarian Follicles
Phenobarb
Phenobarbitol Kinetics
Wheat2
Wheat Yield Trials
Oxboys
Heights of Boys in Oxford
Tetracycline2
Pharmacokinetics of tetracycline
Machines
Productivity Scores for Machines and Workers
Relaxin
Assay for Relaxin
Rail
Evaluation of Stress in Railway Rails
Earthquake
Earthquake Intensity
Orthodont
Growth curve data on an orthdontic measurement