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nlme (version 3.1-34)
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
84,769
Version
3.1-34
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-34)
Search all functions
AIC
Akaike Information Criterion
corAR1
AR(1) Correlation Structure
ACF
Autocorrelation Function
coef.pdMat
pdMat Object Coefficients
Dim.corSpatial
Dimensions of a corSpatial Object
ACF.gls
Autocorrelation Function for gls Residuals
allCoef
Extract Coefficients from a Set of Objects
collapse
Collapse According to Groups
corClasses
Correlation Structure Classes
comparePred
Compare Predictions
Initialize.lmeStruct
Initialize an lmeStruct Object
contr.SAS
Contrast Matrices
coef.lmList
Extract lmList Coefficients
logLik.gls
Log-Likelihood of a gls Object
formula.gnls
Extract gnls Object Formula
corMatrix
Extract Correlation Matrix
print.reStruct
Print an reStruct Object
random.effects
Extract Random Effects
varPower
Power Variance Function
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
ranef.lmList
Extract lmList Random Effects
Matrix
Assign Matrix Values
Initialize.varFunc
Initialize varFunc Object
BIC
Bayesian Information Criterion
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
coef.gnls
Extract gnls Coefficients
Dim.corStruct
Dimensions of a corStruct Object
asOneFormula
Combine Formulas of a Set of Objects
Dim.pdMat
Dimensions of a pdMat Object
fitted.gls
Extract gls Fitted Values
varComb
Combination of Variance Functions
MEdims
Calculate dimensions in mixed-effects
plot.nmGroupedData
Plot an nmGroupedData Object
as.matrix.corStruct
Matrix of a corStruct Object
formula.varFunc
Extract varFunc Formula
Names.formula
Extract Names from a formula
compareFits
Compare Fitted Objects
recalc.varFunc
Recalculate for varFunc Object
print.summary.modelStruct
Print a summary.modelStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
print.summary.pdMat
Print a summary.pdMat Object
print.summary.lmList
Print a summary.lmList Object
as.matrix.pdMat
Matrix of a pdMat Object
residuals.lmList
Extract lmList Residuals
varFixed
Fixed Variance Function
splitFormula
Split a Formula
varWeights.glsStruct
Variance Weights for glsStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
formula.corStruct
Extract corStruct Object Formula
formula.reStruct
Extract reStruct Object Formula
summary.varFunc
Summarize varFunc Object
MEestimate
Estimate mixed-effects parameters
print.corStruct
Print a corStruct Object
print.pdMat
Print a pdMat Object
corFactor.corStruct
Factor of a corStruct Object Matrix
varWeights
Extract Variance Function Weights
formula.modelStruct
Extract modelStruct Object Formula
Covariate.varFunc
Assign varFunc Covariate
getGroups.lmList
Extract lmList Object Groups
isInitialized
Check if Object is Initialized
pruneLevels
Prune Factor Levels
intervals
Confidence Intervals on Coefficients
logLik.gnls
Log-Likelihood of a gnls Object
corFactor
Factor of a Correlation Matrix
summary.pdMat
Summarize a pdMat Object
collapse.groupedData
Collapse a groupedData Object
predict.gnls
Predictions from a gnls Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
BIC.logLik
BIC of a logLik Object
corLin
Linear Correlation Structure
MEEM
EM iterations for mixed-effects
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
coef.modelStruct
Extract modelStruct Object Coefficients
pdSymm
General Positive-Definite Matrix
residuals.lme
Extract lme Residuals
gnlsControl
Control Values for gnls Fit
corCAR1
Continuous AR(1) Correlation Structure
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
summary.nlsList
Summarize an nlsList Object
fitted.lmList
Extract lmList Fitted Values
Variogram
Calculate Semi-variogram
corCompSymm
Compound Symmetry Correlation Structure
corARMA
ARMA(p,q) Correlation Structure
Names.reStruct
Names of an reStruct Object
predict.lme
Predictions from an lme Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
getData.gls
Extract gls Object Data
as.matrix.reStruct
Matrices of an reStruct Object
Variogram.default
Calculate Semi-variogram
getGroups.corStruct
Extract corStruct Groups
formula.nlsList
Extract nlsList Object Formula
residuals.gls
Extract gls Residuals
coef.reStruct
reStruct Object Coefficients
fitted.glsStruct
Calculate glsStruct Fitted Values
summary.modelStruct
Summarize a modelStruct Object
logDet
Extract the Logarithm of the Determinant
plot.augPred
Plot an augPred Object
summary.lmList
Summarize an lmList Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
qqnorm.gls
Normal Plot of Residuals from a gls Object
gapply
Apply a Function by Groups
corNatural
General correlation in natural parameterization
coef.varFunc
varFunc Object Coefficients
print.summary.corStruct
Print a summary.corStruct Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
update.modelStruct
Update a modelStruct Object
lmeControl
Control Values for lme Fit
[.pdMat
Subscript a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
lmeStruct
Linear Mixed-Effects Structure
pdMat
Positive-Definite Matrix
Names
Names Associated with an Object
pairs.lmList
Pairs Plot of an lmList Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
plot.intervals.lmList
Plot lmList Confidence Intervals
print.lmList
Print an lmList Object
quinModel
Model function for the Quinidine data
print.summary.varFunc
Print a summary.varFunc Object
summary.lme
Summarize an lme Object
VarCorr
Extract variance and correlation components
print.varFunc
Print a varFunc Object
summary.corStruct
Summarize a corStruct Object
print.summary.lme
Print a summary.lme Object
getResponseFormula
Extract Formula Specifying Response Variable
predict.lmList
Predictions from an lmList Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
coef.pdIdent
pdIdent Object Coefficients
Names.pdMat
Names of a pdMat Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
varFunc
Variance Function Structure
print.gls
Print a gls Object
pdBlocked
Positive-Definite Block Diagonal Matrix
nlmeStruct
Nonlinear Mixed-Effects Structure
coef.corStruct
Coefficients of a corStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
getData.lmList
Extract lmList Object Data
getResponse.lme
Extract lme Object Response
coef.lme
Extract lme Coefficients
varExp
Exponential Variance Function
logDet.corStruct
Extract corStruct Log-Determinant
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
Initialize.reStruct
Initialize reStruct Object
augPred
Augmented Predictions
gnlsStruct
Generalized Nonlinear Least Squares Structure
coef.pdCompSymm
pdCompSymm Object Coefficients
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Covariate
Assign Covariate Values
predict.nlme
Predictions from an nlme Object
ranef.lme
Extract lme Random Effects
Initialize
Initialize Object
getResponse.data.frame
Extract Response from a Data Frame
corSpatial
Spatial Correlation Structure
Coef
Assign Values to Coefficients
anova.gls
Compare Likelihoods of Fitted Objects
logLik.lme
Log-Likelihood of an lme Object
plot.Variogram
Plot a Variogram Object
varIdent
Constant Variance Function
getResponse
Extract Response Variable from an Object
coef.gls
Extract gls Coefficients
formula.pdMat
Extract pdMat Formula
AIC.lme
Akaike Information Criterion
corSpher
Spherical Correlation Structure
pooledSD
Extract Pooled Standard Deviation
recalc.corStruct
Recalculate for corStruct Object
corMatrix.corStruct
Matrix of a corStruct Object
intervals.lme
Confidence Intervals on lme Parameters
nlme-internal
Internal nlme functions
pdLogChol
General Positive-Definite Matrix
Dim
Extract Dimensions from an Object
Matrix.reStruct
Assign reStruct Matrices
pairs.lme
Pairs Plot of an lme Object
plot.ranef.lmList
Plot a ranef.lmList Object
Initialize.corStruct
Initialize corStruct Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
residuals.gnlsStruct
Calculate gnlsStruct Residuals
intervals.gls
Confidence Intervals on gls Parameters
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pdConstruct
Construct pdMat Objects
ACF.lme
Autocorrelation Function for lme Residuals
balancedGrouped
Create a groupedData object from a matrix
phenoModel
Model function for the Phenobarb data
nlme
Nonlinear Mixed-Effects Models
getResponse.gls
Extract gls Object Response
plot.compareFits
Plot a compareFits Object
logLik.lmList
Log-Likelihood of an lmList Object
isInitialized.reStruct
Check if an reStruct Object is Initialized
varConstPower
Constant Plus Power Variance Function
nlmeObject
Fitted nlme Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
formula.pdBlocked
Extract pdBlocked Formula
getData
Extract Data from an Object
nlsList.selfStart
nlsList Fit from a selfStart Function
formula.lme
Extract lme Object Formula
formula.gls
Extract gls Object Formula
fixef.lmList
Extract lmList Fixed Effects
getGroups.gls
Extract gls Object Groups
Matrix.pdMat
Assign Matrix to a pdMat Object
isBalanced
Check a Design for Balance
fixed.effects
Extract Fixed Effects
logLik.varFunc
Extract varFunc logLik
getGroups.data.frame
Extract Groups from a Data Frame
logLik.reStruct
Calculate reStruct Log-Likelihood
recalc.modelStruct
Recalculate for a modelStruct Object
gsummary
Summarize by Groups
MEdecomp
Decompose a mixed-effects model
formula.lmList
Extract lmList Object Formula
corGaus
Gaussian Correlation Structure
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
getCovariate.corStruct
Extract corStruct Object Covariate
lme.groupedData
LME fit from groupedData Object
Initialize.glsStruct
Initialize a glsStruct Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
LDEsysMat
Generate system matrix for LDEs
solve.reStruct
Apply Solve to an reStruct Object
getGroups.varFunc
Extract varFunc Groups
plot.lme
Plot an lme or nls object
formula.groupedData
Extract groupedData Formula
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
glsStruct
Generalized Least Squares Structure
getCovariateFormula
Extract Covariates Formula
varClasses
Variance Function Classes
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
gls
Fit Linear Model Using Generalized Least Squares
print.groupedData
Print a groupedData Object
model.matrix.reStruct
reStruct Model Matrix
logDet.reStruct
Extract reStruct Log-Determinants
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
plot.gls
Plot a gls Object
residuals.lmeStruct
Calculate lmeStruct Residuals
fdHess
Finite difference Hessian
getGroupsFormula
Extract Grouping Formula
corExp
Exponential Correlation Structure
getData.lme
Extract lme Object Data
corSymm
General Correlation Structure
nlsList
List of nls Objects with a Common Model
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
asTable
Convert groupedData to a matrix
getGroups
Extract Grouping Factors from an Object
nlmeControl
Control Values for nlme Fit
nlme.nlsList
NLME fit from nlsList Object
summary.gls
Summarize a gls Object
residuals.glsStruct
Calculate glsStruct Residuals
logLik.corStruct
Extract corStruct Log-Likelihood
glsObject
Fitted gls Object
recalc.reStruct
Recalculate for an reStruct Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
print.summary.gls
Print a summary.gls Object
lme
Linear Mixed-Effects Models
print.anova.lme
Print an anova.lme Object
coef.pdDiag
pdDiag Object Coefficients
corRatio
Rational Quadratic Correlation Structure
lme.lmList
LME fit from lmList Object
reStruct
Random Effects Structure
fixef.lme
Extract lme Fixed Effects
simulate.lme
simulate lme models
groupedData
Construct a groupedData Object
getVarCov
Extract variance-covariance matrix
recalc
Recalculate Condensed Linear Model Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
pairs.compareFits
Pairs Plot of compareFits Object
needUpdate
Check if Update is Needed
getResponse.lmList
Extract lmList Object Response
glsControl
Control Values for gls Fit
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
print.lme
Print an lme Object
intervals.lmList
Confidence Intervals on lmList Coefficients
plot.ranef.lme
Plot a ranef.lme Object
gnlsObject
Fitted gnls Object
getCovariate
Extract Covariate from an Object
predict.gls
Predictions from a gls Object
fitted.gnls
Extract gnls Fitted Values
getGroups.lme
Extract lme Object Groups
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
lmeScale
Scale for lme Optimization
getCovariate.varFunc
Extract varFunc Covariate
plot.ACF
Plot an ACF Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
plot.nffGroupedData
Plot an nffGroupedData Object
plot.lmList
Plot an lmList Object
pdDiag
Diagonal Positive-Definite Matrix
print.modelStruct
Print a modelStruct Object
formula.nlme
Extract nlme Object Formula
lmList.groupedData
lmList Fit from a groupedData Object
getCovariate.data.frame
Extract Data Frame Covariate
fitted.lme
Extract lme Fitted Values
pdClasses
Positive-Definite Matrix Classes
fitted.lmeStruct
Calculate lmeStruct Fitted Values
lmList
List of lm Objects with a Common Model
lmeObject
Fitted lme Object
update.varFunc
Update varFunc Object
Glucose
Glucose levels over time
Fatigue
Cracks caused by metal fatigue
Spruce
Growth of Spruce Trees
Tetracycline2
Pharmacokinetics of tetracycline
bdf
Language scores
Assay
Bioassay on Cell Culture Plate
Cefamandole
Pharmacokinetics of Cefamandole
Machines
Productivity Scores for Machines and Workers
Gasoline
Refinery yield of gasoline
Earthquake
Earthquake Intensity
RatPupWeight
The weight of rat pups
Meat
Tenderness of meat
Pixel
X-ray pixel intensities over time
Oxide
Variability in Semiconductor Manufacturing
Remifentanil
Pharmacokinetics of remifentanil
Soybean
Growth of soybean plants
Rail
Evaluation of Stress in Railway Rails
Ovary
Counts of Ovarian Follicles
Dialyzer
High-Flux Hemodialyzer
Wheat
Yields by growing conditions
IGF
Radioimmunoassay of IGF-I Protein
MathAchieve
Mathematics achievement scores
Oats
Split-plot Experiment on Varieties of Oats
BodyWeight
Rat weight over time for different diets
ergoStool
Ergometrics experiment with stool types
Wheat2
Wheat Yield Trials
Nitrendipene
Assay of nitrendipene
Muscle
Contraction of heart muscle sections
Tetracycline1
Pharmacokinetics of tetracycline
Glucose2
Glucose Levels Following Alcohol Ingestion
MathAchSchool
School demographic data for MathAchieve
Oxboys
Heights of Boys in Oxford
Relaxin
Assay for Relaxin
Wafer
Modeling of Analog MOS Circuits
Milk
Protein content of cows' milk
PBG
Effect of Phenylbiguanide on Blood Pressure
Orthodont
Growth curve data on an orthdontic measurement
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Gun
Methods for firing naval guns
Quinidine
Quinidine Kinetics
Phenobarb
Phenobarbitol Kinetics