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nlme (version 3.1-38)
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
3.1-38
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-38)
Search all functions
Initialize.corStruct
Initialize corStruct Object
Covariate.varFunc
Assign varFunc Covariate
Dim.corSpatial
Dimensions of a corSpatial Object
coef.gnls
Extract gnls Coefficients
Dim.corStruct
Dimensions of a corStruct Object
AIC
Akaike Information Criterion
ACF.gls
Autocorrelation Function for gls Residuals
Initialize.reStruct
Initialize reStruct Object
MEdims
Calculate dimensions in mixed-effects
coef.lme
Extract lme Coefficients
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
BIC.logLik
BIC of a logLik Object
ACF.lme
Autocorrelation Function for lme Residuals
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Initialize
Initialize Object
Coef
Assign Values to Coefficients
Matrix
Assign Matrix Values
fitted.glsStruct
Calculate glsStruct Fitted Values
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getResponse.lme
Extract lme Object Response
Dim.pdMat
Dimensions of a pdMat Object
AIC.lme
Akaike Information Criterion
Names.pdMat
Names of a pdMat Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
formula.corStruct
Extract corStruct Object Formula
collapse.groupedData
Collapse a groupedData Object
coef.pdCompSymm
pdCompSymm Object Coefficients
Variogram.default
Calculate Semi-variogram
comparePred
Compare Predictions
formula.lme
Extract lme Object Formula
Names.formula
Extract Names from a formula
fixef.lmList
Extract lmList Fixed Effects
corCompSymm
Compound Symmetry Correlation Structure
Dim
Extract Dimensions from an Object
formula.lmList
Extract lmList Object Formula
[.pdMat
Subscript a pdMat Object
MEestimate
Estimate mixed-effects parameters
fixef.lme
Extract lme Fixed Effects
formula.pdBlocked
Extract pdBlocked Formula
Matrix.reStruct
Assign reStruct Matrices
MEEM
EM iterations for mixed-effects
formula.reStruct
Extract reStruct Object Formula
Initialize.varFunc
Initialize varFunc Object
Matrix.pdMat
Assign Matrix to a pdMat Object
lmeControl
Control Values for lme Fit
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
ACF
Autocorrelation Function
BIC
Bayesian Information Criterion
LDEsysMat
Generate system matrix for LDEs
formula.nlsList
Extract nlsList Object Formula
Variogram.corExp
Calculate Semi-variogram for a corExp Object
as.matrix.corStruct
Matrix of a corStruct Object
Covariate
Assign Covariate Values
formula.varFunc
Extract varFunc Formula
as.matrix.reStruct
Matrices of an reStruct Object
Names
Names Associated with an Object
getGroups.varFunc
Extract varFunc Groups
anova.lme
Compare Likelihoods of Fitted Objects
corFactor.corStruct
Factor of a corStruct Object Matrix
coef.pdIdent
pdIdent Object Coefficients
Initialize.lmeStruct
Initialize an lmeStruct Object
as.matrix.pdMat
Matrix of a pdMat Object
MEdecomp
Decompose a mixed-effects model
Initialize.glsStruct
Initialize a glsStruct Object
VarCorr
Extract variance and correlation components
coef.pdDiag
pdDiag Object Coefficients
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
lme.lmList
LME fit from lmList Object
Names.pdBlocked
Names of a pdBlocked Object
collapse
Collapse According to Groups
balancedGrouped
Create a groupedData object from a matrix
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
augPred
Augmented Predictions
formula.modelStruct
Extract modelStruct Object Formula
corClasses
Correlation Structure Classes
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
getResponseFormula
Extract Formula Specifying Response Variable
corAR1
AR(1) Correlation Structure
anova.gls
Compare Likelihoods of Fitted Objects
formula.nlme
Extract nlme Object Formula
coef.pdMat
pdMat Object Coefficients
getData.lme
Extract lme Object Data
glsControl
Control Values for gls Fit
logDet.pdMat
Extract Log-Determinant from a pdMat Object
coef.corStruct
Coefficients of a corStruct Object
coef.modelStruct
Extract modelStruct Object Coefficients
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
coef.gls
Extract gls Coefficients
getGroups.lme
Extract lme Object Groups
gnlsObject
Fitted gnls Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getCovariate.data.frame
Extract Data Frame Covariate
getCovariate
Extract Covariate from an Object
corARMA
ARMA(p,q) Correlation Structure
asOneFormula
Combine Formulas of a Set of Objects
formula.pdMat
Extract pdMat Formula
getData.lmList
Extract lmList Object Data
Variogram
Calculate Semi-variogram
asTable
Convert groupedData to a matrix
corSymm
General Correlation Structure
corSpher
Spherical Correlation Structure
coef.reStruct
reStruct Object Coefficients
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corExp
Exponential Correlation Structure
corLin
Linear Correlation Structure
corNatural
General correlation in natural parameterization
getCovariateFormula
Extract Covariates Formula
getData
Extract Data from an Object
gsummary
Summarize by Groups
corFactor
Factor of a Correlation Matrix
getGroups.corStruct
Extract corStruct Groups
Names.reStruct
Names of an reStruct Object
corMatrix
Extract Correlation Matrix
compareFits
Compare Fitted Objects
gnls
Fit Nonlinear Model Using Generalized Least Squares
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
coef.varFunc
varFunc Object Coefficients
corMatrix.corStruct
Matrix of a corStruct Object
fitted.gnls
Extract gnls Fitted Values
getCovariate.corStruct
Extract corStruct Object Covariate
getData.gls
Extract gls Object Data
pdBlocked
Positive-Definite Block Diagonal Matrix
coef.lmList
Extract lmList Coefficients
fitted.gls
Extract gls Fitted Values
isInitialized
Check if Object is Initialized
plot.intervals.lmList
Plot lmList Confidence Intervals
logDet.reStruct
Extract reStruct Log-Determinants
logDet.corStruct
Extract corStruct Log-Determinant
varIdent
Constant Variance Function
groupedData
Construct a groupedData Object
contr.SAS
Contrast Matrices
fitted.lmList
Extract lmList Fitted Values
getResponse.data.frame
Extract Response from a Data Frame
getResponse.gls
Extract gls Object Response
nlme.nlsList
NLME fit from nlsList Object
formula.gls
Extract gls Object Formula
fitted.lme
Extract lme Fitted Values
corSpatial
Spatial Correlation Structure
getVarCov
Extract variance-covariance matrix
corRatio
Rational Quadratic Correlation Structure
glsObject
Fitted gls Object
intervals
Confidence Intervals on Coefficients
isInitialized.reStruct
Check if an reStruct Object is Initialized
lmeScale
Scale for lme Optimization
plot.nmGroupedData
Plot an nmGroupedData Object
nlme
Nonlinear Mixed-Effects Models
nlsList.selfStart
nlsList Fit from a selfStart Function
lmeObject
Fitted lme Object
logLik.reStruct
Calculate reStruct Log-Likelihood
intervals.gls
Confidence Intervals on gls Parameters
formula.groupedData
Extract groupedData Formula
pairs.compareFits
Pairs Plot of compareFits Object
getGroupsFormula
Extract Grouping Formula
predict.lme
Predictions from an lme Object
logLik.corStruct
Extract corStruct Log-Likelihood
fdHess
Finite difference Hessian
gnlsControl
Control Values for gnls Fit
getGroups.gls
Extract gls Object Groups
getResponse
Extract Response Variable from an Object
summary.modelStruct
Summarize a modelStruct Object
lmList
List of lm Objects with a Common Model
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
predict.gls
Predictions from a gls Object
getGroups.lmList
Extract lmList Object Groups
nlme-internal
Internal nlme functions
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
fixed.effects
Extract Fixed Effects
getCovariate.varFunc
Extract varFunc Covariate
pdLogChol
General Positive-Definite Matrix
getGroups
Extract Grouping Factors from an Object
isBalanced
Check a Design for Balance
pdMat
Positive-Definite Matrix
logDet
Extract the Logarithm of the Determinant
phenoModel
Model function for the Phenobarb data
nlsList
List of nls Objects with a Common Model
corCAR1
Continuous AR(1) Correlation Structure
print.summary.corStruct
Print a summary.corStruct Object
corGaus
Gaussian Correlation Structure
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
formula.gnls
Extract gnls Object Formula
pdConstruct.pdBlocked
Construct pdBlocked Objects
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
nlmeObject
Fitted nlme Object
getResponse.lmList
Extract lmList Object Response
print.gls
Print a gls Object
intervals.lmList
Confidence Intervals on lmList Coefficients
print.summary.modelStruct
Print a summary.modelStruct Object
plot.compareFits
Plot a compareFits Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
quinModel
Model function for the Quinidine data
plot.ACF
Plot an ACF Object
logLik.lme
Log-Likelihood of an lme Object
getGroups.data.frame
Extract Groups from a Data Frame
ranef.lme
Extract lme Random Effects
pdFactor
Square-Root Factor of a Positive-Definite Matrix
splitFormula
Split a Formula
ranef.lmList
Extract lmList Random Effects
plot.Variogram
Plot a Variogram Object
lme
Linear Mixed-Effects Models
pdConstruct
Construct pdMat Objects
intervals.lme
Confidence Intervals on lme Parameters
lmeStruct
Linear Mixed-Effects Structure
gnlsStruct
Generalized Nonlinear Least Squares Structure
reStruct
Random Effects Structure
allCoef
Extract Coefficients from a Set of Objects
predict.gnls
Predictions from a gnls Object
gls
Fit Linear Model Using Generalized Least Squares
summary.pdMat
Summarize a pdMat Object
lme.groupedData
LME fit from groupedData Object
needUpdate
Check if Update is Needed
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
recalc.corStruct
Recalculate for corStruct Object
residuals.lmList
Extract lmList Residuals
gapply
Apply a Function by Groups
varWeights
Extract Variance Function Weights
logLik.gnls
Log-Likelihood of a gnls Object
logLik.lmList
Log-Likelihood of an lmList Object
random.effects
Extract Random Effects
print.reStruct
Print an reStruct Object
pdClasses
Positive-Definite Matrix Classes
print.summary.gls
Print a summary.gls Object
print.varFunc
Print a varFunc Object
nlmeControl
Control Values for nlme Fit
glsStruct
Generalized Least Squares Structure
plot.lmList
Plot an lmList Object
recalc.varFunc
Recalculate for varFunc Object
print.summary.lmList
Print a summary.lmList Object
plot.ranef.lme
Plot a ranef.lme Object
plot.nffGroupedData
Plot an nffGroupedData Object
pdSymm
General Positive-Definite Matrix
print.summary.pdMat
Print a summary.pdMat Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
lmList.groupedData
lmList Fit from a groupedData Object
varConstPower
Constant Plus Power Variance Function
pruneLevels
Prune Factor Levels
plot.lme
Plot an lme or nls object
summary.nlsList
Summarize an nlsList Object
recalc.reStruct
Recalculate for an reStruct Object
print.groupedData
Print a groupedData Object
predict.nlme
Predictions from an nlme Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
logLik.varFunc
Extract varFunc logLik
recalc.modelStruct
Recalculate for a modelStruct Object
simulate.lme
simulate lme models
pdNatural
General Positive-Definite Matrix in Natural Parametrization
solve.reStruct
Apply Solve to an reStruct Object
logLik.gls
Log-Likelihood of a gls Object
summary.lmList
Summarize an lmList Object
residuals.lme
Extract lme Residuals
predict.lmList
Predictions from an lmList Object
summary.gls
Summarize a gls Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
model.matrix.reStruct
reStruct Model Matrix
print.summary.lme
Print a summary.lme Object
print.anova.lme
Print an anova.lme Object
plot.ranef.lmList
Plot a ranef.lmList Object
print.corStruct
Print a corStruct Object
update.modelStruct
Update a modelStruct Object
varExp
Exponential Variance Function
print.summary.varFunc
Print a summary.varFunc Object
varFixed
Fixed Variance Function
residuals.gls
Extract gls Residuals
pooledSD
Extract Pooled Standard Deviation
print.lme
Print an lme Object
pdDiag
Diagonal Positive-Definite Matrix
residuals.gnlsStruct
Calculate gnlsStruct Residuals
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
summary.lme
Summarize an lme Object
pairs.lmList
Pairs Plot of an lmList Object
recalc
Recalculate Condensed Linear Model Object
varWeights.glsStruct
Variance Weights for glsStruct Object
summary.varFunc
Summarize varFunc Object
varFunc
Variance Function Structure
plot.nfnGroupedData
Plot an nfnGroupedData Object
residuals.glsStruct
Calculate glsStruct Residuals
print.pdMat
Print a pdMat Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
residuals.lmeStruct
Calculate lmeStruct Residuals
varComb
Combination of Variance Functions
varPower
Power Variance Function
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
update.varFunc
Update varFunc Object
varClasses
Variance Function Classes
nlmeStruct
Nonlinear Mixed-Effects Structure
summary.corStruct
Summarize a corStruct Object
pairs.lme
Pairs Plot of an lme Object
plot.augPred
Plot an augPred Object
plot.gls
Plot a gls Object
print.lmList
Print an lmList Object
print.modelStruct
Print a modelStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
Gasoline
Refinery yield of gasoline
Oxboys
Heights of Boys in Oxford
Assay
Bioassay on Cell Culture Plate
Gun
Methods for firing naval guns
Cefamandole
Pharmacokinetics of Cefamandole
Dialyzer
High-Flux Hemodialyzer
Muscle
Contraction of heart muscle sections
Orthodont
Growth curve data on an orthdontic measurement
Earthquake
Earthquake Intensity
Nitrendipene
Assay of nitrendipene
Phenobarb
Phenobarbitol Kinetics
Wheat
Yields by growing conditions
MathAchSchool
School demographic data for MathAchieve
Wheat2
Wheat Yield Trials
Fatigue
Cracks caused by metal fatigue
Spruce
Growth of Spruce Trees
Rail
Evaluation of Stress in Railway Rails
Relaxin
Assay for Relaxin
Wafer
Modeling of Analog MOS Circuits
bdf
Language scores
Milk
Protein content of cows' milk
Remifentanil
Pharmacokinetics of remifentanil
Oxide
Variability in Semiconductor Manufacturing
MathAchieve
Mathematics achievement scores
PBG
Effect of Phenylbiguanide on Blood Pressure
ergoStool
Ergometrics experiment with stool types
Soybean
Growth of soybean plants
Glucose2
Glucose Levels Following Alcohol Ingestion
Quinidine
Quinidine Kinetics
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
IGF
Radioimmunoassay of IGF-I Protein
Glucose
Glucose levels over time
Machines
Productivity Scores for Machines and Workers
Meat
Tenderness of meat
Pixel
X-ray pixel intensities over time
BodyWeight
Rat weight over time for different diets
Tetracycline2
Pharmacokinetics of tetracycline
Ovary
Counts of Ovarian Follicles
Tetracycline1
Pharmacokinetics of tetracycline
RatPupWeight
The weight of rat pups
Oats
Split-plot Experiment on Varieties of Oats