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nlme (version 3.1-35)
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
3.1-35
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-35)
Search all functions
Dim
Extract Dimensions from an Object
Names.pdMat
Names of a pdMat Object
MEestimate
Estimate mixed-effects parameters
BIC.logLik
BIC of a logLik Object
MEdecomp
Decompose a mixed-effects model
Covariate
Assign Covariate Values
anova.lme
Compare Likelihoods of Fitted Objects
MEdims
Calculate dimensions in mixed-effects
collapse
Collapse According to Groups
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.default
Calculate Semi-variogram
Matrix.pdMat
Assign Matrix to a pdMat Object
formula.modelStruct
Extract modelStruct Object Formula
[.pdMat
Subscript a pdMat Object
asTable
Convert groupedData to a matrix
Matrix.reStruct
Assign reStruct Matrices
corSpher
Spherical Correlation Structure
as.matrix.pdMat
Matrix of a pdMat Object
as.matrix.reStruct
Matrices of an reStruct Object
asOneFormula
Combine Formulas of a Set of Objects
fixef.lme
Extract lme Fixed Effects
corExp
Exponential Correlation Structure
fitted.gls
Extract gls Fitted Values
coef.reStruct
reStruct Object Coefficients
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corLin
Linear Correlation Structure
comparePred
Compare Predictions
fixed.effects
Extract Fixed Effects
corNatural
General correlation in natural parameterization
corCAR1
Continuous AR(1) Correlation Structure
corCompSymm
Compound Symmetry Correlation Structure
fitted.gnls
Extract gnls Fitted Values
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getCovariateFormula
Extract Covariates Formula
getResponse.gls
Extract gls Object Response
corMatrix.corStruct
Matrix of a corStruct Object
intervals.lmList
Confidence Intervals on lmList Coefficients
gnlsObject
Fitted gnls Object
formula.corStruct
Extract corStruct Object Formula
corClasses
Correlation Structure Classes
getVarCov
Extract variance-covariance matrix
formula.lmList
Extract lmList Object Formula
getGroups.varFunc
Extract varFunc Groups
getGroups.gls
Extract gls Object Groups
lme.lmList
LME fit from lmList Object
needUpdate
Check if Update is Needed
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
getCovariate.data.frame
Extract Data Frame Covariate
summary.gls
Summarize a gls Object
groupedData
Construct a groupedData Object
nlsList
List of nls Objects with a Common Model
formula.varFunc
Extract varFunc Formula
formula.reStruct
Extract reStruct Object Formula
getData.lmList
Extract lmList Object Data
intervals
Confidence Intervals on Coefficients
gnlsControl
Control Values for gnls Fit
nlme
Nonlinear Mixed-Effects Models
logDet.pdMat
Extract Log-Determinant from a pdMat Object
fitted.lme
Extract lme Fitted Values
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdClasses
Positive-Definite Matrix Classes
lmeControl
Control Values for lme Fit
nlmeObject
Fitted nlme Object
residuals.lme
Extract lme Residuals
Initialize.varFunc
Initialize varFunc Object
phenoModel
Model function for the Phenobarb data
pdDiag
Diagonal Positive-Definite Matrix
coef.corStruct
Coefficients of a corStruct Object
nlmeControl
Control Values for nlme Fit
getGroups.data.frame
Extract Groups from a Data Frame
logLik.glsStruct
Log-Likelihood of a glsStruct Object
formula.lme
Extract lme Object Formula
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdBlocked
Positive-Definite Block Diagonal Matrix
print.groupedData
Print a groupedData Object
print.modelStruct
Print a modelStruct Object
nlsList.selfStart
nlsList Fit from a selfStart Function
pairs.lme
Pairs Plot of an lme Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
print.summary.lme
Print a summary.lme Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
print.summary.pdMat
Print a summary.pdMat Object
simulate.lme
simulate lme models
summary.lme
Summarize an lme Object
plot.ranef.lmList
Plot a ranef.lmList Object
predict.lmList
Predictions from an lmList Object
fitted.lmList
Extract lmList Fitted Values
predict.lme
Predictions from an lme Object
pruneLevels
Prune Factor Levels
plot.augPred
Plot an augPred Object
Names.pdBlocked
Names of a pdBlocked Object
varClasses
Variance Function Classes
summary.varFunc
Summarize varFunc Object
print.summary.modelStruct
Print a summary.modelStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
varExp
Exponential Variance Function
lme
Linear Mixed-Effects Models
print.summary.gls
Print a summary.gls Object
logDet
Extract the Logarithm of the Determinant
varWeights.lmeStruct
Variance Weights for lmeStruct Object
quinModel
Model function for the Quinidine data
plot.gls
Plot a gls Object
print.summary.lmList
Print a summary.lmList Object
varFixed
Fixed Variance Function
print.anova.lme
Print an anova.lme Object
varPower
Power Variance Function
summary.corStruct
Summarize a corStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
print.corStruct
Print a corStruct Object
AIC
Akaike Information Criterion
solve.reStruct
Apply Solve to an reStruct Object
ACF
Autocorrelation Function
recalc.varFunc
Recalculate for varFunc Object
summary.lmList
Summarize an lmList Object
Coef
Assign Values to Coefficients
varIdent
Constant Variance Function
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
summary.nlsList
Summarize an nlsList Object
coef.varFunc
varFunc Object Coefficients
varComb
Combination of Variance Functions
glsStruct
Generalized Least Squares Structure
gnlsStruct
Generalized Nonlinear Least Squares Structure
fdHess
Finite difference Hessian
intervals.lme
Confidence Intervals on lme Parameters
formula.nlme
Extract nlme Object Formula
isBalanced
Check a Design for Balance
recalc
Recalculate Condensed Linear Model Object
getGroups.corStruct
Extract corStruct Groups
isInitialized
Check if Object is Initialized
getGroupsFormula
Extract Grouping Formula
gls
Fit Linear Model Using Generalized Least Squares
lme.groupedData
LME fit from groupedData Object
lmeObject
Fitted lme Object
logDet.corStruct
Extract corStruct Log-Determinant
AIC.lme
Akaike Information Criterion
logLik.corStruct
Extract corStruct Log-Likelihood
ACF.lme
Autocorrelation Function for lme Residuals
model.matrix.reStruct
reStruct Model Matrix
pairs.compareFits
Pairs Plot of compareFits Object
Initialize.lmeStruct
Initialize an lmeStruct Object
print.lmList
Print an lmList Object
pairs.lmList
Pairs Plot of an lmList Object
LDEsysMat
Generate system matrix for LDEs
Initialize.corStruct
Initialize corStruct Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
allCoef
Extract Coefficients from a Set of Objects
MEEM
EM iterations for mixed-effects
print.gls
Print a gls Object
coef.modelStruct
Extract modelStruct Object Coefficients
coef.pdIdent
pdIdent Object Coefficients
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
nlme.nlsList
NLME fit from nlsList Object
as.matrix.corStruct
Matrix of a corStruct Object
corMatrix
Extract Correlation Matrix
Matrix
Assign Matrix Values
augPred
Augmented Predictions
compareFits
Compare Fitted Objects
plot.compareFits
Plot a compareFits Object
Names.formula
Extract Names from a formula
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
predict.nlme
Predictions from an nlme Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
print.summary.corStruct
Print a summary.corStruct Object
corFactor
Factor of a Correlation Matrix
getGroups.lme
Extract lme Object Groups
getResponse
Extract Response Variable from an Object
glsControl
Control Values for gls Fit
logLik.gnls
Log-Likelihood of a gnls Object
lmeStruct
Linear Mixed-Effects Structure
logDet.reStruct
Extract reStruct Log-Determinants
logLik.gls
Log-Likelihood of a gls Object
logLik.varFunc
Extract varFunc logLik
pdNatural
General Positive-Definite Matrix in Natural Parametrization
getGroups
Extract Grouping Factors from an Object
plot.lme
Plot an lme or nls object
ranef.lme
Extract lme Random Effects
plot.intervals.lmList
Plot lmList Confidence Intervals
recalc.corStruct
Recalculate for corStruct Object
pdConstruct
Construct pdMat Objects
pooledSD
Extract Pooled Standard Deviation
Dim.corStruct
Dimensions of a corStruct Object
ranef.lmList
Extract lmList Random Effects
Covariate.varFunc
Assign varFunc Covariate
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Names
Names Associated with an Object
anova.gls
Compare Likelihoods of Fitted Objects
print.varFunc
Print a varFunc Object
summary.modelStruct
Summarize a modelStruct Object
Initialize
Initialize Object
Initialize.reStruct
Initialize reStruct Object
coef.lme
Extract lme Coefficients
coef.gnls
Extract gnls Coefficients
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
balancedGrouped
Create a groupedData object from a matrix
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
corRatio
Rational Quadratic Correlation Structure
formula.gls
Extract gls Object Formula
coef.lmList
Extract lmList Coefficients
collapse.groupedData
Collapse a groupedData Object
coef.pdCompSymm
pdCompSymm Object Coefficients
formula.gnls
Extract gnls Object Formula
fitted.glsStruct
Calculate glsStruct Fitted Values
glsObject
Fitted gls Object
corSpatial
Spatial Correlation Structure
formula.groupedData
Extract groupedData Formula
residuals.glsStruct
Calculate glsStruct Residuals
formula.pdMat
Extract pdMat Formula
predict.gls
Predictions from a gls Object
plot.ACF
Plot an ACF Object
getCovariate
Extract Covariate from an Object
getResponse.lmList
Extract lmList Object Response
getCovariate.varFunc
Extract varFunc Covariate
getResponseFormula
Extract Formula Specifying Response Variable
gnls
Fit Nonlinear Model Using Generalized Least Squares
lmList
List of lm Objects with a Common Model
pdMat
Positive-Definite Matrix
getData.gls
Extract gls Object Data
recalc.modelStruct
Recalculate for a modelStruct Object
formula.pdBlocked
Extract pdBlocked Formula
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
residuals.gls
Extract gls Residuals
print.reStruct
Print an reStruct Object
plot.lmList
Plot an lmList Object
print.lme
Print an lme Object
residuals.lmList
Extract lmList Residuals
Variogram.corExp
Calculate Semi-variogram for a corExp Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
summary.pdMat
Summarize a pdMat Object
varFunc
Variance Function Structure
Dim.pdMat
Dimensions of a pdMat Object
coef.gls
Extract gls Coefficients
Variogram
Calculate Semi-variogram
ACF.gls
Autocorrelation Function for gls Residuals
corFactor.corStruct
Factor of a corStruct Object Matrix
splitFormula
Split a Formula
fixef.lmList
Extract lmList Fixed Effects
formula.nlsList
Extract nlsList Object Formula
getData.lme
Extract lme Object Data
getResponse.data.frame
Extract Response from a Data Frame
isInitialized.reStruct
Check if an reStruct Object is Initialized
logLik.lme
Log-Likelihood of an lme Object
plot.nmGroupedData
Plot an nmGroupedData Object
Names.reStruct
Names of an reStruct Object
print.summary.varFunc
Print a summary.varFunc Object
random.effects
Extract Random Effects
corARMA
ARMA(p,q) Correlation Structure
corAR1
AR(1) Correlation Structure
getCovariate.corStruct
Extract corStruct Object Covariate
gsummary
Summarize by Groups
lmeScale
Scale for lme Optimization
Initialize.glsStruct
Initialize a glsStruct Object
contr.SAS
Contrast Matrices
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
nlmeStruct
Nonlinear Mixed-Effects Structure
coef.pdDiag
pdDiag Object Coefficients
pdSymm
General Positive-Definite Matrix
plot.Variogram
Plot a Variogram Object
print.pdMat
Print a pdMat Object
reStruct
Random Effects Structure
corGaus
Gaussian Correlation Structure
coef.pdMat
pdMat Object Coefficients
update.varFunc
Update varFunc Object
getData
Extract Data from an Object
lmList.groupedData
lmList Fit from a groupedData Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
gapply
Apply a Function by Groups
getResponse.lme
Extract lme Object Response
plot.ranef.lme
Plot a ranef.lme Object
intervals.gls
Confidence Intervals on gls Parameters
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
residuals.lmeStruct
Calculate lmeStruct Residuals
recalc.reStruct
Recalculate for an reStruct Object
nlme-internal
Internal nlme functions
update.modelStruct
Update a modelStruct Object
varConstPower
Constant Plus Power Variance Function
varWeights
Extract Variance Function Weights
corSymm
General Correlation Structure
BIC
Bayesian Information Criterion
Dim.corSpatial
Dimensions of a corSpatial Object
VarCorr
Extract variance and correlation components
getGroups.lmList
Extract lmList Object Groups
pdLogChol
General Positive-Definite Matrix
plot.nffGroupedData
Plot an nffGroupedData Object
predict.gnls
Predictions from a gnls Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
RatPupWeight
The weight of rat pups
PBG
Effect of Phenylbiguanide on Blood Pressure
Glucose
Glucose levels over time
Oxide
Variability in Semiconductor Manufacturing
Milk
Protein content of cows' milk
Tetracycline1
Pharmacokinetics of tetracycline
Wafer
Modeling of Analog MOS Circuits
Soybean
Growth of soybean plants
Phenobarb
Phenobarbitol Kinetics
Oxboys
Heights of Boys in Oxford
Ovary
Counts of Ovarian Follicles
Muscle
Contraction of heart muscle sections
BodyWeight
Rat weight over time for different diets
Oats
Split-plot Experiment on Varieties of Oats
Orthodont
Growth curve data on an orthdontic measurement
Fatigue
Cracks caused by metal fatigue
MathAchieve
Mathematics achievement scores
Pixel
X-ray pixel intensities over time
IGF
Radioimmunoassay of IGF-I Protein
Nitrendipene
Assay of nitrendipene
ergoStool
Ergometrics experiment with stool types
Tetracycline2
Pharmacokinetics of tetracycline
Earthquake
Earthquake Intensity
Assay
Bioassay on Cell Culture Plate
MathAchSchool
School demographic data for MathAchieve
Dialyzer
High-Flux Hemodialyzer
Relaxin
Assay for Relaxin
Glucose2
Glucose Levels Following Alcohol Ingestion
Quinidine
Quinidine Kinetics
Meat
Tenderness of meat
Rail
Evaluation of Stress in Railway Rails
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Wheat2
Wheat Yield Trials
Remifentanil
Pharmacokinetics of remifentanil
Cefamandole
Pharmacokinetics of Cefamandole
Wheat
Yields by growing conditions
Spruce
Growth of Spruce Trees
Machines
Productivity Scores for Machines and Workers
Gasoline
Refinery yield of gasoline
Gun
Methods for firing naval guns
bdf
Language scores