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nlme (version 3.1-66)
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
90,554
Version
3.1-66
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-66)
Search all functions
coef.lmList
Extract lmList Coefficients
coef.varFunc
varFunc Object Coefficients
pdBlocked
Positive-Definite Block Diagonal Matrix
Covariate.varFunc
Assign varFunc Covariate
plot.nmGroupedData
Plot an nmGroupedData Object
Matrix.reStruct
Assign reStruct Matrices
allCoef
Extract Coefficients from a Set of Objects
Matrix
Assign Matrix Values
asTable
Convert groupedData to a matrix
corARMA
ARMA(p,q) Correlation Structure
Covariate
Assign Covariate Values
balancedGrouped
Create a groupedData object from a matrix
Names
Names Associated with an Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
corExp
Exponential Correlation Structure
coef.gnls
Extract gnls Coefficients
getCovariate.data.frame
Extract Data Frame Covariate
formula.pdMat
Extract pdMat Formula
corFactor
Factor of a Correlation Matrix
corLin
Linear Correlation Structure
fixed.effects
Extract Fixed Effects
Variogram.corExp
Calculate Semi-variogram for a corExp Object
lmeControl
Control Values for lme Fit
BIC
Bayesian Information Criterion
getGroups.varFunc
Extract varFunc Groups
plot.ACF
Plot an ACF Object
Names.formula
Extract Names from a formula
coef.modelStruct
Extract modelStruct Object Coefficients
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
BIC.logLik
BIC of a logLik Object
corCompSymm
Compound Symmetry Correlation Structure
LDEsysMat
Generate system matrix for LDEs
Initialize
Initialize Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
Dim.corSpatial
Dimensions of a corSpatial Object
[.pdMat
Subscript a pdMat Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
Coef
Assign Values to Coefficients
Initialize.glsStruct
Initialize a glsStruct Object
logDet.corStruct
Extract corStruct Log-Determinant
pdConstruct.pdBlocked
Construct pdBlocked Objects
Names.pdBlocked
Names of a pdBlocked Object
corFactor.corStruct
Factor of a corStruct Object Matrix
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
compareFits
Compare Fitted Objects
Dim
Extract Dimensions from an Object
asOneFormula
Combine Formulas of a Set of Objects
ACF.gls
Autocorrelation Function for gls Residuals
corClasses
Correlation Structure Classes
Initialize.lmeStruct
Initialize an lmeStruct Object
getCovariateFormula
Extract Covariates Formula
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
VarCorr
Extract variance and correlation components
collapse.groupedData
Collapse a groupedData Object
Dim.pdMat
Dimensions of a pdMat Object
coef.reStruct
reStruct Object Coefficients
Names.pdMat
Names of a pdMat Object
corSpher
Spherical Correlation Structure
augPred
Augmented Predictions
Names.reStruct
Names of an reStruct Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
Initialize.corStruct
Initialize corStruct Object
fitted.glsStruct
Calculate glsStruct Fitted Values
getData.lme
Extract lme Object Data
ACF.lme
Autocorrelation Function for lme Residuals
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
corSymm
General Correlation Structure
corGaus
Gaussian Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
isBalanced
Check a Design for Balance
corMatrix.corStruct
Matrix of a corStruct Object
as.matrix.reStruct
Matrices of an reStruct Object
gapply
Apply a Function by Groups
getGroups.gls
Extract gls Object Groups
gls
Fit Linear Model Using Generalized Least Squares
getResponseFormula
Extract Formula Specifying Response Variable
getGroups
Extract Grouping Factors from an Object
getData
Extract Data from an Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
as.matrix.pdMat
Matrix of a pdMat Object
collapse
Collapse According to Groups
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
corNatural
General correlation in natural parameterization
pairs.lmList
Pairs Plot of an lmList Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
getCovariate
Extract Covariate from an Object
Dim.corStruct
Dimensions of a corStruct Object
Initialize.varFunc
Initialize varFunc Object
update.modelStruct
Update a modelStruct Object
anova.gls
Compare Likelihoods of Fitted Objects
coef.pdMat
pdMat Object Coefficients
Initialize.reStruct
Initialize reStruct Object
fixef.lmList
Extract lmList Fixed Effects
getGroups.corStruct
Extract corStruct Groups
fdHess
Finite difference Hessian
gnlsStruct
Generalized Nonlinear Least Squares Structure
plot.compareFits
Plot a compareFits Object
Variogram.default
Calculate Semi-variogram
gnls
Fit Nonlinear Model Using Generalized Least Squares
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
Variogram
Calculate Semi-variogram
getGroups.lme
Extract lme Object Groups
predict.gnls
Predictions from a gnls Object
print.varFunc
Print a varFunc Object
plot.lme
Plot an lme or nls object
residuals.lme
Extract lme Residuals
update.varFunc
Update varFunc Object
glsControl
Control Values for gls Fit
corMatrix
Extract Correlation Matrix
varExp
Exponential Variance Function
summary.pdMat
Summarize a pdMat Object
isInitialized
Check if Object is Initialized
residuals.glsStruct
Calculate glsStruct Residuals
anova.lme
Compare Likelihoods of Fitted Objects
summary.varFunc
Summarize varFunc Object
logLik.varFunc
Extract varFunc logLik
as.matrix.corStruct
Matrix of a corStruct Object
getResponse
Extract Response Variable from an Object
varClasses
Variance Function Classes
varFunc
Variance Function Structure
corAR1
AR(1) Correlation Structure
needUpdate
Check if Update is Needed
summary.nlsList
Summarize an nlsList Object
model.matrix.reStruct
reStruct Model Matrix
lmeScale
Scale for lme Optimization
reStruct
Random Effects Structure
getData.lmList
Extract lmList Object Data
getCovariate.corStruct
Extract corStruct Object Covariate
getGroupsFormula
Extract Grouping Formula
lme.groupedData
LME fit from groupedData Object
summary.lmList
Summarize an lmList Object
corCAR1
Continuous AR(1) Correlation Structure
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
pairs.compareFits
Pairs Plot of compareFits Object
gnlsControl
Control Values for gnls Fit
formula.reStruct
Extract reStruct Object Formula
gsummary
Summarize by Groups
varIdent
Constant Variance Function
lmeStruct
Linear Mixed-Effects Structure
comparePred
Compare Predictions
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
coef.corStruct
Coefficients of a corStruct Object
getData.gls
Extract gls Object Data
nlmeObject
Fitted nlme Object
nlmeControl
Control Values for nlme Fit
glsStruct
Generalized Least Squares Structure
fitted.lme
Extract lme Fitted Values
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
fitted.lmList
Extract lmList Fitted Values
intervals
Confidence Intervals on Coefficients
intervals.gls
Confidence Intervals on gls Parameters
phenoModel
Model function for the Phenobarb data
getGroups.data.frame
Extract Groups from a Data Frame
pdClasses
Positive-Definite Matrix Classes
corSpatial
Spatial Correlation Structure
lmList.groupedData
lmList Fit from a groupedData Object
corRatio
Rational Quadratic Correlation Structure
lmeObject
Fitted lme Object
pdMat
Positive-Definite Matrix
logLik.glsStruct
Log-Likelihood of a glsStruct Object
plot.lmList
Plot an lmList Object
varPower
Power Variance Function
lme
Linear Mixed-Effects Models
plot.gls
Plot a gls Object
pdConstruct
Construct pdMat Objects
gnlsObject
Fitted gnls Object
getCovariate.varFunc
Extract varFunc Covariate
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
intervals.lme
Confidence Intervals on lme Parameters
intervals.lmList
Confidence Intervals on lmList Coefficients
nlsList.selfStart
nlsList Fit from a selfStart Function
pdNatural
General Positive-Definite Matrix in Natural Parametrization
nlme.nlsList
NLME fit from nlsList Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
lme.lmList
LME fit from lmList Object
formula.pdBlocked
Extract pdBlocked Formula
groupedData
Construct a groupedData Object
nlme
Nonlinear Mixed-Effects Models
glsObject
Fitted gls Object
nlsList
List of nls Objects with a Common Model
predict.lme
Predictions from an lme Object
recalc
Recalculate Condensed Linear Model Object
simulate.lme
Simulate results from lme models
predict.nlme
Predictions from an nlme Object
logDet.reStruct
Extract reStruct Log-Determinants
qqnorm.gls
Normal Plot of Residuals from a gls Object
varWeights
Extract Variance Function Weights
pdFactor
Square-Root Factor of a Positive-Definite Matrix
getGroups.lmList
Extract lmList Object Groups
logLik.lmList
Log-Likelihood of an lmList Object
summary.gls
Summarize a gls Object
coef.lme
Extract lme Coefficients
plot.nffGroupedData
Plot an nffGroupedData Object
recalc.corStruct
Recalculate for corStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
pooledSD
Extract Pooled Standard Deviation
logLik.lme
Log-Likelihood of an lme Object
pairs.lme
Pairs Plot of an lme Object
getVarCov
Extract variance-covariance matrix
pdLogChol
General Positive-Definite Matrix
ACF
Autocorrelation Function
residuals.gls
Extract gls Residuals
logLik.corStruct
Extract corStruct Log-Likelihood
pdSymm
General Positive-Definite Matrix
summary.modelStruct
Summarize a modelStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
residuals.lmeStruct
Calculate lmeStruct Residuals
summary.corStruct
Summarize a corStruct Object
solve.reStruct
Apply Solve to an reStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.ranef.lmList
Plot a ranef.lmList Object
plot.Variogram
Plot a Variogram Object
plot.augPred
Plot an augPred Object
predict.gls
Predictions from a gls Object
print.summary.pdMat
Print a summary.pdMat Object
recalc.reStruct
Recalculate for an reStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
nlmeStruct
Nonlinear Mixed-Effects Structure
ranef.lmList
Extract lmList Random Effects
logLik.reStruct
Calculate reStruct Log-Likelihood
varFixed
Fixed Variance Function
splitFormula
Split a Formula
residuals.lmList
Extract lmList Residuals
plot.intervals.lmList
Plot lmList Confidence Intervals
ranef.lme
Extract lme Random Effects
random.effects
Extract Random Effects
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
varWeights.lmeStruct
Variance Weights for lmeStruct Object
predict.lmList
Predictions from an lmList Object
quinModel
Model function for the Quinidine data
varConstPower
Constant Plus Power Variance Function
plot.ranef.lme
Plot a ranef.lme Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
summary.lme
Summarize an lme Object
recalc.varFunc
Recalculate for varFunc Object
lmList
List of lm Objects with a Common Model
Matrix.pdMat
Assign Matrix to a pdMat Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
logDet
Extract the Logarithm of the Determinant
pdDiag
Diagonal Positive-Definite Matrix
varComb
Combination of Variance Functions
varWeights.glsStruct
Variance Weights for glsStruct Object
MathAchSchool
School demographic data for MathAchieve
Oxboys
Heights of Boys in Oxford
Fatigue
Cracks caused by metal fatigue
Dialyzer
High-Flux Hemodialyzer
MathAchieve
Mathematics achievement scores
Glucose
Glucose levels over time
bdf
Language scores
Glucose2
Glucose Levels Following Alcohol Ingestion
Rail
Evaluation of Stress in Railway Rails
Tetracycline1
Pharmacokinetics of tetracycline
Nitrendipene
Assay of nitrendipene
Meat
Tenderness of meat
Wafer
Modeling of Analog MOS Circuits
Soybean
Growth of soybean plants
Orthodont
Growth curve data on an orthdontic measurement
Assay
Bioassay on Cell Culture Plate
Remifentanil
Pharmacokinetics of remifentanil
Ovary
Counts of Ovarian Follicles
Muscle
Contraction of heart muscle sections
Pixel
X-ray pixel intensities over time
ergoStool
Ergometrics experiment with stool types
Relaxin
Assay for Relaxin
Earthquake
Earthquake Intensity
Oxide
Variability in Semiconductor Manufacturing
PBG
Effect of Phenylbiguanide on Blood Pressure
Tetracycline2
Pharmacokinetics of tetracycline
Oats
Split-plot Experiment on Varieties of Oats
Gasoline
Refinery yield of gasoline
Machines
Productivity Scores for Machines and Workers
Spruce
Growth of Spruce Trees
Wheat2
Wheat Yield Trials
Phenobarb
Phenobarbitol Kinetics
RatPupWeight
The weight of rat pups
Cefamandole
Pharmacokinetics of Cefamandole
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Milk
Protein content of cows' milk
Quinidine
Quinidine Kinetics
IGF
Radioimmunoassay of IGF-I Protein
Wheat
Yields by growing conditions
BodyWeight
Rat weight over time for different diets
Gun
Methods for firing naval guns