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nlme (version 3.1-50)
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
93,277
Version
3.1-50
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-50)
Search all functions
getResponse
Extract Response Variable from an Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
Covariate
Assign Covariate Values
summary.varFunc
Summarize varFunc Object
summary.lmList
Summarize an lmList Object
Initialize
Initialize Object
LDEsysMat
Generate system matrix for LDEs
fitted.glsStruct
Calculate glsStruct Fitted Values
Variogram.default
Calculate Semi-variogram
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
compareFits
Compare Fitted Objects
corARMA
ARMA(p,q) Correlation Structure
coef.pdMat
pdMat Object Coefficients
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
getCovariate.data.frame
Extract Data Frame Covariate
getData.lme
Extract lme Object Data
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getGroupsFormula
Extract Grouping Formula
getResponseFormula
Extract Formula Specifying Response Variable
lmList
List of lm Objects with a Common Model
lme.groupedData
LME fit from groupedData Object
logDet.corStruct
Extract corStruct Log-Determinant
intervals.lme
Confidence Intervals on lme Parameters
logLik.lmList
Log-Likelihood of an lmList Object
needUpdate
Check if Update is Needed
pdMat
Positive-Definite Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.compareFits
Plot a compareFits Object
plot.lmList
Plot an lmList Object
plot.nmGroupedData
Plot an nmGroupedData Object
residuals.glsStruct
Calculate glsStruct Residuals
residuals.lmList
Extract lmList Residuals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
summary.corStruct
Summarize a corStruct Object
varClasses
Variance Function Classes
varFunc
Variance Function Structure
varConstPower
Constant Plus Power Variance Function
ranef.lmList
Extract lmList Random Effects
ACF
Autocorrelation Function
Dim.corSpatial
Dimensions of a corSpatial Object
Coef
Assign Values to Coefficients
Initialize.lmeStruct
Initialize an lmeStruct Object
Matrix.pdMat
Assign Matrix to a pdMat Object
ACF.lme
Autocorrelation Function for lme Residuals
Covariate.varFunc
Assign varFunc Covariate
Names.formula
Extract Names from a formula
Matrix
Assign Matrix Values
Dim
Extract Dimensions from an Object
BIC
Bayesian Information Criterion
Dim.pdMat
Dimensions of a pdMat Object
Matrix.reStruct
Assign reStruct Matrices
Names.pdMat
Names of a pdMat Object
coef.varFunc
varFunc Object Coefficients
corGaus
Gaussian Correlation Structure
VarCorr
Extract variance and correlation components
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
corMatrix.corStruct
Matrix of a corStruct Object
Initialize.varFunc
Initialize varFunc Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
balancedGrouped
Create a groupedData object from a matrix
gapply
Apply a Function by Groups
formula.reStruct
Extract reStruct Object Formula
Initialize.reStruct
Initialize reStruct Object
BIC.logLik
BIC of a logLik Object
ACF.gls
Autocorrelation Function for gls Residuals
corSpher
Spherical Correlation Structure
Initialize.corStruct
Initialize corStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
isBalanced
Check a Design for Balance
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
[.pdMat
Subscript a pdMat Object
getGroups.gls
Extract gls Object Groups
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Variogram
Calculate Semi-variogram
getCovariate
Extract Covariate from an Object
Names.pdBlocked
Names of a pdBlocked Object
anova.gls
Compare Likelihoods of Fitted Objects
Names
Names Associated with an Object
getGroups.varFunc
Extract varFunc Groups
getData.gls
Extract gls Object Data
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
contr.SAS
Contrast Matrices
gnlsObject
Fitted gnls Object
glsStruct
Generalized Least Squares Structure
getGroups.corStruct
Extract corStruct Groups
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
fixed.effects
Extract Fixed Effects
collapse.groupedData
Collapse a groupedData Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
model.matrix.reStruct
reStruct Model Matrix
pdConstruct.pdBlocked
Construct pdBlocked Objects
as.matrix.corStruct
Matrix of a corStruct Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pairs.lmList
Pairs Plot of an lmList Object
coef.modelStruct
Extract modelStruct Object Coefficients
Initialize.glsStruct
Initialize a glsStruct Object
getCovariate.corStruct
Extract corStruct Object Covariate
corClasses
Correlation Structure Classes
pdNatural
General Positive-Definite Matrix in Natural Parametrization
Dim.corStruct
Dimensions of a corStruct Object
getGroups.lme
Extract lme Object Groups
asOneFormula
Combine Formulas of a Set of Objects
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
augPred
Augmented Predictions
corCAR1
Continuous AR(1) Correlation Structure
groupedData
Construct a groupedData Object
coef.reStruct
reStruct Object Coefficients
coef.lmList
Extract lmList Coefficients
Names.reStruct
Names of an reStruct Object
fdHess
Finite difference Hessian
getVarCov
Extract variance-covariance matrix
corCompSymm
Compound Symmetry Correlation Structure
splitFormula
Split a Formula
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
allCoef
Extract Coefficients from a Set of Objects
glsControl
Control Values for gls Fit
corNatural
General correlation in natural parameterization
lmList.groupedData
lmList Fit from a groupedData Object
corMatrix
Extract Correlation Matrix
predict.nlme
Predictions from an nlme Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
formula.pdMat
Extract pdMat Formula
coef.corStruct
Coefficients of a corStruct Object
logDet
Extract the Logarithm of the Determinant
as.matrix.reStruct
Matrices of an reStruct Object
as.matrix.pdMat
Matrix of a pdMat Object
asTable
Convert groupedData to a matrix
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
nlmeObject
Fitted nlme Object
pdBlocked
Positive-Definite Block Diagonal Matrix
recalc
Recalculate Condensed Linear Model Object
fitted.lme
Extract lme Fitted Values
gnlsControl
Control Values for gnls Fit
getGroups
Extract Grouping Factors from an Object
corRatio
Rational Quadratic Correlation Structure
plot.intervals.lmList
Plot lmList Confidence Intervals
coef.gnls
Extract gnls Coefficients
corExp
Exponential Correlation Structure
getCovariateFormula
Extract Covariates Formula
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
coef.lme
Extract lme Coefficients
formula.pdBlocked
Extract pdBlocked Formula
isInitialized
Check if Object is Initialized
fitted.lmList
Extract lmList Fitted Values
nlsList.selfStart
nlsList Fit from a selfStart Function
anova.lme
Compare Likelihoods of Fitted Objects
corSymm
General Correlation Structure
nlsList
List of nls Objects with a Common Model
corAR1
AR(1) Correlation Structure
logLik.lme
Log-Likelihood of an lme Object
corFactor
Factor of a Correlation Matrix
collapse
Collapse According to Groups
gnlsStruct
Generalized Nonlinear Least Squares Structure
pdFactor
Square-Root Factor of a Positive-Definite Matrix
lmeStruct
Linear Mixed-Effects Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
recalc.corStruct
Recalculate for corStruct Object
residuals.lme
Extract lme Residuals
logLik.varFunc
Extract varFunc logLik
summary.lme
Summarize an lme Object
nlme.nlsList
NLME fit from nlsList Object
nlmeStruct
Nonlinear Mixed-Effects Structure
pdLogChol
General Positive-Definite Matrix
intervals
Confidence Intervals on Coefficients
glsObject
Fitted gls Object
getData.lmList
Extract lmList Object Data
recalc.reStruct
Recalculate for an reStruct Object
comparePred
Compare Predictions
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
plot.gls
Plot a gls Object
nlmeControl
Control Values for nlme Fit
lmeScale
Scale for lme Optimization
gsummary
Summarize by Groups
residuals.lmeStruct
Calculate lmeStruct Residuals
print.varFunc
Print a varFunc Object
fixef.lmList
Extract lmList Fixed Effects
getData
Extract Data from an Object
recalc.varFunc
Recalculate for varFunc Object
corLin
Linear Correlation Structure
pairs.compareFits
Pairs Plot of compareFits Object
simulate.lme
simulate lme models
lme
Linear Mixed-Effects Models
summary.nlsList
Summarize an nlsList Object
pdClasses
Positive-Definite Matrix Classes
varIdent
Constant Variance Function
pdSymm
General Positive-Definite Matrix
getCovariate.varFunc
Extract varFunc Covariate
corSpatial
Spatial Correlation Structure
getGroups.lmList
Extract lmList Object Groups
gnls
Fit Nonlinear Model Using Generalized Least Squares
summary.gls
Summarize a gls Object
logLik.reStruct
Calculate reStruct Log-Likelihood
plot.Variogram
Plot a Variogram Object
plot.augPred
Plot an augPred Object
intervals.gls
Confidence Intervals on gls Parameters
intervals.lmList
Confidence Intervals on lmList Coefficients
lmeControl
Control Values for lme Fit
update.modelStruct
Update a modelStruct Object
varExp
Exponential Variance Function
predict.lmList
Predictions from an lmList Object
plot.ranef.lmList
Plot a ranef.lmList Object
plot.ACF
Plot an ACF Object
predict.gls
Predictions from a gls Object
varWeights.glsStruct
Variance Weights for glsStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
summary.pdMat
Summarize a pdMat Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
plot.ranef.lme
Plot a ranef.lme Object
varComb
Combination of Variance Functions
predict.gnls
Predictions from a gnls Object
plot.lme
Plot an lme or nls object
gls
Fit Linear Model Using Generalized Least Squares
logDet.reStruct
Extract reStruct Log-Determinants
residuals.gnlsStruct
Calculate gnlsStruct Residuals
lme.lmList
LME fit from lmList Object
lmeObject
Fitted lme Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.gnls
Log-Likelihood of a gnls Object
pairs.lme
Pairs Plot of an lme Object
ranef.lme
Extract lme Random Effects
update.varFunc
Update varFunc Object
pdDiag
Diagonal Positive-Definite Matrix
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdConstruct
Construct pdMat Objects
solve.reStruct
Apply Solve to an reStruct Object
varFixed
Fixed Variance Function
predict.lme
Predictions from an lme Object
logLik.corStruct
Extract corStruct Log-Likelihood
summary.modelStruct
Summarize a modelStruct Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
nlme
Nonlinear Mixed-Effects Models
phenoModel
Model function for the Phenobarb data
plot.nfnGroupedData
Plot an nfnGroupedData Object
reStruct
Random Effects Structure
random.effects
Extract Random Effects
pooledSD
Extract Pooled Standard Deviation
quinModel
Model function for the Quinidine data
residuals.gls
Extract gls Residuals
varPower
Power Variance Function
varWeights
Extract Variance Function Weights
print.summary.pdMat
Print a summary.pdMat Object
recalc.modelStruct
Recalculate for a modelStruct Object
Earthquake
Earthquake Intensity
Glucose
Glucose levels over time
BodyWeight
Rat weight over time for different diets
Dialyzer
High-Flux Hemodialyzer
MathAchSchool
School demographic data for MathAchieve
Quinidine
Quinidine Kinetics
Oats
Split-plot Experiment on Varieties of Oats
Pixel
X-ray pixel intensities over time
Tetracycline2
Pharmacokinetics of tetracycline
Wafer
Modeling of Analog MOS Circuits
Glucose2
Glucose Levels Following Alcohol Ingestion
Nitrendipene
Assay of nitrendipene
Muscle
Contraction of heart muscle sections
Remifentanil
Pharmacokinetics of remifentanil
Milk
Protein content of cows' milk
Oxboys
Heights of Boys in Oxford
RatPupWeight
The weight of rat pups
MathAchieve
Mathematics achievement scores
Orthodont
Growth curve data on an orthdontic measurement
Ovary
Counts of Ovarian Follicles
Wheat
Yields by growing conditions
Tetracycline1
Pharmacokinetics of tetracycline
Assay
Bioassay on Cell Culture Plate
Rail
Evaluation of Stress in Railway Rails
PBG
Effect of Phenylbiguanide on Blood Pressure
Gun
Methods for firing naval guns
Meat
Tenderness of meat
Soybean
Growth of soybean plants
IGF
Radioimmunoassay of IGF-I Protein
Oxide
Variability in Semiconductor Manufacturing
Cefamandole
Pharmacokinetics of Cefamandole
Wheat2
Wheat Yield Trials
bdf
Language scores
Gasoline
Refinery yield of gasoline
Phenobarb
Phenobarbitol Kinetics
ergoStool
Ergometrics experiment with stool types
Relaxin
Assay for Relaxin
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Fatigue
Cracks caused by metal fatigue
Spruce
Growth of Spruce Trees
Machines
Productivity Scores for Machines and Workers