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nlme (version 3.1-19)
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
3.1-19
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-19)
Search all functions
Covariate
Assign Covariate Values
MEEM
EM iterations for mixed-effects
BIC
Bayesian Information Criterion
Names.pdMat
Names of a pdMat Object
as.matrix.pdMat
Matrix of a pdMat Object
Names.reStruct
Names of an reStruct Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
MEestimate
Estimate mixed-effects parameters
getCovariate.corStruct
Extract corStruct Object Covariate
corNatural
General correlation in natural parameterization
fitted.lmList
Extract lmList Fitted Values
formula.nlme
Extract nlme Object Formula
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
corClasses
Correlation Structure Classes
corFactor.corStruct
Factor of a corStruct Object Matrix
corMatrix.corStruct
Matrix of a corStruct Object
coef.reStruct
reStruct Object Coefficients
getCovariate.varFunc
Extract varFunc Covariate
corSpher
Spherical Correlation Structure
corExp
Exponential Correlation Structure
formula.modelStruct
Extract modelStruct Object Formula
getCovariate
Extract Covariate from an Object
anova.lme
Compare Likelihoods of Fitted Objects
VarCorr
Extract variance and correlation components
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
formula.corStruct
Extract corStruct Object Formula
logLik.lme
Log-Likelihood of an lme Object
fixef.lmList
Extract lmList Fixed Effects
formula.pdBlocked
Extract pdBlocked Formula
glsObject
Fitted gls Object
formula.reStruct
Extract reStruct Object Formula
getGroups.corStruct
Extract corStruct Groups
corLin
Linear Correlation Structure
getData.lme
Extract lme Object Data
getGroups.lmList
Extract lmList Object Groups
getData.gls
Extract gls Object Data
getData.lmList
Extract lmList Object Data
formula.lmList
Extract lmList Object Formula
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
AIC
Akaike Information Criterion
fitted.gnls
Extract gnls Fitted Values
corMatrix
Extract Correlation Matrix
as.matrix.reStruct
Matrices of an reStruct Object
fitted.gls
Extract gls Fitted Values
allCoef
Extract Coefficients from a Set of Objects
corFactor
Factor of a Correlation Matrix
augPred
Augmented Predictions
as.matrix.corStruct
Matrix of a corStruct Object
[.pdMat
Subscript a pdMat Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
Matrix.pdMat
Assign Matrix to a pdMat Object
collapse
Collapse According to Groups
Names
Names Associated with an Object
fixed.effects
Extract Fixed Effects
getResponse.lme
Extract lme Object Response
Variogram.corExp
Calculate Semi-variogram for a corExp Object
fixef.lme
Extract lme Fixed Effects
coef.modelStruct
Extract modelStruct Object Coefficients
Names.pdBlocked
Names of a pdBlocked Object
Variogram
Calculate Semi-variogram
getCovariateFormula
Extract Covariates Formula
gnlsObject
Fitted gnls Object
Dim
Extract Dimensions from an Object
print.lmList
Print an lmList Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
logLik.gnls
Log-Likelihood of a gnls Object
corRatio
Rational Quadratic Correlation Structure
Coef
Assign Values to Coefficients
initialize.corStruct
Initialize corStruct Object
comparePred
Compare Predictions
getGroups.gls
Extract gls Object Groups
glsControl
Control Values for gls Fit
getGroups.lme
Extract lme Object Groups
MEdecomp
Decompose a mixed-effects model
Variogram.default
Calculate Semi-variogram
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
nlmeControl
Control Values for nlme Fit
Covariate.varFunc
Assign varFunc Covariate
AIC.lme
Akaike Information Criterion
getResponse.gls
Extract gls Object Response
print.summary.corStruct
Print a summary.corStruct Object
formula.lme
Extract lme Object Formula
anova.gls
Compare Likelihoods of Fitted Objects
gapply
Apply a Function by Groups
BIC.logLik
BIC of a logLik Object
reStruct
Random Effects Structure
recalc
Recalculate Condensed Linear Model Object
residuals.gls
Extract gls Residuals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
recalc.corStruct
Recalculate for corStruct Object
print.summary.modelStruct
Print a summary.modelStruct Object
MEdims
Calculate dimensions in mixed-effects
Matrix.reStruct
Assign reStruct Matrices
model.matrix.reStruct
reStruct Model Matrix
summary.nlsList
Summarize an nlsList Object
ACF.gls
Autocorrelation Function for gls Residuals
getResponse.data.frame
Extract Response from a Data Frame
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corSpatial
Spatial Correlation Structure
coef.lme
Extract lme Coefficients
balancedGrouped
Create a groupedData object from a matrix
getResponseFormula
Extract Formula Specifying Response Variable
ACF
Autocorrelation Function
pdFactor
Square-Root Factor of a Positive-Definite Matrix
ranef.lme
Extract lme Random Effects
plot.augPred
Plot an augPred Object
getResponse
Extract Response Variable from an Object
corGaus
Gaussian Correlation Structure
plot.nfnGroupedData
Plot an nfnGroupedData Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
random.effects
Extract Random Effects
predict.gls
Predictions from a gls Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
compareFits
Compare Fitted Objects
pruneLevels
Prune Factor Levels
varComb
Combination of Variance Functions
formula.pdMat
Extract pdMat Formula
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
predict.gnls
Predictions from a gnls Object
print.groupedData
Print a groupedData Object
asTable
Convert groupedData to a matrix
pooledSD
Extract Pooled Standard Deviation
splitFormula
Split a Formula
print.pdMat
Print a pdMat Object
print.modelStruct
Print a modelStruct Object
plot.Variogram
Plot a Variogram Object
fitted.lme
Extract lme Fitted Values
update.modelStruct
Update a modelStruct Object
getGroups
Extract Grouping Factors from an Object
nlmeObject
Fitted nlme Object
fdHess
Finite difference Hessian
varClasses
Variance Function Classes
getGroups.varFunc
Extract varFunc Groups
plot.intervals.lmList
Plot lmList Confidence Intervals
nlsList.selfStart
nlsList Fit from a selfStart Function
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
print.summary.gls
Print a summary.gls Object
logLik.reStruct
Calculate reStruct Log-Likelihood
plot.compareFits
Plot a compareFits Object
varWeights.glsStruct
Variance Weights for glsStruct Object
varExp
Exponential Variance Function
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
initialize.glsStruct
Initialize a glsStruct Object
nlme
Nonlinear Mixed-Effects Models
gnlsControl
Control Values for gnls Fit
summary.pdMat
Summarize a pdMat Object
initialize.lmeStruct
Initialize an lmeStruct Object
update.gnls
Update a gnls Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.glsStruct
Calculate glsStruct Fitted Values
Dim.corSpatial
Dimensions of a corSpatial Object
initialize.reStruct
Initialize reStruct Object
pdDiag
Diagonal Positive-Definite Matrix
recalc.reStruct
Recalculate for an reStruct Object
lmeStruct
Linear Mixed-Effects Structure
update.lmList
Update an lmList Object
print.summary.lmList
Print a summary.lmList Object
print.gls
Print a gls Object
logLik.lmList
Log-Likelihood of an lmList Object
coef.pdCompSymm
pdCompSymm Object Coefficients
plot.ranef.lme
Plot a ranef.lme Object
residuals.lme
Extract lme Residuals
varFunc
Variance Function Structure
nlsList
List of nls Objects with a Common Model
lmeObject
Fitted lme Object
simulate.lme
simulate lme models
residuals.lmList
Extract lmList Residuals
coef.pdDiag
pdDiag Object Coefficients
update.nlme
Update an nlme Object
pdSymm
General Positive-Definite Matrix
pdNatural
General Positive-Definite Matrix in Natural Parametrization
qqnorm.gls
Normal Plot of Residuals from a gls Object
Dim.corStruct
Dimensions of a corStruct Object
ranef.lmList
Extract lmList Random Effects
pairs.compareFits
Pairs Plot of compareFits Object
intervals.lme
Confidence Intervals on lme Parameters
summary.gls
Summarize a gls Object
corCompSymm
Compound Symmetry Correlation Structure
print.corStruct
Print a corStruct Object
predict.nlme
Predictions from an nlme Object
plot.nmGroupedData
Plot an nmGroupedData Object
residuals.lmeStruct
Calculate lmeStruct Residuals
glsStruct
Generalized Least Squares Structure
plot.gls
Plot a gls Object
pairs.lmList
Pairs Plot of an lmList Object
logLik.varFunc
Extract varFunc logLik
plot.ranef.lmList
Plot a ranef.lmList Object
residuals.glsStruct
Calculate glsStruct Residuals
nlme.nlsList
NLME fit from nlsList Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
update.varFunc
Update varFunc Object
pdBlocked
Positive-Definite Block Diagonal Matrix
summary.lme
Summarize an lme Object
coef.pdIdent
pdIdent Object Coefficients
lme
Linear Mixed-Effects Models
summary.lmList
Summarize an lmList Object
print.varFunc
Print a varFunc Object
print.lme
Print an lme Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
recalc.modelStruct
Recalculate for a modelStruct Object
pdMat
Positive-Definite Matrix
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
intervals.gls
Confidence Intervals on gls Parameters
getResponse.lmList
Extract lmList Object Response
varIdent
Constant Variance Function
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
coef.pdMat
pdMat Object Coefficients
intervals.lmList
Confidence Intervals on lmList Coefficients
lmeScale
Scale for lme Optimization
gls
Fit Linear Model Using Generalized Least Squares
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdConstruct
Construct pdMat Objects
getGroupsFormula
Extract Grouping Formula
pdLogChol
General Positive-Definite Matrix
Names.formula
Extract Names from a formula
gnlsStruct
Generalized Nonlinear Least Squares Structure
solve.reStruct
Apply Solve to an reStruct Object
summary.modelStruct
Summarize a modelStruct Object
getData
Extract Data from an Object
needUpdate
Check if Update is Needed
formula.varFunc
Extract varFunc Formula
coef.corStruct
Coefficients of a corStruct Object
corAR1
AR(1) Correlation Structure
coef.gnls
Extract gnls Coefficients
corCAR1
Continuous AR(1) Correlation Structure
coef.lmList
Extract lmList Coefficients
print.reStruct
Print an reStruct Object
coef.varFunc
varFunc Object Coefficients
contr.SAS
Contrast Matrices
coef.gls
Extract gls Coefficients
print.anova.lme
Print an anova.lme Object
pdClasses
Positive-Definite Matrix Classes
varWeights
Extract Variance Function Weights
varPower
Power Variance Function
formula.groupedData
Extract groupedData Formula
varFixed
Fixed Variance Function
varWeights.lmeStruct
Variance Weights for lmeStruct Object
update.lme
Update an lme Object
formula.nlsList
Extract nlsList Object Formula
varConstPower
Constant Plus Power Variance Function
corSymm
General Correlation Structure
summary.varFunc
Summarize varFunc Object
update.gls
Update a gls Object
update.groupedData
Update a groupedData Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
collapse.groupedData
Collapse a groupedData Object
recalc.varFunc
Recalculate for varFunc Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
asOneFormula
Combine Formulas of a Set of Objects
print.summary.pdMat
Print a summary.pdMat Object
print.summary.varFunc
Print a summary.varFunc Object
print.summary.lme
Print a summary.lme Object
predict.lme
Predictions from an lme Object
predict.lmList
Predictions from an lmList Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
formula.gls
Extract gls Object Formula
summary.corStruct
Summarize a corStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
plot.lmList
Plot an lmList Object
plot.lme
Plot an lme Object
Dim.pdMat
Dimensions of a pdMat Object
formula.gnls
Extract gnls Object Formula
plot.ACF
Plot an ACF Object
update.nlsList
Update an nlsList Object
plot.nffGroupedData
Plot an nffGroupedData Object
corARMA
ARMA(p,q) Correlation Structure
gnls
Fit Nonlinear Model Using Generalized Least Squares
pairs.lme
Pairs Plot of an lme Object
ACF.lme
Autocorrelation Function for lme Residuals
getCovariate.data.frame
Extract Data Frame Covariate
Matrix
Assign Matrix Values
logLik.corStruct
Extract corStruct Log-Likelihood
logDet
Extract the Logarithm of the Determinant
lme.lmList
LME fit from lmList Object
isInitialized.reStruct
Check if an reStruct Object is Initialized
logDet.corStruct
Extract corStruct Log-Determinant
lmList
List of lm Objects with a Common Model
logDet.reStruct
Extract reStruct Log-Determinants
initialize.varFunc
Initialize varFunc Object
lmeControl
Control Values for lme Fit
logLik.gls
Log-Likelihood of a gls Object
isBalanced
Check a Design for Balance
initialize
Initialize Object
lme.groupedData
LME fit from groupedData Object
groupedData
Construct a groupedData Object
gsummary
Summarize by Groups
isInitialized
Check if Object is Initialized
logLik.glsStruct
Log-Likelihood of a glsStruct Object
lmList.groupedData
lmList Fit from a groupedData Object
intervals
Confidence Intervals on Coefficients
nlmeStruct
Nonlinear Mixed-Effects Structure
Earthquake
Earthquake Intensity
Gun
Methods for firing naval guns
Dialyzer
High-Flux Hemodialyzer
Ovary
Counts of Ovarian Follicles
Cefamandole
Pharmacokinetics of Cefamandole
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Fatigue
Cracks caused by metal fatigue
Gasoline
Refinery yield of gasoline
BodyWeight
Rat weight over time for different diets
Pixel
X-ray pixel intensities over time
Glucose
Glucose levels over time
PBG
Effect of Phenylbiguanide on Blood Pressure
Relaxin
Assay for Relaxin
Nitrendipene
Assay of nitrendipene
Assay
Bioassay on Cell Culture Plate
Rail
Evaluation of Stress in Railway Rails
RatPupWeight
The weight of rat pups
Oxide
Variability in Semiconductor Manufacturing
Machines
Productivity Scores for Machines and Workers
Soybean
Growth of soybean plants
Quinidine
Quinidine Kinetics
Orthodont
Growth curve data on an orthdontic measurement
MathAchSchool
School demographic data for MathAchieve
Wheat
Yields by growing conditions
Phenobarb
Phenobarbitol Kinetics
IGF
Radioimmunoassay of IGF-I Protein
MathAchieve
Mathematics achievement scores
Wheat2
Wheat Yield Trials
Glucose2
Glucose Levels Following Alcohol Ingestion
Meat
Tenderness of meat
Milk
Protein content of cows' milk
Tetracycline2
Pharmacokinetics of tetracycline
Wafer
Modeling of Analog MOS Circuits
Muscle
Contraction of heart muscle sections
ergoStool
Ergometrics experiment with stool types
Oxboys
Heights of Boys in Oxford
Spruce
Growth of Spruce Trees
Remifentanil
Pharmacokinetics of remifentanil
bdf
Language scores
Tetracycline1
Pharmacokinetics of tetracycline
Oats
Split-plot Experiment on Varieties of Oats