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nlme (version 3.1-80)
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
84,769
Version
3.1-80
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-80)
Search all functions
Covariate
Assign Covariate Values
Initialize.glsStruct
Initialize a glsStruct Object
Initialize.varFunc
Initialize varFunc Object
Covariate.varFunc
Assign varFunc Covariate
ACF.lme
Autocorrelation Function for lme Residuals
BIC
Bayesian Information Criterion
Coef
Assign Values to Coefficients
[.pdMat
Subscript a pdMat Object
Names
Names Associated with an Object
Variogram.default
Calculate Semi-variogram
Matrix.pdMat
Assign Matrix to a pdMat Object
Matrix.reStruct
Assign reStruct Matrices
corClasses
Correlation Structure Classes
LDEsysMat
Generate system matrix for LDEs
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
Matrix
Assign Matrix Values
formula.pdMat
Extract pdMat Formula
predict.gnls
Predictions from a gnls Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
collapse
Collapse According to Groups
varExp
Exponential Variance Function
update.varFunc
Update varFunc Object
varWeights.glsStruct
Variance Weights for glsStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
intervals.lmList
Confidence Intervals on lmList Coefficients
summary.varFunc
Summarize varFunc Object
predict.lme
Predictions from an lme Object
intervals.gls
Confidence Intervals on gls Parameters
summary.nlsList
Summarize an nlsList Object
Dim.pdMat
Dimensions of a pdMat Object
asOneFormula
Combine Formulas of a Set of Objects
lme.lmList
LME fit from lmList Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Dim
Extract Dimensions from an Object
ACF
Autocorrelation Function
corNatural
General correlation in natural parameterization
Dim.corSpatial
Dimensions of a corSpatial Object
coef.pdMat
pdMat Object Coefficients
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
Names.pdBlocked
Names of a pdBlocked Object
random.effects
Extract Random Effects
Names.reStruct
Names of an reStruct Object
asTable
Convert groupedData to a matrix
compareFits
Compare Fitted Objects
as.matrix.pdMat
Matrix of a pdMat Object
coef.gnls
Extract gnls Coefficients
corAR1
AR(1) Correlation Structure
varWeights.lmeStruct
Variance Weights for lmeStruct Object
fixef.lmList
Extract lmList Fixed Effects
splitFormula
Split a Formula
fitted.lmList
Extract lmList Fitted Values
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Names.pdMat
Names of a pdMat Object
corExp
Exponential Correlation Structure
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.lme
Extract lme Fitted Values
fdHess
Finite difference Hessian
corCAR1
Continuous AR(1) Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
fixed.effects
Extract Fixed Effects
getGroupsFormula
Extract Grouping Formula
getResponse
Extract Response Variable from an Object
Names.formula
Extract Names from a formula
getGroups.lmList
Extract lmList Object Groups
predict.nlme
Predictions from an nlme Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram
Calculate Semi-variogram
summary.pdMat
Summarize a pdMat Object
getData.gls
Extract gls Object Data
varPower
Power Variance Function
getGroups.data.frame
Extract Groups from a Data Frame
getGroups.gls
Extract gls Object Groups
corSymm
General Correlation Structure
Initialize.corStruct
Initialize corStruct Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
residuals.glsStruct
Calculate glsStruct Residuals
getCovariate.data.frame
Extract Data Frame Covariate
varFixed
Fixed Variance Function
as.matrix.corStruct
Matrix of a corStruct Object
Initialize.reStruct
Initialize reStruct Object
residuals.lmList
Extract lmList Residuals
formula.reStruct
Extract reStruct Object Formula
intervals
Confidence Intervals on Coefficients
ACF.gls
Autocorrelation Function for gls Residuals
getGroups.lme
Extract lme Object Groups
pooledSD
Extract Pooled Standard Deviation
ranef.lmList
Extract lmList Random Effects
plot.ranef.lme
Plot a ranef.lme Object
corFactor.corStruct
Factor of a corStruct Object Matrix
pdSymm
General Positive-Definite Matrix
gnlsStruct
Generalized Nonlinear Least Squares Structure
logLik.varFunc
Extract varFunc logLik
augPred
Augmented Predictions
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
coef.lmList
Extract lmList Coefficients
corFactor
Factor of a Correlation Matrix
logLik.lme
Log-Likelihood of an lme Object
recalc.varFunc
Recalculate for varFunc Object
residuals.lmeStruct
Calculate lmeStruct Residuals
varConstPower
Constant Plus Power Variance Function
reStruct
Random Effects Structure
lmList
List of lm Objects with a Common Model
gnls
Fit Nonlinear Model Using Generalized Least Squares
allCoef
Extract Coefficients from a Set of Objects
recalc.reStruct
Recalculate for an reStruct Object
solve.reStruct
Apply Solve to an reStruct Object
lmeControl
Control Values for lme Fit
update.modelStruct
Update a modelStruct Object
summary.corStruct
Summarize a corStruct Object
print.summary.pdMat
Print a summary.pdMat Object
VarCorr
Extract variance and correlation components
getCovariate
Extract Covariate from an Object
logLik.lmList
Log-Likelihood of an lmList Object
corLin
Linear Correlation Structure
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
getData
Extract Data from an Object
corARMA
ARMA(p,q) Correlation Structure
groupedData
Construct a groupedData Object
corMatrix.corStruct
Matrix of a corStruct Object
getData.lme
Extract lme Object Data
getCovariate.corStruct
Extract corStruct Object Covariate
summary.lmList
Summarize an lmList Object
residuals.gls
Extract gls Residuals
predict.lmList
Predictions from an lmList Object
summary.gls
Summarize a gls Object
ranef.lme
Extract lme Random Effects
Initialize.lmeStruct
Initialize an lmeStruct Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
recalc
Recalculate Condensed Linear Model Object
varIdent
Constant Variance Function
coef.corStruct
Coefficients of a corStruct Object
comparePred
Compare Predictions
nlsList.selfStart
nlsList Fit from a selfStart Function
recalc.corStruct
Recalculate for corStruct Object
residuals.lme
Extract lme Residuals
glsControl
Control Values for gls Fit
plot.nffGroupedData
Plot an nffGroupedData Object
lme.groupedData
LME fit from groupedData Object
getData.lmList
Extract lmList Object Data
summary.modelStruct
Summarize a modelStruct Object
simulate.lme
Simulate results from lme models
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
balancedGrouped
Create a groupedData object from a matrix
getVarCov
Extract variance-covariance matrix
gapply
Apply a Function by Groups
fitted.glsStruct
Calculate glsStruct Fitted Values
getGroups.corStruct
Extract corStruct Groups
coef.reStruct
reStruct Object Coefficients
Dim.corStruct
Dimensions of a corStruct Object
coef.lme
Extract lme Coefficients
getResponseFormula
Extract Formula Specifying Response Variable
needUpdate
Check if Update is Needed
intervals.lme
Confidence Intervals on lme Parameters
collapse.groupedData
Collapse a groupedData Object
corSpatial
Spatial Correlation Structure
pdNatural
General Positive-Definite Matrix in Natural Parametrization
corGaus
Gaussian Correlation Structure
pdConstruct
Construct pdMat Objects
getGroups
Extract Grouping Factors from an Object
lmeScale
Scale for lme Optimization
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
print.varFunc
Print a varFunc Object
glsStruct
Generalized Least Squares Structure
Initialize
Initialize Object
gls
Fit Linear Model Using Generalized Least Squares
coef.modelStruct
Extract modelStruct Object Coefficients
pdDiag
Diagonal Positive-Definite Matrix
logLik.glsStruct
Log-Likelihood of a glsStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
corSpher
Spherical Correlation Structure
getGroups.varFunc
Extract varFunc Groups
plot.augPred
Plot an augPred Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdMat
Positive-Definite Matrix
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
logLik.reStruct
Calculate reStruct Log-Likelihood
nlmeStruct
Nonlinear Mixed-Effects Structure
phenoModel
Model function for the Phenobarb data
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
coef.varFunc
varFunc Object Coefficients
pairs.lme
Pairs Plot of an lme Object
gsummary
Summarize by Groups
anova.gls
Compare Likelihoods of Fitted Objects
anova.lme
Compare Likelihoods of Fitted Objects
lme
Linear Mixed-Effects Models
summary.lme
Summarize an lme Object
nlmeControl
Control Values for nlme Fit
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
getCovariateFormula
Extract Covariates Formula
logLik.gnls
Log-Likelihood of a gnls Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
pdConstruct.pdBlocked
Construct pdBlocked Objects
plot.lme
Plot an lme or nls object
pdClasses
Positive-Definite Matrix Classes
varWeights
Extract Variance Function Weights
predict.gls
Predictions from a gls Object
glsObject
Fitted gls Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
plot.intervals.lmList
Plot lmList Confidence Intervals
nlmeObject
Fitted nlme Object
logDet.reStruct
Extract reStruct Log-Determinants
corMatrix
Extract Correlation Matrix
plot.ranef.lmList
Plot a ranef.lmList Object
gnlsObject
Fitted gnls Object
varFunc
Variance Function Structure
corRatio
Rational Quadratic Correlation Structure
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
isBalanced
Check a Design for Balance
corCompSymm
Compound Symmetry Correlation Structure
nlme.nlsList
NLME fit from nlsList Object
logDet.corStruct
Extract corStruct Log-Determinant
varComb
Combination of Variance Functions
lmeObject
Fitted lme Object
nlme
Nonlinear Mixed-Effects Models
isInitialized
Check if Object is Initialized
plot.nmGroupedData
Plot an nmGroupedData Object
formula.pdBlocked
Extract pdBlocked Formula
BIC.logLik
BIC of a logLik Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
lmeStruct
Linear Mixed-Effects Structure
varClasses
Variance Function Classes
getCovariate.varFunc
Extract varFunc Covariate
as.matrix.reStruct
Matrices of an reStruct Object
model.matrix.reStruct
reStruct Model Matrix
nlsList
List of nls Objects with a Common Model
quinModel
Model function for the Quinidine data
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdBlocked
Positive-Definite Block Diagonal Matrix
pairs.lmList
Pairs Plot of an lmList Object
logDet
Extract the Logarithm of the Determinant
gnlsControl
Control Values for gnls Fit
logLik.corStruct
Extract corStruct Log-Likelihood
lmList.groupedData
lmList Fit from a groupedData Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdLogChol
General Positive-Definite Matrix
plot.lmList
Plot an lmList Object
pairs.compareFits
Pairs Plot of compareFits Object
plot.ACF
Plot an ACF Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
plot.compareFits
Plot a compareFits Object
plot.gls
Plot a gls Object
plot.Variogram
Plot a Variogram Object
BodyWeight
Rat weight over time for different diets
Gun
Methods for firing naval guns
Glucose
Glucose levels over time
Cefamandole
Pharmacokinetics of Cefamandole
Earthquake
Earthquake Intensity
Glucose2
Glucose Levels Following Alcohol Ingestion
Milk
Protein content of cows' milk
Dialyzer
High-Flux Hemodialyzer
Assay
Bioassay on Cell Culture Plate
Fatigue
Cracks caused by metal fatigue
Phenobarb
Phenobarbitol Kinetics
MathAchieve
Mathematics achievement scores
Tetracycline1
Pharmacokinetics of tetracycline
Tetracycline2
Pharmacokinetics of tetracycline
Spruce
Growth of Spruce Trees
Rail
Evaluation of Stress in Railway Rails
Machines
Productivity Scores for Machines and Workers
Wafer
Modeling of Analog MOS Circuits
Remifentanil
Pharmacokinetics of remifentanil
Relaxin
Assay for Relaxin
PBG
Effect of Phenylbiguanide on Blood Pressure
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Muscle
Contraction of heart muscle sections
Soybean
Growth of soybean plants
Pixel
X-ray pixel intensities over time
Orthodont
Growth curve data on an orthdontic measurement
Oxboys
Heights of Boys in Oxford
IGF
Radioimmunoassay of IGF-I Protein
Oxide
Variability in Semiconductor Manufacturing
Nitrendipene
Assay of nitrendipene
Quinidine
Quinidine Kinetics
bdf
Language scores
ergoStool
Ergometrics experiment with stool types
MathAchSchool
School demographic data for MathAchieve
Oats
Split-plot Experiment on Varieties of Oats
Wheat2
Wheat Yield Trials
Gasoline
Refinery yield of gasoline
Meat
Tenderness of meat
Wheat
Yields by growing conditions
RatPupWeight
The weight of rat pups
Ovary
Counts of Ovarian Follicles