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nlme (version 3.1-82)
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
62,596
Version
3.1-82
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-82)
Search all functions
logDet
Extract the Logarithm of the Determinant
collapse
Collapse According to Groups
glsObject
Fitted gls Object
BIC.logLik
BIC of a logLik Object
ACF.lme
Autocorrelation Function for lme Residuals
Coef
Assign Values to Coefficients
Names
Names Associated with an Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Names.pdMat
Names of a pdMat Object
LDEsysMat
Generate system matrix for LDEs
asOneFormula
Combine Formulas of a Set of Objects
as.matrix.reStruct
Matrices of an reStruct Object
coef.lme
Extract lme Coefficients
as.matrix.pdMat
Matrix of a pdMat Object
VarCorr
Extract variance and correlation components
balancedGrouped
Create a groupedData object from a matrix
Initialize.glsStruct
Initialize a glsStruct Object
coef.reStruct
reStruct Object Coefficients
[.pdMat
Subscript a pdMat Object
augPred
Augmented Predictions
allCoef
Extract Coefficients from a Set of Objects
as.matrix.corStruct
Matrix of a corStruct Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
plot.augPred
Plot an augPred Object
random.effects
Extract Random Effects
fitted.glsStruct
Calculate glsStruct Fitted Values
Covariate
Assign Covariate Values
corRatio
Rational Quadratic Correlation Structure
pdBlocked
Positive-Definite Block Diagonal Matrix
lmeObject
Fitted lme Object
Dim.pdMat
Dimensions of a pdMat Object
ACF
Autocorrelation Function
reStruct
Random Effects Structure
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
corMatrix
Extract Correlation Matrix
Initialize
Initialize Object
Matrix
Assign Matrix Values
plot.compareFits
Plot a compareFits Object
Covariate.varFunc
Assign varFunc Covariate
Matrix.pdMat
Assign Matrix to a pdMat Object
getGroupsFormula
Extract Grouping Formula
varComb
Combination of Variance Functions
Dim
Extract Dimensions from an Object
Initialize.varFunc
Initialize varFunc Object
plot.nffGroupedData
Plot an nffGroupedData Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
summary.pdMat
Summarize a pdMat Object
Initialize.lmeStruct
Initialize an lmeStruct Object
getData.lmList
Extract lmList Object Data
corFactor.corStruct
Factor of a corStruct Object Matrix
pdConstruct
Construct pdMat Objects
corFactor
Factor of a Correlation Matrix
Initialize.reStruct
Initialize reStruct Object
coef.modelStruct
Extract modelStruct Object Coefficients
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
ACF.gls
Autocorrelation Function for gls Residuals
residuals.gls
Extract gls Residuals
varWeights.lmeStruct
Variance Weights for lmeStruct Object
collapse.groupedData
Collapse a groupedData Object
splitFormula
Split a Formula
Matrix.reStruct
Assign reStruct Matrices
corARMA
ARMA(p,q) Correlation Structure
summary.corStruct
Summarize a corStruct Object
getGroups
Extract Grouping Factors from an Object
getGroups.corStruct
Extract corStruct Groups
getGroups.varFunc
Extract varFunc Groups
coef.varFunc
varFunc Object Coefficients
Names.reStruct
Names of an reStruct Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Dim.corSpatial
Dimensions of a corSpatial Object
BIC
Bayesian Information Criterion
residuals.lmeStruct
Calculate lmeStruct Residuals
logLik.reStruct
Calculate reStruct Log-Likelihood
corCompSymm
Compound Symmetry Correlation Structure
plot.ACF
Plot an ACF Object
Names.pdBlocked
Names of a pdBlocked Object
varPower
Power Variance Function
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
Variogram
Calculate Semi-variogram
Initialize.corStruct
Initialize corStruct Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
asTable
Convert groupedData to a matrix
comparePred
Compare Predictions
Names.formula
Extract Names from a formula
corMatrix.corStruct
Matrix of a corStruct Object
getData.gls
Extract gls Object Data
getCovariateFormula
Extract Covariates Formula
coef.pdMat
pdMat Object Coefficients
summary.gls
Summarize a gls Object
corClasses
Correlation Structure Classes
nlme
Nonlinear Mixed-Effects Models
plot.nfnGroupedData
Plot an nfnGroupedData Object
coef.corStruct
Coefficients of a corStruct Object
pdLogChol
General Positive-Definite Matrix
lmList
List of lm Objects with a Common Model
corCAR1
Continuous AR(1) Correlation Structure
summary.lmList
Summarize an lmList Object
varConstPower
Constant Plus Power Variance Function
gapply
Apply a Function by Groups
lmeScale
Scale for lme Optimization
isInitialized
Check if Object is Initialized
nlsList.selfStart
nlsList Fit from a selfStart Function
recalc
Recalculate Condensed Linear Model Object
formula.pdMat
Extract pdMat Formula
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
varIdent
Constant Variance Function
pdSymm
General Positive-Definite Matrix
needUpdate
Check if Update is Needed
getGroups.data.frame
Extract Groups from a Data Frame
gsummary
Summarize by Groups
plot.lmList
Plot an lmList Object
fitted.lme
Extract lme Fitted Values
anova.gls
Compare Likelihoods of Fitted Objects
varWeights.glsStruct
Variance Weights for glsStruct Object
logLik.varFunc
Extract varFunc logLik
nlmeStruct
Nonlinear Mixed-Effects Structure
model.matrix.reStruct
reStruct Model Matrix
corSpatial
Spatial Correlation Structure
predict.gnls
Predictions from a gnls Object
compareFits
Compare Fitted Objects
residuals.lme
Extract lme Residuals
pairs.lme
Pairs Plot of an lme Object
varClasses
Variance Function Classes
corNatural
General correlation in natural parameterization
getVarCov
Extract variance-covariance matrix
Variogram.corLin
Calculate Semi-variogram for a corLin Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
simulate.lme
Simulate results from lme models
coef.lmList
Extract lmList Coefficients
Variogram.corExp
Calculate Semi-variogram for a corExp Object
intervals.lme
Confidence Intervals on lme Parameters
getData.lme
Extract lme Object Data
summary.modelStruct
Summarize a modelStruct Object
Dim.corStruct
Dimensions of a corStruct Object
getGroups.gls
Extract gls Object Groups
recalc.varFunc
Recalculate for varFunc Object
varFunc
Variance Function Structure
pdClasses
Positive-Definite Matrix Classes
pdConstruct.pdBlocked
Construct pdBlocked Objects
getCovariate.varFunc
Extract varFunc Covariate
corGaus
Gaussian Correlation Structure
varWeights
Extract Variance Function Weights
corAR1
AR(1) Correlation Structure
summary.lme
Summarize an lme Object
anova.lme
Compare Likelihoods of Fitted Objects
corSpher
Spherical Correlation Structure
coef.gnls
Extract gnls Coefficients
varExp
Exponential Variance Function
nlmeControl
Control Values for nlme Fit
phenoModel
Model function for the Phenobarb data
varFixed
Fixed Variance Function
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
recalc.corStruct
Recalculate for corStruct Object
nlme.nlsList
NLME fit from nlsList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
getCovariate
Extract Covariate from an Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
qqnorm.gls
Normal Plot of Residuals from a gls Object
nlsList
List of nls Objects with a Common Model
plot.intervals.lmList
Plot lmList Confidence Intervals
predict.lmList
Predictions from an lmList Object
predict.lme
Predictions from an lme Object
print.summary.pdMat
Print a summary.pdMat Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
summary.nlsList
Summarize an nlsList Object
lme.lmList
LME fit from lmList Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
getCovariate.corStruct
Extract corStruct Object Covariate
fitted.lmList
Extract lmList Fitted Values
Variogram.default
Calculate Semi-variogram
update.varFunc
Update varFunc Object
plot.nmGroupedData
Plot an nmGroupedData Object
plot.gls
Plot a gls Object
gnlsObject
Fitted gnls Object
fdHess
Finite difference Hessian
getData
Extract Data from an Object
corSymm
General Correlation Structure
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
pdMat
Positive-Definite Matrix
formula.pdBlocked
Extract pdBlocked Formula
intervals
Confidence Intervals on Coefficients
isBalanced
Check a Design for Balance
print.varFunc
Print a varFunc Object
residuals.lmList
Extract lmList Residuals
getCovariate.data.frame
Extract Data Frame Covariate
lmList.groupedData
lmList Fit from a groupedData Object
logDet.reStruct
Extract reStruct Log-Determinants
summary.varFunc
Summarize varFunc Object
getResponse
Extract Response Variable from an Object
lmeStruct
Linear Mixed-Effects Structure
intervals.lmList
Confidence Intervals on lmList Coefficients
logLik.gnls
Log-Likelihood of a gnls Object
plot.ranef.lme
Plot a ranef.lme Object
glsStruct
Generalized Least Squares Structure
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
getResponseFormula
Extract Formula Specifying Response Variable
recalc.reStruct
Recalculate for an reStruct Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
groupedData
Construct a groupedData Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
logDet.corStruct
Extract corStruct Log-Determinant
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.corStruct
Extract corStruct Log-Likelihood
plot.ranef.lmList
Plot a ranef.lmList Object
predict.gls
Predictions from a gls Object
ranef.lme
Extract lme Random Effects
fixef.lmList
Extract lmList Fixed Effects
gnls
Fit Nonlinear Model Using Generalized Least Squares
gls
Fit Linear Model Using Generalized Least Squares
lme
Linear Mixed-Effects Models
solve.reStruct
Apply Solve to an reStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdDiag
Diagonal Positive-Definite Matrix
lmeControl
Control Values for lme Fit
pairs.compareFits
Pairs Plot of compareFits Object
lme.groupedData
LME fit from groupedData Object
predict.nlme
Predictions from an nlme Object
corExp
Exponential Correlation Structure
nlmeObject
Fitted nlme Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
getGroups.lme
Extract lme Object Groups
logLik.glsStruct
Log-Likelihood of a glsStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
ranef.lmList
Extract lmList Random Effects
plot.lme
Plot an lme or nls object
quinModel
Model function for the Quinidine data
plot.Variogram
Plot a Variogram Object
pooledSD
Extract Pooled Standard Deviation
pairs.lmList
Pairs Plot of an lmList Object
intervals.gls
Confidence Intervals on gls Parameters
glsControl
Control Values for gls Fit
update.modelStruct
Update a modelStruct Object
fixed.effects
Extract Fixed Effects
corLin
Linear Correlation Structure
residuals.glsStruct
Calculate glsStruct Residuals
getGroups.lmList
Extract lmList Object Groups
logLik.lme
Log-Likelihood of an lme Object
gnlsControl
Control Values for gnls Fit
fitted.lmeStruct
Calculate lmeStruct Fitted Values
logLik.lmList
Log-Likelihood of an lmList Object
formula.reStruct
Extract reStruct Object Formula
Pixel
X-ray pixel intensities over time
RatPupWeight
The weight of rat pups
Assay
Bioassay on Cell Culture Plate
Tetracycline1
Pharmacokinetics of tetracycline
Glucose
Glucose levels over time
Soybean
Growth of soybean plants
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
IGF
Radioimmunoassay of IGF-I Protein
Cefamandole
Pharmacokinetics of Cefamandole
Dialyzer
High-Flux Hemodialyzer
BodyWeight
Rat weight over time for different diets
Tetracycline2
Pharmacokinetics of tetracycline
Quinidine
Quinidine Kinetics
Remifentanil
Pharmacokinetics of remifentanil
Rail
Evaluation of Stress in Railway Rails
PBG
Effect of Phenylbiguanide on Blood Pressure
Muscle
Contraction of heart muscle sections
bdf
Language scores
Machines
Productivity Scores for Machines and Workers
Spruce
Growth of Spruce Trees
Wheat
Yields by growing conditions
Gun
Methods for firing naval guns
Milk
Protein content of cows' milk
MathAchieve
Mathematics achievement scores
Glucose2
Glucose Levels Following Alcohol Ingestion
Oats
Split-plot Experiment on Varieties of Oats
Wheat2
Wheat Yield Trials
Orthodont
Growth curve data on an orthdontic measurement
Wafer
Modeling of Analog MOS Circuits
Relaxin
Assay for Relaxin
MathAchSchool
School demographic data for MathAchieve
Oxide
Variability in Semiconductor Manufacturing
Meat
Tenderness of meat
Ovary
Counts of Ovarian Follicles
Nitrendipene
Assay of nitrendipene
Phenobarb
Phenobarbitol Kinetics
Gasoline
Refinery yield of gasoline
Oxboys
Heights of Boys in Oxford
ergoStool
Ergometrics experiment with stool types
Earthquake
Earthquake Intensity
Fatigue
Cracks caused by metal fatigue