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nlme (version 3.1-76)
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
3.1-76
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-76)
Search all functions
BIC
Bayesian Information Criterion
Coef
Assign Values to Coefficients
BIC.logLik
BIC of a logLik Object
corMatrix
Extract Correlation Matrix
intervals.gls
Confidence Intervals on gls Parameters
Dim.corStruct
Dimensions of a corStruct Object
Initialize.varFunc
Initialize varFunc Object
ACF.gls
Autocorrelation Function for gls Residuals
Dim
Extract Dimensions from an Object
Covariate
Assign Covariate Values
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
as.matrix.reStruct
Matrices of an reStruct Object
corCAR1
Continuous AR(1) Correlation Structure
Variogram.corExp
Calculate Semi-variogram for a corExp Object
collapse
Collapse According to Groups
coef.gnls
Extract gnls Coefficients
augPred
Augmented Predictions
corFactor.corStruct
Factor of a corStruct Object Matrix
Dim.pdMat
Dimensions of a pdMat Object
coef.corStruct
Coefficients of a corStruct Object
getCovariate.corStruct
Extract corStruct Object Covariate
coef.reStruct
reStruct Object Coefficients
VarCorr
Extract variance and correlation components
recalc.modelStruct
Recalculate for a modelStruct Object
isInitialized
Check if Object is Initialized
summary.lmList
Summarize an lmList Object
Initialize.lmeStruct
Initialize an lmeStruct Object
[.pdMat
Subscript a pdMat Object
Matrix.reStruct
Assign reStruct Matrices
as.matrix.pdMat
Matrix of a pdMat Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
coef.varFunc
varFunc Object Coefficients
Initialize
Initialize Object
ACF
Autocorrelation Function
Names.reStruct
Names of an reStruct Object
Names.formula
Extract Names from a formula
Names.pdBlocked
Names of a pdBlocked Object
Variogram
Calculate Semi-variogram
Matrix
Assign Matrix Values
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Matrix.pdMat
Assign Matrix to a pdMat Object
corNatural
General correlation in natural parameterization
Names.pdMat
Names of a pdMat Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
Dim.corSpatial
Dimensions of a corSpatial Object
corAR1
AR(1) Correlation Structure
asOneFormula
Combine Formulas of a Set of Objects
summary.nlsList
Summarize an nlsList Object
residuals.glsStruct
Calculate glsStruct Residuals
residuals.gls
Extract gls Residuals
summary.corStruct
Summarize a corStruct Object
recalc
Recalculate Condensed Linear Model Object
ranef.lmList
Extract lmList Random Effects
varFixed
Fixed Variance Function
getGroupsFormula
Extract Grouping Formula
summary.pdMat
Summarize a pdMat Object
getVarCov
Extract variance-covariance matrix
getCovariate.data.frame
Extract Data Frame Covariate
summary.varFunc
Summarize varFunc Object
recalc.varFunc
Recalculate for varFunc Object
comparePred
Compare Predictions
pairs.compareFits
Pairs Plot of compareFits Object
nlme.nlsList
NLME fit from nlsList Object
coef.pdMat
pdMat Object Coefficients
getGroups.lmList
Extract lmList Object Groups
corCompSymm
Compound Symmetry Correlation Structure
ACF.lme
Autocorrelation Function for lme Residuals
corGaus
Gaussian Correlation Structure
corRatio
Rational Quadratic Correlation Structure
qqnorm.gls
Normal Plot of Residuals from a gls Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
nlsList
List of nls Objects with a Common Model
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
plot.Variogram
Plot a Variogram Object
summary.gls
Summarize a gls Object
intervals.lmList
Confidence Intervals on lmList Coefficients
Initialize.glsStruct
Initialize a glsStruct Object
Initialize.corStruct
Initialize corStruct Object
Names
Names Associated with an Object
update.modelStruct
Update a modelStruct Object
varComb
Combination of Variance Functions
varIdent
Constant Variance Function
formula.reStruct
Extract reStruct Object Formula
gapply
Apply a Function by Groups
fitted.lmList
Extract lmList Fitted Values
corFactor
Factor of a Correlation Matrix
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
varWeights
Extract Variance Function Weights
pairs.lmList
Pairs Plot of an lmList Object
Variogram.default
Calculate Semi-variogram
varFunc
Variance Function Structure
print.varFunc
Print a varFunc Object
corSpher
Spherical Correlation Structure
corSpatial
Spatial Correlation Structure
lmeObject
Fitted lme Object
plot.compareFits
Plot a compareFits Object
anova.gls
Compare Likelihoods of Fitted Objects
lmeScale
Scale for lme Optimization
lmeStruct
Linear Mixed-Effects Structure
getCovariateFormula
Extract Covariates Formula
plot.ranef.lmList
Plot a ranef.lmList Object
splitFormula
Split a Formula
recalc.corStruct
Recalculate for corStruct Object
coef.lmList
Extract lmList Coefficients
collapse.groupedData
Collapse a groupedData Object
simulate.lme
Simulate results from lme models
predict.gls
Predictions from a gls Object
ranef.lme
Extract lme Random Effects
getGroups.data.frame
Extract Groups from a Data Frame
recalc.reStruct
Recalculate for an reStruct Object
plot.intervals.lmList
Plot lmList Confidence Intervals
formula.pdBlocked
Extract pdBlocked Formula
corClasses
Correlation Structure Classes
nlmeStruct
Nonlinear Mixed-Effects Structure
getCovariate
Extract Covariate from an Object
getGroups
Extract Grouping Factors from an Object
logLik.reStruct
Calculate reStruct Log-Likelihood
pooledSD
Extract Pooled Standard Deviation
getGroups.varFunc
Extract varFunc Groups
gnlsControl
Control Values for gnls Fit
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
pdClasses
Positive-Definite Matrix Classes
fdHess
Finite difference Hessian
balancedGrouped
Create a groupedData object from a matrix
plot.ranef.lme
Plot a ranef.lme Object
pdConstruct
Construct pdMat Objects
gnlsObject
Fitted gnls Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
pairs.lme
Pairs Plot of an lme Object
logDet.reStruct
Extract reStruct Log-Determinants
Covariate.varFunc
Assign varFunc Covariate
allCoef
Extract Coefficients from a Set of Objects
LDEsysMat
Generate system matrix for LDEs
logLik.glsStruct
Log-Likelihood of a glsStruct Object
asTable
Convert groupedData to a matrix
getResponseFormula
Extract Formula Specifying Response Variable
fitted.glsStruct
Calculate glsStruct Fitted Values
getCovariate.varFunc
Extract varFunc Covariate
nlme
Nonlinear Mixed-Effects Models
residuals.lmeStruct
Calculate lmeStruct Residuals
random.effects
Extract Random Effects
varWeights.glsStruct
Variance Weights for glsStruct Object
residuals.lme
Extract lme Residuals
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varConstPower
Constant Plus Power Variance Function
getData
Extract Data from an Object
getResponse
Extract Response Variable from an Object
glsStruct
Generalized Least Squares Structure
plot.nmGroupedData
Plot an nmGroupedData Object
lme
Linear Mixed-Effects Models
nlsList.selfStart
nlsList Fit from a selfStart Function
summary.lme
Summarize an lme Object
fitted.lme
Extract lme Fitted Values
anova.lme
Compare Likelihoods of Fitted Objects
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
residuals.lmList
Extract lmList Residuals
pdSymm
General Positive-Definite Matrix
coef.modelStruct
Extract modelStruct Object Coefficients
corLin
Linear Correlation Structure
corExp
Exponential Correlation Structure
getData.lme
Extract lme Object Data
lme.lmList
LME fit from lmList Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
Initialize.reStruct
Initialize reStruct Object
formula.pdMat
Extract pdMat Formula
pdIdent
Multiple of the Identity Positive-Definite Matrix
lmeControl
Control Values for lme Fit
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
glsControl
Control Values for gls Fit
pdMat
Positive-Definite Matrix
fixef.lmList
Extract lmList Fixed Effects
varExp
Exponential Variance Function
pdBlocked
Positive-Definite Block Diagonal Matrix
varPower
Power Variance Function
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
groupedData
Construct a groupedData Object
plot.ACF
Plot an ACF Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
isBalanced
Check a Design for Balance
logLik.lmList
Log-Likelihood of an lmList Object
gls
Fit Linear Model Using Generalized Least Squares
gnls
Fit Nonlinear Model Using Generalized Least Squares
nlmeObject
Fitted nlme Object
logLik.varFunc
Extract varFunc logLik
glsObject
Fitted gls Object
corMatrix.corStruct
Matrix of a corStruct Object
logLik.corStruct
Extract corStruct Log-Likelihood
predict.lme
Predictions from an lme Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
print.summary.pdMat
Print a summary.pdMat Object
intervals.lme
Confidence Intervals on lme Parameters
plot.gls
Plot a gls Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
logDet
Extract the Logarithm of the Determinant
gnlsStruct
Generalized Nonlinear Least Squares Structure
plot.lme
Plot an lme or nls object
lmList.groupedData
lmList Fit from a groupedData Object
summary.modelStruct
Summarize a modelStruct Object
update.varFunc
Update varFunc Object
predict.gnls
Predictions from a gnls Object
logLik.lme
Log-Likelihood of an lme Object
plot.nffGroupedData
Plot an nffGroupedData Object
getGroups.lme
Extract lme Object Groups
varClasses
Variance Function Classes
coef.lme
Extract lme Coefficients
predict.lmList
Predictions from an lmList Object
intervals
Confidence Intervals on Coefficients
lmList
List of lm Objects with a Common Model
model.matrix.reStruct
reStruct Model Matrix
getGroups.corStruct
Extract corStruct Groups
logDet.corStruct
Extract corStruct Log-Determinant
needUpdate
Check if Update is Needed
getGroups.gls
Extract gls Object Groups
fixed.effects
Extract Fixed Effects
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getData.gls
Extract gls Object Data
plot.lmList
Plot an lmList Object
getData.lmList
Extract lmList Object Data
nlmeControl
Control Values for nlme Fit
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
predict.nlme
Predictions from an nlme Object
pdDiag
Diagonal Positive-Definite Matrix
gsummary
Summarize by Groups
lme.groupedData
LME fit from groupedData Object
reStruct
Random Effects Structure
solve.reStruct
Apply Solve to an reStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
corSymm
General Correlation Structure
corARMA
ARMA(p,q) Correlation Structure
compareFits
Compare Fitted Objects
plot.nfnGroupedData
Plot an nfnGroupedData Object
quinModel
Model function for the Quinidine data
plot.augPred
Plot an augPred Object
phenoModel
Model function for the Phenobarb data
pdLogChol
General Positive-Definite Matrix
pdNatural
General Positive-Definite Matrix in Natural Parametrization
Rail
Evaluation of Stress in Railway Rails
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
BodyWeight
Rat weight over time for different diets
Dialyzer
High-Flux Hemodialyzer
Cefamandole
Pharmacokinetics of Cefamandole
Assay
Bioassay on Cell Culture Plate
Muscle
Contraction of heart muscle sections
MathAchieve
Mathematics achievement scores
Meat
Tenderness of meat
Nitrendipene
Assay of nitrendipene
Glucose2
Glucose Levels Following Alcohol Ingestion
RatPupWeight
The weight of rat pups
Oats
Split-plot Experiment on Varieties of Oats
Gasoline
Refinery yield of gasoline
Remifentanil
Pharmacokinetics of remifentanil
Milk
Protein content of cows' milk
Earthquake
Earthquake Intensity
Oxboys
Heights of Boys in Oxford
Relaxin
Assay for Relaxin
PBG
Effect of Phenylbiguanide on Blood Pressure
IGF
Radioimmunoassay of IGF-I Protein
Fatigue
Cracks caused by metal fatigue
Oxide
Variability in Semiconductor Manufacturing
Wheat
Yields by growing conditions
Glucose
Glucose levels over time
Quinidine
Quinidine Kinetics
Gun
Methods for firing naval guns
Wheat2
Wheat Yield Trials
Tetracycline1
Pharmacokinetics of tetracycline
Tetracycline2
Pharmacokinetics of tetracycline
Phenobarb
Phenobarbitol Kinetics
Wafer
Modeling of Analog MOS Circuits
Machines
Productivity Scores for Machines and Workers
bdf
Language scores
Ovary
Counts of Ovarian Follicles
Soybean
Growth of soybean plants
MathAchSchool
School demographic data for MathAchieve
Pixel
X-ray pixel intensities over time
ergoStool
Ergometrics experiment with stool types
Spruce
Growth of Spruce Trees
Orthodont
Growth curve data on an orthdontic measurement