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nlme (version 3.1-74)
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
3.1-74
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-74)
Search all functions
Covariate
Assign Covariate Values
Dim.corSpatial
Dimensions of a corSpatial Object
Dim
Extract Dimensions from an Object
Dim.pdMat
Dimensions of a pdMat Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
Initialize.reStruct
Initialize reStruct Object
Names
Names Associated with an Object
ACF.gls
Autocorrelation Function for gls Residuals
pdMat
Positive-Definite Matrix
getGroups.data.frame
Extract Groups from a Data Frame
getCovariateFormula
Extract Covariates Formula
quinModel
Model function for the Quinidine data
random.effects
Extract Random Effects
lmeScale
Scale for lme Optimization
residuals.glsStruct
Calculate glsStruct Residuals
lme.groupedData
LME fit from groupedData Object
Initialize
Initialize Object
predict.gnls
Predictions from a gnls Object
Names.pdMat
Names of a pdMat Object
corCompSymm
Compound Symmetry Correlation Structure
Initialize.corStruct
Initialize corStruct Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Names.pdBlocked
Names of a pdBlocked Object
coef.lme
Extract lme Coefficients
ACF
Autocorrelation Function
ACF.lme
Autocorrelation Function for lme Residuals
as.matrix.reStruct
Matrices of an reStruct Object
LDEsysMat
Generate system matrix for LDEs
collapse.groupedData
Collapse a groupedData Object
[.pdMat
Subscript a pdMat Object
Names.reStruct
Names of an reStruct Object
coef.gnls
Extract gnls Coefficients
Variogram.default
Calculate Semi-variogram
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Matrix
Assign Matrix Values
corCAR1
Continuous AR(1) Correlation Structure
Coef
Assign Values to Coefficients
coef.pdMat
pdMat Object Coefficients
BIC
Bayesian Information Criterion
Matrix.pdMat
Assign Matrix to a pdMat Object
as.matrix.corStruct
Matrix of a corStruct Object
Initialize.lmeStruct
Initialize an lmeStruct Object
Initialize.glsStruct
Initialize a glsStruct Object
Variogram
Calculate Semi-variogram
anova.gls
Compare Likelihoods of Fitted Objects
coef.corStruct
Coefficients of a corStruct Object
BIC.logLik
BIC of a logLik Object
getGroups
Extract Grouping Factors from an Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
getData.gls
Extract gls Object Data
gnlsStruct
Generalized Nonlinear Least Squares Structure
corSpatial
Spatial Correlation Structure
pdClasses
Positive-Definite Matrix Classes
asTable
Convert groupedData to a matrix
plot.lmList
Plot an lmList Object
fdHess
Finite difference Hessian
allCoef
Extract Coefficients from a Set of Objects
fixef.lmList
Extract lmList Fixed Effects
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
augPred
Augmented Predictions
lme.lmList
LME fit from lmList Object
getVarCov
Extract variance-covariance matrix
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
plot.ranef.lmList
Plot a ranef.lmList Object
getGroups.corStruct
Extract corStruct Groups
fitted.lmeStruct
Calculate lmeStruct Fitted Values
plot.augPred
Plot an augPred Object
Initialize.varFunc
Initialize varFunc Object
plot.ACF
Plot an ACF Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
varExp
Exponential Variance Function
pdDiag
Diagonal Positive-Definite Matrix
predict.gls
Predictions from a gls Object
asOneFormula
Combine Formulas of a Set of Objects
Covariate.varFunc
Assign varFunc Covariate
Names.formula
Extract Names from a formula
Dim.corStruct
Dimensions of a corStruct Object
gsummary
Summarize by Groups
gapply
Apply a Function by Groups
Matrix.reStruct
Assign reStruct Matrices
model.matrix.reStruct
reStruct Model Matrix
logLik.glsStruct
Log-Likelihood of a glsStruct Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
corNatural
General correlation in natural parameterization
coef.lmList
Extract lmList Coefficients
formula.pdMat
Extract pdMat Formula
gls
Fit Linear Model Using Generalized Least Squares
corClasses
Correlation Structure Classes
corLin
Linear Correlation Structure
getData.lme
Extract lme Object Data
coef.reStruct
reStruct Object Coefficients
pdLogChol
General Positive-Definite Matrix
balancedGrouped
Create a groupedData object from a matrix
getCovariate.data.frame
Extract Data Frame Covariate
getGroupsFormula
Extract Grouping Formula
getResponseFormula
Extract Formula Specifying Response Variable
formula.reStruct
Extract reStruct Object Formula
getCovariate.varFunc
Extract varFunc Covariate
fitted.glsStruct
Calculate glsStruct Fitted Values
isBalanced
Check a Design for Balance
getCovariate.corStruct
Extract corStruct Object Covariate
corFactor.corStruct
Factor of a corStruct Object Matrix
getData
Extract Data from an Object
logLik.corStruct
Extract corStruct Log-Likelihood
plot.nffGroupedData
Plot an nffGroupedData Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
VarCorr
Extract variance and correlation components
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
compareFits
Compare Fitted Objects
glsStruct
Generalized Least Squares Structure
glsObject
Fitted gls Object
predict.lme
Predictions from an lme Object
pairs.lme
Pairs Plot of an lme Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
ranef.lme
Extract lme Random Effects
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
getGroups.varFunc
Extract varFunc Groups
lmList.groupedData
lmList Fit from a groupedData Object
intervals.gls
Confidence Intervals on gls Parameters
corARMA
ARMA(p,q) Correlation Structure
qqnorm.gls
Normal Plot of Residuals from a gls Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
lme
Linear Mixed-Effects Models
formula.pdBlocked
Extract pdBlocked Formula
corAR1
AR(1) Correlation Structure
collapse
Collapse According to Groups
fixed.effects
Extract Fixed Effects
corRatio
Rational Quadratic Correlation Structure
logLik.gnls
Log-Likelihood of a gnls Object
isInitialized
Check if Object is Initialized
gnlsObject
Fitted gnls Object
getGroups.lme
Extract lme Object Groups
lmeStruct
Linear Mixed-Effects Structure
splitFormula
Split a Formula
gnlsControl
Control Values for gnls Fit
intervals.lme
Confidence Intervals on lme Parameters
varWeights.glsStruct
Variance Weights for glsStruct Object
getCovariate
Extract Covariate from an Object
getResponse
Extract Response Variable from an Object
update.modelStruct
Update a modelStruct Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
varComb
Combination of Variance Functions
nlmeStruct
Nonlinear Mixed-Effects Structure
fitted.lmList
Extract lmList Fitted Values
logLik.reStruct
Calculate reStruct Log-Likelihood
corSymm
General Correlation Structure
recalc.modelStruct
Recalculate for a modelStruct Object
pdBlocked
Positive-Definite Block Diagonal Matrix
logLik.varFunc
Extract varFunc logLik
corFactor
Factor of a Correlation Matrix
pdConstruct.pdBlocked
Construct pdBlocked Objects
groupedData
Construct a groupedData Object
intervals
Confidence Intervals on Coefficients
lmeControl
Control Values for lme Fit
lmeObject
Fitted lme Object
needUpdate
Check if Update is Needed
nlmeObject
Fitted nlme Object
coef.modelStruct
Extract modelStruct Object Coefficients
glsControl
Control Values for gls Fit
lmList
List of lm Objects with a Common Model
nlme
Nonlinear Mixed-Effects Models
coef.varFunc
varFunc Object Coefficients
pdSymm
General Positive-Definite Matrix
varIdent
Constant Variance Function
ranef.lmList
Extract lmList Random Effects
getData.lmList
Extract lmList Object Data
predict.lmList
Predictions from an lmList Object
plot.intervals.lmList
Plot lmList Confidence Intervals
logDet.corStruct
Extract corStruct Log-Determinant
phenoModel
Model function for the Phenobarb data
as.matrix.pdMat
Matrix of a pdMat Object
nlsList.selfStart
nlsList Fit from a selfStart Function
pdNatural
General Positive-Definite Matrix in Natural Parametrization
plot.ranef.lme
Plot a ranef.lme Object
varClasses
Variance Function Classes
recalc.reStruct
Recalculate for an reStruct Object
nlme.nlsList
NLME fit from nlsList Object
update.varFunc
Update varFunc Object
simulate.lme
Simulate results from lme models
print.summary.pdMat
Print a summary.pdMat Object
intervals.lmList
Confidence Intervals on lmList Coefficients
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
summary.gls
Summarize a gls Object
recalc
Recalculate Condensed Linear Model Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.lme
Plot an lme or nls object
varConstPower
Constant Plus Power Variance Function
recalc.corStruct
Recalculate for corStruct Object
pooledSD
Extract Pooled Standard Deviation
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
residuals.lmList
Extract lmList Residuals
print.varFunc
Print a varFunc Object
pairs.compareFits
Pairs Plot of compareFits Object
summary.corStruct
Summarize a corStruct Object
corMatrix
Extract Correlation Matrix
summary.lmList
Summarize an lmList Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
plot.nmGroupedData
Plot an nmGroupedData Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
summary.lme
Summarize an lme Object
reStruct
Random Effects Structure
predict.nlme
Predictions from an nlme Object
plot.Variogram
Plot a Variogram Object
residuals.lmeStruct
Calculate lmeStruct Residuals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
summary.pdMat
Summarize a pdMat Object
summary.modelStruct
Summarize a modelStruct Object
varWeights
Extract Variance Function Weights
pdIdent
Multiple of the Identity Positive-Definite Matrix
varPower
Power Variance Function
varFixed
Fixed Variance Function
plot.compareFits
Plot a compareFits Object
residuals.gls
Extract gls Residuals
residuals.gnlsStruct
Calculate gnlsStruct Residuals
summary.nlsList
Summarize an nlsList Object
summary.varFunc
Summarize varFunc Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
corSpher
Spherical Correlation Structure
logDet.reStruct
Extract reStruct Log-Determinants
recalc.varFunc
Recalculate for varFunc Object
nlsList
List of nls Objects with a Common Model
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
pairs.lmList
Pairs Plot of an lmList Object
pdConstruct
Construct pdMat Objects
varFunc
Variance Function Structure
solve.reStruct
Apply Solve to an reStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
comparePred
Compare Predictions
corExp
Exponential Correlation Structure
corMatrix.corStruct
Matrix of a corStruct Object
fitted.lme
Extract lme Fitted Values
corGaus
Gaussian Correlation Structure
gnls
Fit Nonlinear Model Using Generalized Least Squares
logDet
Extract the Logarithm of the Determinant
getGroups.lmList
Extract lmList Object Groups
logLik.lme
Log-Likelihood of an lme Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
nlmeControl
Control Values for nlme Fit
plot.gls
Plot a gls Object
residuals.lme
Extract lme Residuals
getGroups.gls
Extract gls Object Groups
Tetracycline1
Pharmacokinetics of tetracycline
Machines
Productivity Scores for Machines and Workers
Oxboys
Heights of Boys in Oxford
Earthquake
Earthquake Intensity
Wafer
Modeling of Analog MOS Circuits
Soybean
Growth of soybean plants
Relaxin
Assay for Relaxin
Gun
Methods for firing naval guns
Ovary
Counts of Ovarian Follicles
Meat
Tenderness of meat
Wheat
Yields by growing conditions
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Milk
Protein content of cows' milk
RatPupWeight
The weight of rat pups
MathAchieve
Mathematics achievement scores
Tetracycline2
Pharmacokinetics of tetracycline
Orthodont
Growth curve data on an orthdontic measurement
Pixel
X-ray pixel intensities over time
Oxide
Variability in Semiconductor Manufacturing
MathAchSchool
School demographic data for MathAchieve
Glucose
Glucose levels over time
Assay
Bioassay on Cell Culture Plate
Fatigue
Cracks caused by metal fatigue
Gasoline
Refinery yield of gasoline
Muscle
Contraction of heart muscle sections
Oats
Split-plot Experiment on Varieties of Oats
Wheat2
Wheat Yield Trials
Quinidine
Quinidine Kinetics
Spruce
Growth of Spruce Trees
Remifentanil
Pharmacokinetics of remifentanil
Rail
Evaluation of Stress in Railway Rails
Cefamandole
Pharmacokinetics of Cefamandole
bdf
Language scores
ergoStool
Ergometrics experiment with stool types
PBG
Effect of Phenylbiguanide on Blood Pressure
Nitrendipene
Assay of nitrendipene
Glucose2
Glucose Levels Following Alcohol Ingestion
Phenobarb
Phenobarbitol Kinetics
BodyWeight
Rat weight over time for different diets
IGF
Radioimmunoassay of IGF-I Protein
Dialyzer
High-Flux Hemodialyzer