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nlme (version 3.1-81)
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
3.1-81
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-81)
Search all functions
Initialize.lmeStruct
Initialize an lmeStruct Object
Matrix.reStruct
Assign reStruct Matrices
Dim
Extract Dimensions from an Object
Names.formula
Extract Names from a formula
Dim.corSpatial
Dimensions of a corSpatial Object
Covariate
Assign Covariate Values
Initialize.glsStruct
Initialize a glsStruct Object
ACF
Autocorrelation Function
Names.reStruct
Names of an reStruct Object
Coef
Assign Values to Coefficients
asTable
Convert groupedData to a matrix
Matrix
Assign Matrix Values
asOneFormula
Combine Formulas of a Set of Objects
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Matrix.pdMat
Assign Matrix to a pdMat Object
Initialize.reStruct
Initialize reStruct Object
Initialize.corStruct
Initialize corStruct Object
gapply
Apply a Function by Groups
as.matrix.reStruct
Matrices of an reStruct Object
Variogram.default
Calculate Semi-variogram
predict.lme
Predictions from an lme Object
comparePred
Compare Predictions
summary.corStruct
Summarize a corStruct Object
collapse.groupedData
Collapse a groupedData Object
[.pdMat
Subscript a pdMat Object
lmeObject
Fitted lme Object
coef.corStruct
Coefficients of a corStruct Object
Initialize
Initialize Object
getCovariate.varFunc
Extract varFunc Covariate
fitted.lmeStruct
Calculate lmeStruct Fitted Values
as.matrix.corStruct
Matrix of a corStruct Object
coef.modelStruct
Extract modelStruct Object Coefficients
corFactor.corStruct
Factor of a corStruct Object Matrix
logLik.gnls
Log-Likelihood of a gnls Object
corLin
Linear Correlation Structure
coef.reStruct
reStruct Object Coefficients
LDEsysMat
Generate system matrix for LDEs
corARMA
ARMA(p,q) Correlation Structure
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
formula.reStruct
Extract reStruct Object Formula
varConstPower
Constant Plus Power Variance Function
pooledSD
Extract Pooled Standard Deviation
ACF.lme
Autocorrelation Function for lme Residuals
ranef.lmList
Extract lmList Random Effects
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Names
Names Associated with an Object
Dim.corStruct
Dimensions of a corStruct Object
BIC
Bayesian Information Criterion
logDet
Extract the Logarithm of the Determinant
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
anova.lme
Compare Likelihoods of Fitted Objects
fixed.effects
Extract Fixed Effects
recalc.modelStruct
Recalculate for a modelStruct Object
corSpher
Spherical Correlation Structure
getData.lmList
Extract lmList Object Data
corGaus
Gaussian Correlation Structure
glsStruct
Generalized Least Squares Structure
corNatural
General correlation in natural parameterization
simulate.lme
Simulate results from lme models
Variogram.corLin
Calculate Semi-variogram for a corLin Object
corClasses
Correlation Structure Classes
print.varFunc
Print a varFunc Object
coef.pdMat
pdMat Object Coefficients
getCovariateFormula
Extract Covariates Formula
getData.lme
Extract lme Object Data
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
corAR1
AR(1) Correlation Structure
gnlsStruct
Generalized Nonlinear Least Squares Structure
isInitialized
Check if Object is Initialized
getGroups.data.frame
Extract Groups from a Data Frame
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
summary.modelStruct
Summarize a modelStruct Object
summary.lme
Summarize an lme Object
allCoef
Extract Coefficients from a Set of Objects
ACF.gls
Autocorrelation Function for gls Residuals
Names.pdMat
Names of a pdMat Object
update.modelStruct
Update a modelStruct Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
logDet.reStruct
Extract reStruct Log-Determinants
intervals.gls
Confidence Intervals on gls Parameters
coef.gnls
Extract gnls Coefficients
corMatrix.corStruct
Matrix of a corStruct Object
summary.pdMat
Summarize a pdMat Object
Initialize.varFunc
Initialize varFunc Object
balancedGrouped
Create a groupedData object from a matrix
predict.gnls
Predictions from a gnls Object
fitted.lme
Extract lme Fitted Values
gsummary
Summarize by Groups
pdClasses
Positive-Definite Matrix Classes
residuals.gnlsStruct
Calculate gnlsStruct Residuals
getData
Extract Data from an Object
plot.intervals.lmList
Plot lmList Confidence Intervals
varFunc
Variance Function Structure
splitFormula
Split a Formula
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
Dim.pdMat
Dimensions of a pdMat Object
gls
Fit Linear Model Using Generalized Least Squares
corFactor
Factor of a Correlation Matrix
solve.reStruct
Apply Solve to an reStruct Object
getCovariate.corStruct
Extract corStruct Object Covariate
formula.pdBlocked
Extract pdBlocked Formula
summary.gls
Summarize a gls Object
update.varFunc
Update varFunc Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
intervals.lmList
Confidence Intervals on lmList Coefficients
fdHess
Finite difference Hessian
predict.gls
Predictions from a gls Object
lmeScale
Scale for lme Optimization
as.matrix.pdMat
Matrix of a pdMat Object
fixef.lmList
Extract lmList Fixed Effects
compareFits
Compare Fitted Objects
getCovariate.data.frame
Extract Data Frame Covariate
augPred
Augmented Predictions
getData.gls
Extract gls Object Data
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
summary.nlsList
Summarize an nlsList Object
varFixed
Fixed Variance Function
Variogram.corExp
Calculate Semi-variogram for a corExp Object
glsControl
Control Values for gls Fit
formula.pdMat
Extract pdMat Formula
lmList.groupedData
lmList Fit from a groupedData Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
VarCorr
Extract variance and correlation components
groupedData
Construct a groupedData Object
getGroups.lme
Extract lme Object Groups
getResponseFormula
Extract Formula Specifying Response Variable
plot.Variogram
Plot a Variogram Object
lme.lmList
LME fit from lmList Object
getGroups.lmList
Extract lmList Object Groups
corSpatial
Spatial Correlation Structure
logLik.corStruct
Extract corStruct Log-Likelihood
collapse
Collapse According to Groups
getVarCov
Extract variance-covariance matrix
corCAR1
Continuous AR(1) Correlation Structure
plot.lme
Plot an lme or nls object
residuals.lmeStruct
Calculate lmeStruct Residuals
varComb
Combination of Variance Functions
varWeights
Extract Variance Function Weights
varWeights.lmeStruct
Variance Weights for lmeStruct Object
Names.pdBlocked
Names of a pdBlocked Object
Covariate.varFunc
Assign varFunc Covariate
predict.nlme
Predictions from an nlme Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
varIdent
Constant Variance Function
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
coef.varFunc
varFunc Object Coefficients
intervals
Confidence Intervals on Coefficients
gnlsControl
Control Values for gnls Fit
residuals.glsStruct
Calculate glsStruct Residuals
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
coef.lmList
Extract lmList Coefficients
pdMat
Positive-Definite Matrix
summary.lmList
Summarize an lmList Object
plot.ranef.lmList
Plot a ranef.lmList Object
varExp
Exponential Variance Function
pairs.lme
Pairs Plot of an lme Object
fitted.glsStruct
Calculate glsStruct Fitted Values
plot.ACF
Plot an ACF Object
corSymm
General Correlation Structure
gnlsObject
Fitted gnls Object
fitted.lmList
Extract lmList Fitted Values
logLik.glsStruct
Log-Likelihood of a glsStruct Object
pdDiag
Diagonal Positive-Definite Matrix
residuals.lme
Extract lme Residuals
glsObject
Fitted gls Object
lme
Linear Mixed-Effects Models
varClasses
Variance Function Classes
getGroupsFormula
Extract Grouping Formula
print.summary.pdMat
Print a summary.pdMat Object
pairs.compareFits
Pairs Plot of compareFits Object
lmList
List of lm Objects with a Common Model
getGroups.corStruct
Extract corStruct Groups
pdLogChol
General Positive-Definite Matrix
plot.nmGroupedData
Plot an nmGroupedData Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.compareFits
Plot a compareFits Object
lmeControl
Control Values for lme Fit
varWeights.glsStruct
Variance Weights for glsStruct Object
residuals.gls
Extract gls Residuals
Variogram
Calculate Semi-variogram
nlmeObject
Fitted nlme Object
ranef.lme
Extract lme Random Effects
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getGroups
Extract Grouping Factors from an Object
corMatrix
Extract Correlation Matrix
predict.lmList
Predictions from an lmList Object
plot.nffGroupedData
Plot an nffGroupedData Object
isBalanced
Check a Design for Balance
recalc.reStruct
Recalculate for an reStruct Object
residuals.lmList
Extract lmList Residuals
BIC.logLik
BIC of a logLik Object
logDet.corStruct
Extract corStruct Log-Determinant
recalc.varFunc
Recalculate for varFunc Object
corExp
Exponential Correlation Structure
lmeStruct
Linear Mixed-Effects Structure
recalc.corStruct
Recalculate for corStruct Object
plot.lmList
Plot an lmList Object
corRatio
Rational Quadratic Correlation Structure
plot.augPred
Plot an augPred Object
getGroups.gls
Extract gls Object Groups
recalc
Recalculate Condensed Linear Model Object
quinModel
Model function for the Quinidine data
getGroups.varFunc
Extract varFunc Groups
random.effects
Extract Random Effects
getCovariate
Extract Covariate from an Object
phenoModel
Model function for the Phenobarb data
getResponse
Extract Response Variable from an Object
nlme
Nonlinear Mixed-Effects Models
coef.lme
Extract lme Coefficients
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
anova.gls
Compare Likelihoods of Fitted Objects
lme.groupedData
LME fit from groupedData Object
plot.ranef.lme
Plot a ranef.lme Object
corCompSymm
Compound Symmetry Correlation Structure
intervals.lme
Confidence Intervals on lme Parameters
reStruct
Random Effects Structure
nlme.nlsList
NLME fit from nlsList Object
varPower
Power Variance Function
summary.varFunc
Summarize varFunc Object
pdSymm
General Positive-Definite Matrix
plot.gls
Plot a gls Object
nlsList
List of nls Objects with a Common Model
logLik.lme
Log-Likelihood of an lme Object
logLik.varFunc
Extract varFunc logLik
nlmeStruct
Nonlinear Mixed-Effects Structure
logLik.lmList
Log-Likelihood of an lmList Object
pairs.lmList
Pairs Plot of an lmList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
nlsList.selfStart
nlsList Fit from a selfStart Function
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
needUpdate
Check if Update is Needed
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pdBlocked
Positive-Definite Block Diagonal Matrix
model.matrix.reStruct
reStruct Model Matrix
logLik.reStruct
Calculate reStruct Log-Likelihood
nlmeControl
Control Values for nlme Fit
pdConstruct
Construct pdMat Objects
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdIdent
Multiple of the Identity Positive-Definite Matrix
Pixel
X-ray pixel intensities over time
Gun
Methods for firing naval guns
Fatigue
Cracks caused by metal fatigue
Machines
Productivity Scores for Machines and Workers
IGF
Radioimmunoassay of IGF-I Protein
Orthodont
Growth curve data on an orthdontic measurement
MathAchieve
Mathematics achievement scores
Oats
Split-plot Experiment on Varieties of Oats
Dialyzer
High-Flux Hemodialyzer
MathAchSchool
School demographic data for MathAchieve
Glucose
Glucose levels over time
Glucose2
Glucose Levels Following Alcohol Ingestion
Earthquake
Earthquake Intensity
Assay
Bioassay on Cell Culture Plate
Wheat2
Wheat Yield Trials
Muscle
Contraction of heart muscle sections
Milk
Protein content of cows' milk
BodyWeight
Rat weight over time for different diets
Ovary
Counts of Ovarian Follicles
Wafer
Modeling of Analog MOS Circuits
Spruce
Growth of Spruce Trees
Soybean
Growth of soybean plants
Nitrendipene
Assay of nitrendipene
Oxide
Variability in Semiconductor Manufacturing
Meat
Tenderness of meat
Quinidine
Quinidine Kinetics
Cefamandole
Pharmacokinetics of Cefamandole
bdf
Language scores
Gasoline
Refinery yield of gasoline
Tetracycline2
Pharmacokinetics of tetracycline
PBG
Effect of Phenylbiguanide on Blood Pressure
Relaxin
Assay for Relaxin
Tetracycline1
Pharmacokinetics of tetracycline
Rail
Evaluation of Stress in Railway Rails
Phenobarb
Phenobarbitol Kinetics
Oxboys
Heights of Boys in Oxford
Remifentanil
Pharmacokinetics of remifentanil
RatPupWeight
The weight of rat pups
ergoStool
Ergometrics experiment with stool types
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Wheat
Yields by growing conditions