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nlme (version 3.1-57)
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
149,202
Version
3.1-57
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-57)
Search all functions
ACF
Autocorrelation Function
ACF.gls
Autocorrelation Function for gls Residuals
Initialize.lmeStruct
Initialize an lmeStruct Object
Dim.pdMat
Dimensions of a pdMat Object
Names.formula
Extract Names from a formula
Variogram.default
Calculate Semi-variogram
Dim.corSpatial
Dimensions of a corSpatial Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
LDEsysMat
Generate system matrix for LDEs
Dim.corStruct
Dimensions of a corStruct Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
fitted.lme
Extract lme Fitted Values
corLin
Linear Correlation Structure
Covariate
Assign Covariate Values
Variogram.corExp
Calculate Semi-variogram for a corExp Object
getGroupsFormula
Extract Grouping Formula
balancedGrouped
Create a groupedData object from a matrix
Coef
Assign Values to Coefficients
Names.pdBlocked
Names of a pdBlocked Object
collapse.groupedData
Collapse a groupedData Object
asOneFormula
Combine Formulas of a Set of Objects
allCoef
Extract Coefficients from a Set of Objects
VarCorr
Extract variance and correlation components
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Initialize.varFunc
Initialize varFunc Object
compareFits
Compare Fitted Objects
Names.pdMat
Names of a pdMat Object
as.matrix.reStruct
Matrices of an reStruct Object
Initialize.corStruct
Initialize corStruct Object
corCAR1
Continuous AR(1) Correlation Structure
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
coef.varFunc
varFunc Object Coefficients
asTable
Convert groupedData to a matrix
Covariate.varFunc
Assign varFunc Covariate
lmList
List of lm Objects with a Common Model
Matrix.reStruct
Assign reStruct Matrices
coef.gnls
Extract gnls Coefficients
ACF.lme
Autocorrelation Function for lme Residuals
fitted.lmeStruct
Calculate lmeStruct Fitted Values
comparePred
Compare Predictions
corCompSymm
Compound Symmetry Correlation Structure
Variogram.corLin
Calculate Semi-variogram for a corLin Object
corFactor
Factor of a Correlation Matrix
corExp
Exponential Correlation Structure
corMatrix
Extract Correlation Matrix
lmeControl
Control Values for lme Fit
nlmeObject
Fitted nlme Object
getVarCov
Extract variance-covariance matrix
formula.reStruct
Extract reStruct Object Formula
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
fixed.effects
Extract Fixed Effects
Matrix
Assign Matrix Values
coef.corStruct
Coefficients of a corStruct Object
corMatrix.corStruct
Matrix of a corStruct Object
Variogram
Calculate Semi-variogram
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
gnlsControl
Control Values for gnls Fit
fdHess
Finite difference Hessian
getData.lmList
Extract lmList Object Data
getGroups.lmList
Extract lmList Object Groups
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
contr.SAS
Contrast Matrices
augPred
Augmented Predictions
lme.lmList
LME fit from lmList Object
corFactor.corStruct
Factor of a corStruct Object Matrix
corSymm
General Correlation Structure
getGroups.gls
Extract gls Object Groups
getGroups.corStruct
Extract corStruct Groups
glsStruct
Generalized Least Squares Structure
isBalanced
Check a Design for Balance
coef.reStruct
reStruct Object Coefficients
corClasses
Correlation Structure Classes
fitted.glsStruct
Calculate glsStruct Fitted Values
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
corGaus
Gaussian Correlation Structure
corSpher
Spherical Correlation Structure
anova.gls
Compare Likelihoods of Fitted Objects
getCovariateFormula
Extract Covariates Formula
BIC
Bayesian Information Criterion
glsControl
Control Values for gls Fit
logLik.corStruct
Extract corStruct Log-Likelihood
BIC.logLik
BIC of a logLik Object
getCovariate
Extract Covariate from an Object
coef.lmList
Extract lmList Coefficients
gapply
Apply a Function by Groups
corAR1
AR(1) Correlation Structure
getCovariate.data.frame
Extract Data Frame Covariate
getCovariate.varFunc
Extract varFunc Covariate
gnls
Fit Nonlinear Model Using Generalized Least Squares
glsObject
Fitted gls Object
formula.pdBlocked
Extract pdBlocked Formula
lme
Linear Mixed-Effects Models
[.pdMat
Subscript a pdMat Object
pdBlocked
Positive-Definite Block Diagonal Matrix
getData.gls
Extract gls Object Data
coef.pdMat
pdMat Object Coefficients
pdSymm
General Positive-Definite Matrix
model.matrix.reStruct
reStruct Model Matrix
getData.lme
Extract lme Object Data
getResponseFormula
Extract Formula Specifying Response Variable
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
lmList.groupedData
lmList Fit from a groupedData Object
groupedData
Construct a groupedData Object
pooledSD
Extract Pooled Standard Deviation
corRatio
Rational Quadratic Correlation Structure
Matrix.pdMat
Assign Matrix to a pdMat Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
getGroups.varFunc
Extract varFunc Groups
nlme.nlsList
NLME fit from nlsList Object
varFunc
Variance Function Structure
solve.reStruct
Apply Solve to an reStruct Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
pdDiag
Diagonal Positive-Definite Matrix
logLik.lme
Log-Likelihood of an lme Object
Names
Names Associated with an Object
lmeObject
Fitted lme Object
plot.lmList
Plot an lmList Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
intervals
Confidence Intervals on Coefficients
predict.lmList
Predictions from an lmList Object
pdMat
Positive-Definite Matrix
ranef.lme
Extract lme Random Effects
residuals.lme
Extract lme Residuals
pairs.lme
Pairs Plot of an lme Object
quinModel
Model function for the Quinidine data
corNatural
General correlation in natural parameterization
predict.nlme
Predictions from an nlme Object
gsummary
Summarize by Groups
nlmeStruct
Nonlinear Mixed-Effects Structure
plot.ranef.lmList
Plot a ranef.lmList Object
getGroups
Extract Grouping Factors from an Object
plot.lme
Plot an lme or nls object
Initialize
Initialize Object
recalc.reStruct
Recalculate for an reStruct Object
nlmeControl
Control Values for nlme Fit
ranef.lmList
Extract lmList Random Effects
logDet.corStruct
Extract corStruct Log-Determinant
gls
Fit Linear Model Using Generalized Least Squares
intervals.lme
Confidence Intervals on lme Parameters
plot.ranef.lme
Plot a ranef.lme Object
varConstPower
Constant Plus Power Variance Function
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.varFunc
Extract varFunc logLik
corARMA
ARMA(p,q) Correlation Structure
lme.groupedData
LME fit from groupedData Object
varWeights
Extract Variance Function Weights
residuals.gnlsStruct
Calculate gnlsStruct Residuals
formula.pdMat
Extract pdMat Formula
reStruct
Random Effects Structure
summary.corStruct
Summarize a corStruct Object
summary.lme
Summarize an lme Object
intervals.lmList
Confidence Intervals on lmList Coefficients
phenoModel
Model function for the Phenobarb data
logLik.gnls
Log-Likelihood of a gnls Object
summary.lmList
Summarize an lmList Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
predict.lme
Predictions from an lme Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
logDet.reStruct
Extract reStruct Log-Determinants
varPower
Power Variance Function
plot.Variogram
Plot a Variogram Object
pdClasses
Positive-Definite Matrix Classes
lmeStruct
Linear Mixed-Effects Structure
getData
Extract Data from an Object
pairs.lmList
Pairs Plot of an lmList Object
plot.nmGroupedData
Plot an nmGroupedData Object
nlsList.selfStart
nlsList Fit from a selfStart Function
varClasses
Variance Function Classes
pdLogChol
General Positive-Definite Matrix
plot.intervals.lmList
Plot lmList Confidence Intervals
logDet
Extract the Logarithm of the Determinant
Initialize.reStruct
Initialize reStruct Object
print.summary.pdMat
Print a summary.pdMat Object
summary.modelStruct
Summarize a modelStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
varFixed
Fixed Variance Function
qqnorm.gls
Normal Plot of Residuals from a gls Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
summary.pdMat
Summarize a pdMat Object
residuals.lmList
Extract lmList Residuals
getCovariate.corStruct
Extract corStruct Object Covariate
isInitialized
Check if Object is Initialized
pdConstruct
Construct pdMat Objects
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
varComb
Combination of Variance Functions
getResponse
Extract Response Variable from an Object
coef.modelStruct
Extract modelStruct Object Coefficients
recalc
Recalculate Condensed Linear Model Object
print.varFunc
Print a varFunc Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
summary.nlsList
Summarize an nlsList Object
summary.varFunc
Summarize varFunc Object
getGroups.lme
Extract lme Object Groups
predict.gnls
Predictions from a gnls Object
as.matrix.corStruct
Matrix of a corStruct Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
as.matrix.pdMat
Matrix of a pdMat Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
lmeScale
Scale for lme Optimization
varExp
Exponential Variance Function
recalc.modelStruct
Recalculate for a modelStruct Object
residuals.gls
Extract gls Residuals
recalc.corStruct
Recalculate for corStruct Object
update.varFunc
Update varFunc Object
summary.gls
Summarize a gls Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
update.modelStruct
Update a modelStruct Object
collapse
Collapse According to Groups
nlme
Nonlinear Mixed-Effects Models
varIdent
Constant Variance Function
random.effects
Extract Random Effects
simulate.lme
simulate lme models
coef.lme
Extract lme Coefficients
recalc.varFunc
Recalculate for varFunc Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
fixef.lmList
Extract lmList Fixed Effects
logLik.reStruct
Calculate reStruct Log-Likelihood
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
gnlsObject
Fitted gnls Object
pairs.compareFits
Pairs Plot of compareFits Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
plot.ACF
Plot an ACF Object
fitted.lmList
Extract lmList Fitted Values
getGroups.data.frame
Extract Groups from a Data Frame
pdConstruct.pdBlocked
Construct pdBlocked Objects
Initialize.glsStruct
Initialize a glsStruct Object
Names.reStruct
Names of an reStruct Object
Dim
Extract Dimensions from an Object
corSpatial
Spatial Correlation Structure
residuals.glsStruct
Calculate glsStruct Residuals
residuals.lmeStruct
Calculate lmeStruct Residuals
varWeights.glsStruct
Variance Weights for glsStruct Object
intervals.gls
Confidence Intervals on gls Parameters
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
needUpdate
Check if Update is Needed
nlsList
List of nls Objects with a Common Model
plot.gls
Plot a gls Object
plot.augPred
Plot an augPred Object
plot.compareFits
Plot a compareFits Object
splitFormula
Split a Formula
predict.gls
Predictions from a gls Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
Machines
Productivity Scores for Machines and Workers
Ovary
Counts of Ovarian Follicles
MathAchSchool
School demographic data for MathAchieve
Muscle
Contraction of heart muscle sections
Spruce
Growth of Spruce Trees
Wheat
Yields by growing conditions
Relaxin
Assay for Relaxin
Wheat2
Wheat Yield Trials
Gasoline
Refinery yield of gasoline
Dialyzer
High-Flux Hemodialyzer
Wafer
Modeling of Analog MOS Circuits
PBG
Effect of Phenylbiguanide on Blood Pressure
Earthquake
Earthquake Intensity
Remifentanil
Pharmacokinetics of remifentanil
MathAchieve
Mathematics achievement scores
Assay
Bioassay on Cell Culture Plate
Tetracycline2
Pharmacokinetics of tetracycline
Cefamandole
Pharmacokinetics of Cefamandole
IGF
Radioimmunoassay of IGF-I Protein
Soybean
Growth of soybean plants
BodyWeight
Rat weight over time for different diets
ergoStool
Ergometrics experiment with stool types
Rail
Evaluation of Stress in Railway Rails
Fatigue
Cracks caused by metal fatigue
Glucose2
Glucose Levels Following Alcohol Ingestion
Pixel
X-ray pixel intensities over time
Nitrendipene
Assay of nitrendipene
Gun
Methods for firing naval guns
bdf
Language scores
Tetracycline1
Pharmacokinetics of tetracycline
Oxide
Variability in Semiconductor Manufacturing
Glucose
Glucose levels over time
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Meat
Tenderness of meat
RatPupWeight
The weight of rat pups
Quinidine
Quinidine Kinetics
Milk
Protein content of cows' milk
Orthodont
Growth curve data on an orthdontic measurement
Oxboys
Heights of Boys in Oxford
Oats
Split-plot Experiment on Varieties of Oats
Phenobarb
Phenobarbitol Kinetics