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nlme (version 3.1-10)
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
85,005
Version
3.1-10
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 31st, 2025
Functions in nlme (3.1-10)
Search all functions
formula.reStruct
Extract reStruct Object Formula
getCovariate
Extract Covariate from an Object
intervals
Confidence Intervals on Coefficients
pairs.compareFits
Pairs Plot of compareFits Object
MEdims
Calculate dimensions in mixed-effects
Matrix
Assign Matrix Values
MEEM
EM iterations for mixed-effects
formula.pdMat
Extract pdMat Formula
fixed.effects.lmList
Extract lmList Fixed Effects
logLik.varFunc
Extract varFunc logLik
allCoef
Extract Coefficients from a Set of Objects
solve.reStruct
Apply Solve to an reStruct Object
getGroups.varFunc
Extract varFunc Groups
formula.lme
Extract lme Object Formula
logLik.reStruct
Calculate reStruct Log-Likelihood
varFunc
Variance Function Structure
formula.modelStruct
Extract modelStruct Object Formula
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varIdent
Constant Variance Function
getData.gls
Extract gls Object Data
Variogram.corExp
Calculate Semi-variogram for a corExp Object
plot.nffGroupedData
Plot an nffGroupedData Object
coef.lmList
Extract lmList Coefficients
as.matrix.reStruct
Matrices of an reStruct Object
asTable
Convert groupedData to a matrix
getGroups.lmList
Extract lmList Object Groups
Covariate
Assign Covariate Values
ACF.gls
Autocorrelation Function for gls Residuals
plot.intervals.lmList
Plot lmList Confidence Intervals
getCovariateFormula
Extract Covariates Formula
varPower
Power Variance Function
Gun
Methods for firing naval guns
varWeights.glsStruct
Variance Weights for glsStruct Object
Dialyzer
High-Flux Hemodialyzer
Coef
Assign Values to Coefficients
Dim.corStruct
Dimensions of a corStruct Object
Dim.pdMat
Dimensions of a pdMat Object
update.varFunc
Update varFunc Object
Dim.corSpatial
Dimensions of a corSpatial Object
Matrix.pdMat
Assign Matrix to a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
Names.formula
Extract Names from a formula
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
Matrix.reStruct
Assign reStruct Matrices
Ovary
Counts of Ovarian Follicles
MathAchSchool
School demographic data for MathAchieve
Machines
Productivity Scores for Machines and Workers
IGF
Radioimmunoassay of IGF-I Protein
Pixel
X-ray pixel intensities over time
MathAchieve
Mathematics achievement scores
as.matrix.corStruct
Matrix of a corStruct Object
getGroups
Extract Grouping Factors from an Object
coef.pdMat
pdMat Object Coefficients
fdHess
Finite difference Hessian
pairs.lmList
Pairs Plot of an lmList Object
bdf
Language scores
getResponse.data.frame
Extract Response from a Data Frame
pairs.lme
Pairs Plot of an lme Object
glsObject
Fitted gls Object
formula.nlsList
Extract nlsList Object Formula
formula.gls
Extract gls Object Formula
getGroups.lme
Extract lme Object Groups
Cefamandole
Pharmacokinetics of Cefamandole
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
getGroupsFormula.gls
Extract gls Object Grouping Formula
varConstPower
Constant Plus Power Variance Function
getData.lmList
Extract lmList Object Data
corAR1
AR(1) Correlation Structure
initialize.glsStruct
Initialize a glsStruct Object
getGroupsFormula.reStruct
Extract reStruct Grouping Formula
getGroups.corStruct
Extract corStruct Groups
formula.gnls
Extract gnls Object Formula
getResponse.lme
Extract lme Object Response
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
varClasses
Variance Function Classes
logLik.lmList
Log-Likelihood of an lmList Object
corRatio
Rational Quadratic Correlation Structure
logLik.glsStruct
Log-Likelihood of a glsStruct Object
ACF
Autocorrelation Function
getData
Extract Data from an Object
pdClasses
Positive-Definite Matrix Classes
getGroups.gls
Extract gls Object Groups
Covariate.varFunc
Assign varFunc Covariate
asOneFormula
Combine Formulas of a Set of Objects
corCAR1
Continuous AR(1) Correlation Structure
[.pdMat
Subscript a pdMat Object
Names.reStruct
Names of an reStruct Object
corSpher
Spherical Correlation Structure
ACF.lme
Autocorrelation Function for lme Residuals
formula.groupedData
Extract groupedData Formula
coef.pdIdent
pdIdent Object Coefficients
BIC.logLik
BIC of a logLik Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
fitted.gls
Extract gls Fitted Values
Dim
Extract Dimensions from an Object
BIC
Bayesian Information Criterion
coef.reStruct
reStruct Object Coefficients
corSymm
General Correlation Structure
coef.lme
Extract lme Coefficients
initialize.corStruct
Initialize corStruct Object
AIC.logLik
AIC of a logLik Object
update.modelStruct
Update a modelStruct Object
contr.SAS
Contrast Matrices
model.matrix.reStruct
reStruct Model Matrix
fitted.glsStruct
Calculate glsStruct Fitted Values
corClasses
Correlation Structure Classes
getGroups.data.frame
Extract Groups from a Data Frame
pdConstruct.pdBlocked
Construct pdBlocked Objects
gnls
Fit Nonlinear Model Using Generalized Least Squares
nlmeControl
Control Values for nlme Fit
nlme.nlsList
NLME fit from nlsList Object
pdLogChol
General Positive-Definite Matrix
collapse.groupedData
Collapse a groupedData Object
fitted.lmList
Extract lmList Fitted Values
getGroupsFormula
Extract Grouping Formula
pdMat
Positive-Definite Matrix
plot.compareFits
Plot a compareFits Object
nlmeStruct
Nonlinear Mixed-Effects Structure
summary.gls
Summarize a gls Object
balancedGrouped
Create a groupedData object from a matrix
predict.gnls
Predictions from a gnls Object
plot.ACF
Plot an ACF Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
corMatrix
Extract Correlation Matrix
Remifentanil
Pharmacokinetics of remifentanil
Initialize.lmeStruct
Initialize an lmeStruct Object
plot.nmGroupedData
Plot an nmGroupedData Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
intervals.gls
Confidence Intervals on gls Parameters
glsStruct
Generalized Least Squares Structure
summary.pdMat
Summarize a pdMat Object
Oats
Split-plot Experiment on Varieties of Oats
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
plot.ranef.lmList
Plot a ranef.lmList Object
summary.corStruct
Summarize a corStruct Object
ranef.lme
Extract lme Random Effects
getData.lme
Extract lme Object Data
residuals.lmList
Extract lmList Residuals
intervals.lmList
Confidence Intervals on lmList Coefficients
summary.lme
Summarize an lme Object
phenoModel
Model function for the Phenobarb data
recalc.reStruct
Recalculate for an reStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
quinModel
Model function for the Quinidine data
Glucose2
Glucose Levels Following Alcohol Ingestion
residuals.nlmeStruct
Calculate nlmeStruct Residuals
augPred
Augmented Predictions
Rail
Evaluation of Stress in Railway Rails
corLin
Linear Correlation Structure
gnlsStruct
Generalized Nonlinear Least Squares Structure
coef.modelStruct
Extract modelStruct Object Coefficients
MEestimate
Estimate mixed-effects parameters
isBalanced
Check a Design for Balance
logLik.gls
Log-Likelihood of a gls Object
logDet
Extract the Logarithm of the Determinant
lmeControl
Control Values for lme Fit
VarCorr
Extract variance and correlation components
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
logLik.lme
Log-Likelihood of an lme Object
pdConstruct
Construct pdMat Objects
coef.corStruct
Coefficients of a corStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
anova.gls
Compare Likelihoods of Fitted Objects
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
getResponseFormula
Extract Formula Specifying Response Variable
fitted.lmeStruct
Calculate lmeStruct Fitted Values
fitted.gnls
Extract gnls Fitted Values
coef.pdDiag
pdDiag Object Coefficients
formula.nlme
Extract nlme Object Formula
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
intervals.lme
Confidence Intervals on lme Parameters
corFactor.corStruct
Factor of a corStruct Object Matrix
getCovariate.corStruct
Extract corStruct Object Covariate
Relaxin
Assay for Relaxin
print.summary.pdMat
Print a summary.pdMat Object
needUpdate
Check if Update is Needed
formula.nls
Extract Model Formula from nls Object
collapse
Collapse According to Groups
varComb
Combination of Variance Functions
Names.pdMat
Names of a pdMat Object
getCovariate.data.frame
Extract Data Frame Covariate
Milk
Protein content of cows' milk
logDet.corStruct
Extract corStruct Log-Determinant
corCompSymm
Compound Symmetry Correlation Structure
plot.Variogram
Plot a Variogram Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
gnlsObject
Fitted gnls Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
logDet.pdMat
Extract Log-Determinant from a pdMat Object
varFixed
Fixed Variance Function
gnlsControl
Control Values for gnls Fit
initialize.varFunc
Initialize varFunc Object
gls
Fit Linear Model Using Generalized Least Squares
summary.lmList
Summarize an lmList Object
gsummary
Summarize by Groups
lme.lmList
LME fit from lmList Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
groupedData
Construct a groupedData Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
recalc.corStruct
Recalculate for corStruct Object
Initialize
Initialize Object
pdBlocked
Positive-Definite Block Diagonal Matrix
Oxboys
Heights of Boys in Oxford
Quinidine
Quinidine Kinetics
varExp
Exponential Variance Function
plot.lmList
Plot an lmList Object
coef.pdCompSymm
pdCompSymm Object Coefficients
Oxide
Variability in Semiconductor Manufacturing
pdSymm
General Positive-Definite Matrix
lme
Linear Mixed-Effects Models
lmeScale
Scale for lme Optimization
Wheat2
Wheat Yield Trials
Wheat
Yields by growing conditions
pdIdent
Multiple of the Identity Positive-Definite Matrix
corARMA
ARMA(p,q) Correlation Structure
getVarCov
Extract variance-covariance matrix
lmeObject
Fitted lme Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
splitFormula
Split a Formula
Glucose
Glucose levels over time
gapply
Apply a Function by Groups
Soybean
Growth of soybean plants
comparePred
Compare Predictions
LDEsysMat
Generate system matrix for LDEs
varWeights
Extract Variance Function Weights
nlsList
List of nls Objects with a Common Model
Variogram.default
Calculate Semi-variogram
corGaus
Gaussian Correlation Structure
reStruct
Random Effects Structure
Initialize.reStruct
Initialize reStruct Object
residuals.lmeStruct
Calculate lmeStruct Residuals
Names
Names Associated with an Object
compareFits
Compare Fitted Objects
MEdecomp
Decompose a mixed-effects model
coef.gls
Extract gls Coefficients
pdDiag
Diagonal Positive-Definite Matrix
getCovariate.varFunc
Extract varFunc Covariate
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
nlmeObject
Fitted nlme Object
recalc.varFunc
Recalculate for varFunc Object
logLik.corStruct
Extract corStruct Log-Likelihood
plot.lme
Plot an lme or nls object
recalc
Recalculate Condensed Linear Model Object
formula.lmList
Extract lmList Object Formula
getResponse
Extract Response Variable from an Object
corFactor
Factor of a Correlation Matrix
lmList.groupedData
lmList Fit from a groupedData Object
Nitrendipene
Assay of nitrendipene
nlsList.selfStart
nlsList Fit from a selfStart Function
PBG
Effect of Phenylbiguanide on Blood Pressure
logLik.lm
Extract Log-Likelihood from an lm Object
summary.modelStruct
Summarize a modelStruct Object
summary.varFunc
Summarize varFunc Object
Fatigue
Cracks caused by metal fatigue
predict.lmList
Predictions from an lmList Object
BodyWeight
Rat weight over time for different diets
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
lme.groupedData
LME fit from groupedData Object
glsControl
Control Values for gls Fit
fixef.lmList
Extract lmList Fixed Effects
corMatrix.corStruct
Matrix of a corStruct Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
formula.pdBlocked
Extract pdBlocked Formula
predict.gls
Predictions from a gls Object
as.matrix.pdMat
Matrix of a pdMat Object
corNatural
General correlation in natural parameterization
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Gasoline
Refinery yield of gasoline
print.varFunc
Print a varFunc Object
Wafer
Modeling of Analog MOS Circuits
coef.varFunc
varFunc Object Coefficients
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.gls
Plot a gls Object
isInitialized
Check if Object is Initialized
residuals.gnlsStruct
Calculate gnlsStruct Residuals
fitted.lme
Extract lme Fitted Values
random.effects
Extract Random Effects
Muscle
Contraction of heart muscle sections
plot.ranef.lme
Plot a ranef.lme Object
lmList
List of lm Objects with a Common Model
residuals.gls
Extract gls Residuals
corSpatial
Spatial Correlation Structure
Variogram
Calculate Semi-variogram
anova.lme
Compare Likelihoods of Fitted Objects
corExp
Exponential Correlation Structure
predict.nlme
Predictions from an nlme Object
summary.nlsList
Summarize an nlsList Object
formula.corStruct
Extract corStruct Object Formula
Phenobarb
Phenobarbitol Kinetics
lmeStruct
Linear Mixed-Effects Structure
plot.augPred
Plot an augPred Object
residuals.lme
Extract lme Residuals
residuals.glsStruct
Calculate glsStruct Residuals
Spruce
Growth of Spruce Trees
getResponse.lmList
Extract lmList Object Response
Meat
Tenderness of meat
RatPupWeight
The weight of rat pups
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
Orthodont
Growth curve data on an orthdontic measurement
fixed.effects.lme
Extract lme Fixed Effects
Earthquake
Earthquake Intensity
Assay
Bioassay on Cell Culture Plate
Tetracycline2
Pharmacokinetics of tetracycline
fixed.effects
Extract Fixed Effects
Tetracycline1
Pharmacokinetics of tetracycline
coef.gnls
Extract gnls Coefficients
getResponse.gls
Extract gls Object Response
pooledSD
Extract Pooled Standard Deviation
ranef.lmList
Extract lmList Random Effects
nlme
Nonlinear Mixed-Effects Models
predict.lme
Predictions from an lme Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
simulate.lme
Simulate results from lme models
print.anova.lme
Print an anova.lme Object
print.summary.varFunc
Print a summary.varFunc Object
isInitialized.reStruct
Check if an reStruct Object is Initialized
print.groupedData
Print a groupedData Object
print.summary.modelStruct
Print a summary.modelStruct Object
print.lme
Print an lme Object
print.intervals.gls
Print an intervals.gls Object
update.lme
Update an lme Object
print.modelStruct
Print a modelStruct Object
print.corStruct
Print a corStruct Object
logDet.reStruct
Extract reStruct Log-Determinants
random.effects.lmList
Extract lmList Random Effects
print.lmList
Print an lmList Object
update.nlsList
Update an nlsList Object
print.summary.gls
Print a summary.gls Object
print.gls
Print a gls Object
ergoStool
Ergometrics experiment with stool types
AIC
Akaike Information Criterion
update.gls
Update a gls Object
update.gnls
Update a gnls Object
random.effects.lme
Extract lme Random Effects
print.summary.lmList
Print a summary.lmList Object
update.lmList
Update an lmList Object
print.intervals.lme
Print an intervals.lme Object
print.reStruct
Print an reStruct Object
update.groupedData
Update a groupedData Object
print.pdMat
Print a pdMat Object
pruneLevels
Prune Factor Levels
residuals.gnls
Extract gnls Residuals
print.summary.lme
Print a summary.lme Object
formula.varFunc
Extract varFunc Formula
update.nlme
Update an nlme Object
print.summary.corStruct
Print a summary.corStruct Object
getGroupsFormula.lmList
Extract lmList Object Grouping Formula
getGroupsFormula.lme
Extract lme Object Grouping Formula