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nlme (version 3.1-87)
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
3.1-87
License
GPL (>=2)
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-87)
Search all functions
Machines
Productivity Scores for Machines and Workers
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Matrix.pdMat
Assign Matrix to a pdMat Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
Initialize
Initialize Object
ACF
Autocorrelation Function
print.varFunc
Print a varFunc Object
Dialyzer
High-Flux Hemodialyzer
Fatigue
Cracks caused by metal fatigue
Initialize.corStruct
Initialize corStruct Object
Milk
Protein content of cows' milk
Variogram.default
Calculate Semi-variogram
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Earthquake
Earthquake Intensity
Nitrendipene
Assay of nitrendipene
balancedGrouped
Create a groupedData object from a matrix
comparePred
Compare Predictions
Wheat2
Wheat Yield Trials
Glucose2
Glucose Levels Following Alcohol Ingestion
Names
Names Associated with an Object
getData.lme
Extract lme Object Data
corExp
Exponential Correlation Structure
Phenobarb
Phenobarbitol Kinetics
Remifentanil
Pharmacokinetics of remifentanil
Matrix.reStruct
Assign reStruct Matrices
Names.pdBlocked
Names of a pdBlocked Object
Oxboys
Heights of Boys in Oxford
Dim.corStruct
Dimensions of a corStruct Object
PBG
Effect of Phenylbiguanide on Blood Pressure
Names.pdMat
Names of a pdMat Object
getCovariateFormula
Extract Covariates Formula
corFactor
Factor of a Correlation Matrix
Dim
Extract Dimensions from an Object
Initialize.glsStruct
Initialize a glsStruct Object
MathAchieve
Mathematics achievement scores
anova.lme
Compare Likelihoods of Fitted Objects
coef.lmList
Extract lmList Coefficients
Initialize.reStruct
Initialize reStruct Object
IGF
Radioimmunoassay of IGF-I Protein
asOneFormula
Combine Formulas of a Set of Objects
coef.gnls
Extract gnls Coefficients
ACF.gls
Autocorrelation Function for gls Residuals
BIC.logLik
BIC of a logLik Object
plot.compareFits
Plot a compareFits Object
Ovary
Counts of Ovarian Follicles
Oats
Split-plot Experiment on Varieties of Oats
Variogram
Calculate Semi-variogram
BIC
Bayesian Information Criterion
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Matrix
Assign Matrix Values
asTable
Convert groupedData to a matrix
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Quinidine
Quinidine Kinetics
Variogram.corExp
Calculate Semi-variogram for a corExp Object
RatPupWeight
The weight of rat pups
Assay
Bioassay on Cell Culture Plate
nlme
Nonlinear Mixed-Effects Models
Names.formula
Extract Names from a formula
Dim.pdMat
Dimensions of a pdMat Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Covariate.varFunc
Assign varFunc Covariate
fitted.lme
Extract lme Fitted Values
gls
Fit Linear Model Using Generalized Least Squares
Coef
Assign Values to Coefficients
Initialize.varFunc
Initialize varFunc Object
Wafer
Modeling of Analog MOS Circuits
coef.varFunc
varFunc Object Coefficients
Orthodont
Growth curve data on an orthdontic measurement
coef.modelStruct
Extract modelStruct Object Coefficients
gnls
Fit Nonlinear Model Using Generalized Least Squares
getGroupsFormula
Extract Grouping Formula
isInitialized
Check if Object is Initialized
Muscle
Contraction of heart muscle sections
ACF.lme
Autocorrelation Function for lme Residuals
glsControl
Control Values for gls Fit
corAR1
AR(1) Correlation Structure
MathAchSchool
School demographic data for MathAchieve
as.matrix.corStruct
Matrix of a corStruct Object
Glucose
Glucose levels over time
allCoef
Extract Coefficients from a Set of Objects
Meat
Tenderness of meat
Wheat
Yields by growing conditions
coef.lme
Extract lme Coefficients
getGroups.lme
Extract lme Object Groups
lmeControl
Control Values for lme Fit
lmList
List of lm Objects with a Common Model
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
intervals.lme
Confidence Intervals on lme Parameters
formula.pdMat
Extract pdMat Formula
[.pdMat
Subscript a pdMat Object
predict.lmList
Predictions from an lmList Object
corFactor.corStruct
Factor of a corStruct Object Matrix
getResponse
Extract Response Variable from an Object
lme.lmList
LME fit from lmList Object
getData
Extract Data from an Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
ergoStool
Ergometrics experiment with stool types
collapse.groupedData
Collapse a groupedData Object
lmList.groupedData
lmList Fit from a groupedData Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
getData.gls
Extract gls Object Data
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
getVarCov
Extract variance-covariance matrix
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
VarCorr
Extract variance and correlation components
update.modelStruct
Update a modelStruct Object
getCovariate.corStruct
Extract corStruct Object Covariate
residuals.lmList
Extract lmList Residuals
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
corLin
Linear Correlation Structure
pdNatural
General Positive-Definite Matrix in Natural Parametrization
lme
Linear Mixed-Effects Models
isBalanced
Check a Design for Balance
getGroups
Extract Grouping Factors from an Object
summary.nlsList
Summarize an nlsList Object
corClasses
Correlation Structure Classes
fixed.effects
Extract Fixed Effects
getData.lmList
Extract lmList Object Data
recalc.reStruct
Recalculate for an reStruct Object
formula.reStruct
Extract reStruct Object Formula
gnlsObject
Fitted gnls Object
model.matrix.reStruct
reStruct Model Matrix
pairs.lmList
Pairs Plot of an lmList Object
varComb
Combination of Variance Functions
logLik.corStruct
Extract corStruct Log-Likelihood
corARMA
ARMA(p,q) Correlation Structure
nlmeObject
Fitted nlme Object
corCAR1
Continuous AR(1) Correlation Structure
logLik.glsStruct
Log-Likelihood of a glsStruct Object
corMatrix
Extract Correlation Matrix
corNatural
General correlation in natural parameterization
coef.corStruct
Coefficients of a corStruct Object
corSymm
General Correlation Structure
summary.gls
Summarize a gls Object
augPred
Augmented Predictions
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corSpher
Spherical Correlation Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
pdConstruct
Construct pdMat Objects
plot.Variogram
Plot a Variogram Object
nlsList.selfStart
nlsList Fit from a selfStart Function
as.matrix.pdMat
Matrix of a pdMat Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
pairs.compareFits
Pairs Plot of compareFits Object
gapply
Apply a Function by Groups
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
lme.groupedData
LME fit from groupedData Object
plot.gls
Plot a gls Object
residuals.glsStruct
Calculate glsStruct Residuals
lmeScale
Scale for lme Optimization
getGroups.corStruct
Extract corStruct Groups
anova.gls
Compare Likelihoods of Fitted Objects
plot.nmGroupedData
Plot an nmGroupedData Object
residuals.gls
Extract gls Residuals
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
glsStruct
Generalized Least Squares Structure
varFixed
Fixed Variance Function
logLik.gnls
Log-Likelihood of a gnls Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdDiag
Diagonal Positive-Definite Matrix
gnlsControl
Control Values for gnls Fit
fitted.lmList
Extract lmList Fitted Values
needUpdate
Check if Update is Needed
pdClasses
Positive-Definite Matrix Classes
intervals.gls
Confidence Intervals on gls Parameters
formula.pdBlocked
Extract pdBlocked Formula
plot.nfnGroupedData
Plot an nfnGroupedData Object
varWeights
Extract Variance Function Weights
plot.ranef.lmList
Plot a ranef.lmList Object
plot.lme
Plot an lme or nls object
quinModel
Model function for the Quinidine data
summary.corStruct
Summarize a corStruct Object
varIdent
Constant Variance Function
fdHess
Finite difference Hessian
predict.gnls
Predictions from a gnls Object
varPower
Power Variance Function
intervals
Confidence Intervals on Coefficients
plot.intervals.lmList
Plot lmList Confidence Intervals
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logDet
Extract the Logarithm of the Determinant
nlsList
List of nls Objects with a Common Model
getCovariate.data.frame
Extract Data Frame Covariate
pdLogChol
General Positive-Definite Matrix
getGroups.gls
Extract gls Object Groups
pdMat
Positive-Definite Matrix
intervals.lmList
Confidence Intervals on lmList Coefficients
varClasses
Variance Function Classes
getResponseFormula
Extract Formula Specifying Response Variable
glsObject
Fitted gls Object
phenoModel
Model function for the Phenobarb data
ranef.lmList
Extract lmList Random Effects
logLik.lme
Log-Likelihood of an lme Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
Pixel
X-ray pixel intensities over time
residuals.lme
Extract lme Residuals
random.effects
Extract Random Effects
recalc.corStruct
Recalculate for corStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
nlmeStruct
Nonlinear Mixed-Effects Structure
update.varFunc
Update varFunc Object
splitFormula
Split a Formula
plot.augPred
Plot an augPred Object
BodyWeight
Rat weight over time for different diets
residuals.gnlsStruct
Calculate gnlsStruct Residuals
varConstPower
Constant Plus Power Variance Function
varWeights.glsStruct
Variance Weights for glsStruct Object
predict.lme
Predictions from an lme Object
simulate.lme
Simulate results from lme models
summary.varFunc
Summarize varFunc Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
summary.lmList
Summarize an lmList Object
residuals.lmeStruct
Calculate lmeStruct Residuals
qqnorm.gls
Normal Plot of Residuals from a gls Object
bdf
Language scores
getGroups.lmList
Extract lmList Object Groups
summary.lme
Summarize an lme Object
reStruct
Random Effects Structure
pairs.lme
Pairs Plot of an lme Object
predict.nlme
Predictions from an nlme Object
Covariate
Assign Covariate Values
Initialize.lmeStruct
Initialize an lmeStruct Object
Gun
Methods for firing naval guns
Names.reStruct
Names of an reStruct Object
Rail
Evaluation of Stress in Railway Rails
Soybean
Growth of soybean plants
summary.pdMat
Summarize a pdMat Object
recalc.varFunc
Recalculate for varFunc Object
Relaxin
Assay for Relaxin
Tetracycline2
Pharmacokinetics of tetracycline
collapse
Collapse According to Groups
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
coef.reStruct
reStruct Object Coefficients
getGroups.data.frame
Extract Groups from a Data Frame
groupedData
Construct a groupedData Object
as.matrix.reStruct
Matrices of an reStruct Object
fixef.lmList
Extract lmList Fixed Effects
logDet.reStruct
Extract reStruct Log-Determinants
plot.ranef.lme
Plot a ranef.lme Object
Gasoline
Refinery yield of gasoline
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
corRatio
Rational Quadratic Correlation Structure
LDEsysMat
Generate system matrix for LDEs
Cefamandole
Pharmacokinetics of Cefamandole
compareFits
Compare Fitted Objects
Oxide
Variability in Semiconductor Manufacturing
getCovariate.varFunc
Extract varFunc Covariate
coef.pdMat
pdMat Object Coefficients
nlme.nlsList
NLME fit from nlsList Object
getGroups.varFunc
Extract varFunc Groups
corCompSymm
Compound Symmetry Correlation Structure
pooledSD
Extract Pooled Standard Deviation
logLik.varFunc
Extract varFunc logLik
ranef.lme
Extract lme Random Effects
gsummary
Summarize by Groups
print.summary.pdMat
Print a summary.pdMat Object
lmeObject
Fitted lme Object
getCovariate
Extract Covariate from an Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
Dim.corSpatial
Dimensions of a corSpatial Object
Spruce
Growth of Spruce Trees
summary.modelStruct
Summarize a modelStruct Object
nlmeControl
Control Values for nlme Fit
varExp
Exponential Variance Function
pdBlocked
Positive-Definite Block Diagonal Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
logDet.corStruct
Extract corStruct Log-Determinant
predict.gls
Predictions from a gls Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
lmeStruct
Linear Mixed-Effects Structure
plot.lmList
Plot an lmList Object
plot.nffGroupedData
Plot an nffGroupedData Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
solve.reStruct
Apply Solve to an reStruct Object
varFunc
Variance Function Structure
Tetracycline1
Pharmacokinetics of tetracycline
plot.ACF
Plot an ACF Object
corMatrix.corStruct
Matrix of a corStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
corGaus
Gaussian Correlation Structure
pdSymm
General Positive-Definite Matrix
recalc
Recalculate Condensed Linear Model Object
corSpatial
Spatial Correlation Structure