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nlme (version 3.1-168)
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
122,138
Version
3.1-168
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-168)
Search all functions
Dim.corStruct
Dimensions of a corStruct Object
Dialyzer
High-Flux Hemodialyzer
Gasoline
Refinery yield of gasoline
[.pdMat
Subscript a pdMat Object
Glucose
Glucose levels over time
Dim.corSpatial
Dimensions of a corSpatial Object
Dim
Extract Dimensions from an Object
Dim.pdMat
Dimensions of a pdMat Object
Earthquake
Earthquake Intensity
Fatigue
Cracks caused by metal fatigue
Initialize.reStruct
Initialize reStruct Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Initialize
Initialize Object
Initialize.lmeStruct
Initialize an lmeStruct Object
LDEsysMat
Generate system matrix for LDEs
Initialize.corStruct
Initialize corStruct Object
Initialize.glsStruct
Initialize a glsStruct Object
IGF
Radioimmunoassay of IGF-I Protein
Initialize.varFunc
Initialize varFunc Object
Gun
Methods for firing naval guns
Matrix
Assign Matrix Values
Milk
Protein content of cows' milk
Meat
Tenderness of meat
MathAchieve
Mathematics achievement scores
Names.reStruct
Names of an reStruct Object
Machines
Productivity Scores for Machines and Workers
MathAchSchool
School demographic data for MathAchieve
Names.pdMat
Names of a pdMat Object
Phenobarb
Phenobarbitol Kinetics
PBG
Effect of Phenylbiguanide on Blood Pressure
Oxboys
Heights of Boys in Oxford
Orthodont
Growth curve data on an orthdontic measurement
Ovary
Counts of Ovarian Follicles
VarCorr
Extract variance and correlation components
Matrix.reStruct
Assign reStruct Matrices
Nitrendipene
Assay of nitrendipene
Oats
Split-plot Experiment on Varieties of Oats
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Soybean
Growth of soybean plants
Names
Names Associated with an Object
Pixel
X-ray pixel intensities over time
Muscle
Contraction of heart muscle sections
Variogram
Calculate Semi-variogram
Oxide
Variability in Semiconductor Manufacturing
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Names.formula
Extract Names from a formula
Variogram.corExp
Calculate Semi-variogram for a corExp Object
allCoef
Extract Coefficients from a Set of Objects
anova.gls
Compare Likelihoods of Fitted Objects
Wheat2
Wheat Yield Trials
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Spruce
Growth of Spruce Trees
Wheat
Yields by growing conditions
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Wafer
Modeling of Analog MOS Circuits
Names.pdBlocked
Names of a pdBlocked Object
RatPupWeight
The weight of rat pups
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Rail
Evaluation of Stress in Railway Rails
as.matrix.corStruct
Matrix of a corStruct Object
bdf
Language scores
anova.lme
Compare Likelihoods of Fitted Objects
coef.gnls
Extract gnls Coefficients
coef.corStruct
Coefficients of a corStruct Object
coef.pdMat
pdMat Object Coefficients
coef.lmList
Extract lmList Coefficients
Quinidine
Quinidine Kinetics
comparePred
Compare Predictions
coef.reStruct
reStruct Object Coefficients
Tetracycline1
Pharmacokinetics of tetracycline
Tetracycline2
Pharmacokinetics of tetracycline
augPred
Augmented Predictions
as.matrix.pdMat
Matrix of a pdMat Object
Relaxin
Assay for Relaxin
Remifentanil
Pharmacokinetics of Remifentanil
corExp
Exponential Correlation Structure
asOneFormula
Combine Formulas of a Set of Objects
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
balancedGrouped
Create a groupedData object from a matrix
Variogram.default
Calculate Semi-variogram
coef.varFunc
varFunc Object Coefficients
asTable
Convert groupedData to a matrix
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
collapse
Collapse According to Groups
corFactor
Factor of a Correlation Matrix
as.matrix.reStruct
Matrices of an reStruct Object
collapse.groupedData
Collapse a groupedData Object
corClasses
Correlation Structure Classes
compareFits
Compare Fitted Objects
corSpher
Spherical Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
corGaus
Gaussian Correlation Structure
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corCompSymm
Compound Symmetry Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
corRatio
Rational Quadratic Correlation Structure
fitted.lmList
Extract lmList Fitted Values
fitted.lme
Extract lme Fitted Values
corMatrix.corStruct
Matrix of a corStruct Object
corAR1
AR(1) Correlation Structure
coef.lme
Extract lme Coefficients
corLin
Linear Correlation Structure
corNatural
General correlation in natural parameterization
corMatrix
Extract Correlation Matrix
corSpatial
Spatial Correlation Structure
formula.pdBlocked
Extract pdBlocked Formula
getCovariateFormula
Extract Covariates Formula
formula.pdMat
Extract pdMat Formula
fitted.glsStruct
Calculate glsStruct Fitted Values
coef.modelStruct
Extract modelStruct Object Coefficients
corARMA
ARMA(p,q) Correlation Structure
getGroups.varFunc
Extract varFunc Groups
fixed.effects
Extract Fixed Effects
corSymm
General Correlation Structure
gapply
Apply a Function by Groups
corCAR1
Continuous AR(1) Correlation Structure
getGroups.lme
Extract lme Object Groups
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
fixef.lmList
Extract lmList Fixed Effects
formula.reStruct
Extract reStruct Object Formula
getCovariate.data.frame
Extract Data Frame Covariate
getResponseFormula
Extract Formula Specifying Response Variable
getData
Extract Data from an Object
glsControl
Control Values for gls Fit
glsObject
Fitted gls Object
getData.gls
Extract gls Object Data
getData.lmList
Extract lmList Object Data
getGroups.corStruct
Extract corStruct Groups
getGroups.data.frame
Extract Groups from a Data Frame
glsStruct
Generalized Least Squares Structure
getGroupsFormula
Extract Grouping Formula
gls
Fit Linear Model Using Generalized Least Squares
getResponse
Extract Response Variable from an Object
gls-internal
Auxiliary functions used by gls
lmList
List of lm Objects with a Common Model
gnls
Fit Nonlinear Model Using Generalized Least Squares
isInitialized
Check if Object is Initialized
getCovariate.varFunc
Extract varFunc Covariate
intervals.lme
Confidence Intervals on lme Parameters
getGroups
Extract Grouping Factors from an Object
getVarCov
Extract variance-covariance matrix
ergoStool
Ergometrics experiment with stool types
gnlsStruct
Generalized Nonlinear Least Squares Structure
getData.lme
Extract lme Object Data
intervals.gls
Confidence Intervals on gls Parameters
groupedData
Construct a groupedData Object
lmeStruct
Linear Mixed-Effects Structure
getCovariate.corStruct
Extract corStruct Object Covariate
fdHess
Finite difference Hessian
lmeControl
Specifying Control Values for lme Fit
getCovariate
Extract Covariate from an Object
isBalanced
Check a Design for Balance
lmeObject
Fitted lme Object
lme.lmList
LME fit from lmList Object
getGroups.lmList
Extract lmList Object Groups
getGroups.gls
Extract gls Object Groups
logDet.corStruct
Extract corStruct Log-Determinant
lme.groupedData
LME fit from groupedData Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.gnls
Log-Likelihood of a gnls Object
gnlsControl
Control Values for gnls Fit
intervals.lmList
Confidence Intervals on lmList Coefficients
logLik.lme
Log-Likelihood of an lme Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
lmList.groupedData
lmList Fit from a groupedData Object
logLik.reStruct
Calculate reStruct Log-Likelihood
lme
Linear Mixed-Effects Models
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logDet
Extract the Logarithm of the Determinant
nlmeStruct
Nonlinear Mixed-Effects Structure
gsummary
Summarize by Groups
logLik.varFunc
Extract varFunc logLik
nlme
Nonlinear Mixed-Effects Models
intervals
Confidence Intervals on Coefficients
gnlsObject
Fitted gnls Object
nlme.nlsList
NLME fit from nlsList Object
logLik.lmList
Log-Likelihood of an lmList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdClasses
Positive-Definite Matrix Classes
pdBlocked
Positive-Definite Block Diagonal Matrix
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdConstruct
Construct pdMat Objects
nlme-deprecated
Deprecated Functions in Package
nlme
pairs.lme
Pairs Plot of an lme Object
pairs.lmList
Pairs Plot of an lmList Object
pairs.compareFits
Pairs Plot of compareFits Object
nlsList
List of nls Objects with a Common Model
nlsList.selfStart
nlsList Fit from a selfStart Function
pdMat
Positive-Definite Matrix
needUpdate
Check if Update is Needed
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
phenoModel
Model function for the Phenobarb data
pdSymm
General Positive-Definite Matrix
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
plot.lmList
Plot an lmList Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
plot.augPred
Plot an augPred Object
model.matrix.reStruct
reStruct Model Matrix
pdLogChol
General Positive-Definite Matrix
plot.nffGroupedData
Plot an nffGroupedData Object
plot.lme
Plot an lme or nls object
logDet.reStruct
Extract reStruct Log-Determinants
plot.gls
Plot a gls Object
nlmeControl
Control Values for nlme Fit
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.compareFits
Plot a compareFits Object
predict.gls
Predictions from a gls Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdDiag
Diagonal Positive-Definite Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
logLik.corStruct
Extract corStruct Log-Likelihood
pdNatural
General Positive-Definite Matrix in Natural Parametrization
nlmeObject
Fitted nlme Object
plot.ACF
Plot an ACF Object
plot.ranef.lmList
Plot a ranef.lmList Object
pooledSD
Extract Pooled Standard Deviation
plot.ranef.lme
Plot a ranef.lme Object
plot.Variogram
Plot a Variogram Object
predict.lmList
Predictions from an lmList Object
plot.nmGroupedData
Plot an nmGroupedData Object
ranef.lme
Extract lme Random Effects
predict.nlme
Predictions from an nlme Object
predict.lme
Predictions from an lme Object
recalc.corStruct
Recalculate for corStruct Object
recalc
Recalculate Condensed Linear Model Object
reStruct
Random Effects Structure
recalc.modelStruct
Recalculate for a modelStruct Object
simulate.lme
Simulate Results from
lme
Models
recalc.reStruct
Recalculate for an reStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
predict.gnls
Predictions from a gnls Object
print.varFunc
Print a varFunc Object
residuals.lmList
Extract lmList Residuals
residuals.lme
Extract lme Residuals
residuals.gnlsStruct
Calculate gnlsStruct Residuals
recalc.varFunc
Recalculate for varFunc Object
splitFormula
Split a Formula
qqnorm.gls
Normal Plot of Residuals from a gls Object
solve.reStruct
Apply Solve to an reStruct Object
varComb
Combination of Variance Functions
summary.nlsList
Summarize an nlsList Object
summary.modelStruct
Summarize a modelStruct Object
varConstPower
Constant Plus Power Variance Function
ranef.lmList
Extract lmList Random Effects
varClasses
Variance Function Classes
print.summary.pdMat
Print a summary.pdMat Object
varExp
Exponential Variance Function
random.effects
Extract Random Effects
residuals.gls
Extract gls Residuals
varFixed
Fixed Variance Function
varConstProp
Constant Plus Proportion Variance Function
summary.corStruct
Summarize a corStruct Object
quinModel
Model function for the Quinidine data
residuals.nlmeStruct
Calculate nlmeStruct Residuals
residuals.lmeStruct
Calculate lmeStruct Residuals
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
summary.lmList
Summarize an lmList Object
varPower
Power Variance Function
update.modelStruct
Update a modelStruct Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
varWeights
Extract Variance Function Weights
summary.lme
Summarize an lme Object
summary.pdMat
Summarize a pdMat Object
varWeights.glsStruct
Variance Weights for glsStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
update.varFunc
Update varFunc Object
summary.varFunc
Summarize "varFunc" Object
varFunc
Variance Function Structure
varIdent
Constant Variance Function
Covariate
Assign Covariate Values
ACF
Autocorrelation Function
Cefamandole
Pharmacokinetics of Cefamandole
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Coef
Assign Values to Coefficients
Covariate.varFunc
Assign varFunc Covariate
Assay
Bioassay on Cell Culture Plate
BodyWeight
Rat weight over time for different diets
ACF.gls
Autocorrelation Function for gls Residuals
ACF.lme
Autocorrelation Function for lme Residuals