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nlme (version 3.1-78)
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
3.1-78
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-78)
Search all functions
Covariate
Assign Covariate Values
Covariate.varFunc
Assign varFunc Covariate
Matrix.pdMat
Assign Matrix to a pdMat Object
Dim.corStruct
Dimensions of a corStruct Object
Initialize
Initialize Object
Initialize.reStruct
Initialize reStruct Object
ACF
Autocorrelation Function
BIC.logLik
BIC of a logLik Object
Initialize.glsStruct
Initialize a glsStruct Object
Dim.pdMat
Dimensions of a pdMat Object
Coef
Assign Values to Coefficients
compareFits
Compare Fitted Objects
Variogram.corLin
Calculate Semi-variogram for a corLin Object
formula.reStruct
Extract reStruct Object Formula
augPred
Augmented Predictions
getCovariateFormula
Extract Covariates Formula
corFactor
Factor of a Correlation Matrix
formula.pdMat
Extract pdMat Formula
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
getData.gls
Extract gls Object Data
fitted.glsStruct
Calculate glsStruct Fitted Values
getGroups.corStruct
Extract corStruct Groups
fitted.lmeStruct
Calculate lmeStruct Fitted Values
comparePred
Compare Predictions
fitted.lmList
Extract lmList Fitted Values
fixed.effects
Extract Fixed Effects
getData
Extract Data from an Object
getGroups.gls
Extract gls Object Groups
getGroupsFormula
Extract Grouping Formula
intervals.lme
Confidence Intervals on lme Parameters
logDet
Extract the Logarithm of the Determinant
Names.reStruct
Names of an reStruct Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
plot.augPred
Plot an augPred Object
print.varFunc
Print a varFunc Object
predict.nlme
Predictions from an nlme Object
recalc
Recalculate Condensed Linear Model Object
recalc.varFunc
Recalculate for varFunc Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
recalc.corStruct
Recalculate for corStruct Object
Initialize.lmeStruct
Initialize an lmeStruct Object
lmeObject
Fitted lme Object
ACF.lme
Autocorrelation Function for lme Residuals
Names.formula
Extract Names from a formula
collapse
Collapse According to Groups
VarCorr
Extract variance and correlation components
as.matrix.corStruct
Matrix of a corStruct Object
varIdent
Constant Variance Function
allCoef
Extract Coefficients from a Set of Objects
getGroups.data.frame
Extract Groups from a Data Frame
getData.lmList
Extract lmList Object Data
pairs.lme
Pairs Plot of an lme Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
coef.pdMat
pdMat Object Coefficients
[.pdMat
Subscript a pdMat Object
logDet.reStruct
Extract reStruct Log-Determinants
corClasses
Correlation Structure Classes
getGroups
Extract Grouping Factors from an Object
nlmeStruct
Nonlinear Mixed-Effects Structure
residuals.gls
Extract gls Residuals
corRatio
Rational Quadratic Correlation Structure
gnlsStruct
Generalized Nonlinear Least Squares Structure
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
summary.gls
Summarize a gls Object
pairs.compareFits
Pairs Plot of compareFits Object
solve.reStruct
Apply Solve to an reStruct Object
intervals.lmList
Confidence Intervals on lmList Coefficients
corSymm
General Correlation Structure
Names.pdBlocked
Names of a pdBlocked Object
residuals.lme
Extract lme Residuals
Names
Names Associated with an Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
asTable
Convert groupedData to a matrix
getCovariate.data.frame
Extract Data Frame Covariate
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
BIC
Bayesian Information Criterion
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
balancedGrouped
Create a groupedData object from a matrix
quinModel
Model function for the Quinidine data
as.matrix.pdMat
Matrix of a pdMat Object
phenoModel
Model function for the Phenobarb data
logLik.reStruct
Calculate reStruct Log-Likelihood
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
corNatural
General correlation in natural parameterization
varWeights.lmeStruct
Variance Weights for lmeStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
getCovariate.varFunc
Extract varFunc Covariate
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
plot.ACF
Plot an ACF Object
coef.gnls
Extract gnls Coefficients
pairs.lmList
Pairs Plot of an lmList Object
as.matrix.reStruct
Matrices of an reStruct Object
fitted.lme
Extract lme Fitted Values
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
residuals.lmList
Extract lmList Residuals
logLik.glsStruct
Log-Likelihood of a glsStruct Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
varWeights
Extract Variance Function Weights
varFixed
Fixed Variance Function
nlsList.selfStart
nlsList Fit from a selfStart Function
recalc.reStruct
Recalculate for an reStruct Object
Variogram
Calculate Semi-variogram
update.modelStruct
Update a modelStruct Object
getResponse
Extract Response Variable from an Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
coef.modelStruct
Extract modelStruct Object Coefficients
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
corFactor.corStruct
Factor of a corStruct Object Matrix
getCovariate
Extract Covariate from an Object
predict.gnls
Predictions from a gnls Object
random.effects
Extract Random Effects
coef.varFunc
varFunc Object Coefficients
predict.gls
Predictions from a gls Object
needUpdate
Check if Update is Needed
summary.pdMat
Summarize a pdMat Object
print.summary.pdMat
Print a summary.pdMat Object
fdHess
Finite difference Hessian
plot.nmGroupedData
Plot an nmGroupedData Object
Matrix
Assign Matrix Values
summary.modelStruct
Summarize a modelStruct Object
corExp
Exponential Correlation Structure
varClasses
Variance Function Classes
model.matrix.reStruct
reStruct Model Matrix
getGroups.lmList
Extract lmList Object Groups
varExp
Exponential Variance Function
varPower
Power Variance Function
varWeights.glsStruct
Variance Weights for glsStruct Object
ranef.lmList
Extract lmList Random Effects
corARMA
ARMA(p,q) Correlation Structure
nlmeObject
Fitted nlme Object
getGroups.varFunc
Extract varFunc Groups
corCompSymm
Compound Symmetry Correlation Structure
pdIdent
Multiple of the Identity Positive-Definite Matrix
logLik.varFunc
Extract varFunc logLik
getResponseFormula
Extract Formula Specifying Response Variable
asOneFormula
Combine Formulas of a Set of Objects
plot.lme
Plot an lme or nls object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
coef.corStruct
Coefficients of a corStruct Object
corSpatial
Spatial Correlation Structure
summary.lmList
Summarize an lmList Object
corMatrix.corStruct
Matrix of a corStruct Object
gnlsControl
Control Values for gnls Fit
residuals.lmeStruct
Calculate lmeStruct Residuals
summary.corStruct
Summarize a corStruct Object
fixef.lmList
Extract lmList Fixed Effects
Initialize.corStruct
Initialize corStruct Object
lme
Linear Mixed-Effects Models
pooledSD
Extract Pooled Standard Deviation
coef.lme
Extract lme Coefficients
logLik.corStruct
Extract corStruct Log-Likelihood
lmeScale
Scale for lme Optimization
plot.ranef.lmList
Plot a ranef.lmList Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
Names.pdMat
Names of a pdMat Object
update.varFunc
Update varFunc Object
ACF.gls
Autocorrelation Function for gls Residuals
summary.varFunc
Summarize varFunc Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
LDEsysMat
Generate system matrix for LDEs
pdMat
Positive-Definite Matrix
Matrix.reStruct
Assign reStruct Matrices
predict.lme
Predictions from an lme Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
Dim.corSpatial
Dimensions of a corSpatial Object
intervals.gls
Confidence Intervals on gls Parameters
corLin
Linear Correlation Structure
recalc.modelStruct
Recalculate for a modelStruct Object
getVarCov
Extract variance-covariance matrix
pdConstruct
Construct pdMat Objects
corGaus
Gaussian Correlation Structure
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
glsObject
Fitted gls Object
Dim
Extract Dimensions from an Object
nlsList
List of nls Objects with a Common Model
summary.lme
Summarize an lme Object
plot.gls
Plot a gls Object
varFunc
Variance Function Structure
corCAR1
Continuous AR(1) Correlation Structure
getData.lme
Extract lme Object Data
Variogram.default
Calculate Semi-variogram
gsummary
Summarize by Groups
plot.ranef.lme
Plot a ranef.lme Object
varConstPower
Constant Plus Power Variance Function
logLik.lme
Log-Likelihood of an lme Object
plot.Variogram
Plot a Variogram Object
intervals
Confidence Intervals on Coefficients
anova.lme
Compare Likelihoods of Fitted Objects
pdDiag
Diagonal Positive-Definite Matrix
pdClasses
Positive-Definite Matrix Classes
lmList
List of lm Objects with a Common Model
getGroups.lme
Extract lme Object Groups
summary.nlsList
Summarize an nlsList Object
lme.lmList
LME fit from lmList Object
pdLogChol
General Positive-Definite Matrix
pdBlocked
Positive-Definite Block Diagonal Matrix
qqnorm.gls
Normal Plot of Residuals from a gls Object
plot.intervals.lmList
Plot lmList Confidence Intervals
collapse.groupedData
Collapse a groupedData Object
lmeStruct
Linear Mixed-Effects Structure
corSpher
Spherical Correlation Structure
residuals.gnlsStruct
Calculate gnlsStruct Residuals
coef.lmList
Extract lmList Coefficients
Initialize.varFunc
Initialize varFunc Object
simulate.lme
Simulate results from lme models
varComb
Combination of Variance Functions
corMatrix
Extract Correlation Matrix
glsStruct
Generalized Least Squares Structure
pdSymm
General Positive-Definite Matrix
isInitialized
Check if Object is Initialized
plot.nffGroupedData
Plot an nffGroupedData Object
nlmeControl
Control Values for nlme Fit
lmList.groupedData
lmList Fit from a groupedData Object
isBalanced
Check a Design for Balance
splitFormula
Split a Formula
plot.lmList
Plot an lmList Object
nlme.nlsList
NLME fit from nlsList Object
residuals.glsStruct
Calculate glsStruct Residuals
reStruct
Random Effects Structure
lme.groupedData
LME fit from groupedData Object
logLik.gnls
Log-Likelihood of a gnls Object
gls
Fit Linear Model Using Generalized Least Squares
plot.nfnGroupedData
Plot an nfnGroupedData Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
logDet.corStruct
Extract corStruct Log-Determinant
nlme
Nonlinear Mixed-Effects Models
pdFactor
Square-Root Factor of a Positive-Definite Matrix
predict.lmList
Predictions from an lmList Object
formula.pdBlocked
Extract pdBlocked Formula
getCovariate.corStruct
Extract corStruct Object Covariate
coef.reStruct
reStruct Object Coefficients
ranef.lme
Extract lme Random Effects
anova.gls
Compare Likelihoods of Fitted Objects
lmeControl
Control Values for lme Fit
corAR1
AR(1) Correlation Structure
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
plot.compareFits
Plot a compareFits Object
glsControl
Control Values for gls Fit
gnlsObject
Fitted gnls Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
groupedData
Construct a groupedData Object
gapply
Apply a Function by Groups
Cefamandole
Pharmacokinetics of Cefamandole
MathAchSchool
School demographic data for MathAchieve
Machines
Productivity Scores for Machines and Workers
Quinidine
Quinidine Kinetics
Gasoline
Refinery yield of gasoline
Wheat
Yields by growing conditions
Glucose2
Glucose Levels Following Alcohol Ingestion
Glucose
Glucose levels over time
Oxide
Variability in Semiconductor Manufacturing
Muscle
Contraction of heart muscle sections
Fatigue
Cracks caused by metal fatigue
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
IGF
Radioimmunoassay of IGF-I Protein
Soybean
Growth of soybean plants
Earthquake
Earthquake Intensity
Phenobarb
Phenobarbitol Kinetics
Spruce
Growth of Spruce Trees
Meat
Tenderness of meat
Nitrendipene
Assay of nitrendipene
Tetracycline1
Pharmacokinetics of tetracycline
PBG
Effect of Phenylbiguanide on Blood Pressure
bdf
Language scores
Oats
Split-plot Experiment on Varieties of Oats
Rail
Evaluation of Stress in Railway Rails
Pixel
X-ray pixel intensities over time
MathAchieve
Mathematics achievement scores
Tetracycline2
Pharmacokinetics of tetracycline
RatPupWeight
The weight of rat pups
Oxboys
Heights of Boys in Oxford
ergoStool
Ergometrics experiment with stool types
Orthodont
Growth curve data on an orthdontic measurement
Relaxin
Assay for Relaxin
Wheat2
Wheat Yield Trials
BodyWeight
Rat weight over time for different diets
Ovary
Counts of Ovarian Follicles
Dialyzer
High-Flux Hemodialyzer
Wafer
Modeling of Analog MOS Circuits
Milk
Protein content of cows' milk
Remifentanil
Pharmacokinetics of remifentanil
Gun
Methods for firing naval guns
Assay
Bioassay on Cell Culture Plate