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nlme (version 3.1-79)
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
3.1-79
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-79)
Search all functions
[.pdMat
Subscript a pdMat Object
Initialize
Initialize Object
ACF
Autocorrelation Function
ACF.gls
Autocorrelation Function for gls Residuals
BIC
Bayesian Information Criterion
Dim.corSpatial
Dimensions of a corSpatial Object
Initialize.lmeStruct
Initialize an lmeStruct Object
ACF.lme
Autocorrelation Function for lme Residuals
Matrix
Assign Matrix Values
BIC.logLik
BIC of a logLik Object
Initialize.corStruct
Initialize corStruct Object
Initialize.reStruct
Initialize reStruct Object
getCovariate.varFunc
Extract varFunc Covariate
getGroups.lmList
Extract lmList Object Groups
getGroups.gls
Extract gls Object Groups
getGroups.varFunc
Extract varFunc Groups
as.matrix.corStruct
Matrix of a corStruct Object
glsObject
Fitted gls Object
Variogram
Calculate Semi-variogram
coef.gnls
Extract gnls Coefficients
corFactor
Factor of a Correlation Matrix
gapply
Apply a Function by Groups
varFunc
Variance Function Structure
varClasses
Variance Function Classes
summary.varFunc
Summarize varFunc Object
summary.gls
Summarize a gls Object
Dim.pdMat
Dimensions of a pdMat Object
collapse.groupedData
Collapse a groupedData Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
varComb
Combination of Variance Functions
summary.modelStruct
Summarize a modelStruct Object
recalc.reStruct
Recalculate for an reStruct Object
Dim
Extract Dimensions from an Object
Matrix.reStruct
Assign reStruct Matrices
anova.gls
Compare Likelihoods of Fitted Objects
LDEsysMat
Generate system matrix for LDEs
Variogram.default
Calculate Semi-variogram
getGroups.data.frame
Extract Groups from a Data Frame
coef.pdMat
pdMat Object Coefficients
Names.pdMat
Names of a pdMat Object
as.matrix.reStruct
Matrices of an reStruct Object
residuals.gls
Extract gls Residuals
getGroups
Extract Grouping Factors from an Object
corARMA
ARMA(p,q) Correlation Structure
allCoef
Extract Coefficients from a Set of Objects
VarCorr
Extract variance and correlation components
phenoModel
Model function for the Phenobarb data
residuals.lmList
Extract lmList Residuals
coef.reStruct
reStruct Object Coefficients
asOneFormula
Combine Formulas of a Set of Objects
corClasses
Correlation Structure Classes
Names.pdBlocked
Names of a pdBlocked Object
collapse
Collapse According to Groups
residuals.lme
Extract lme Residuals
random.effects
Extract Random Effects
fitted.lmList
Extract lmList Fitted Values
recalc.modelStruct
Recalculate for a modelStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
augPred
Augmented Predictions
logLik.lmList
Log-Likelihood of an lmList Object
Initialize.varFunc
Initialize varFunc Object
getCovariate.corStruct
Extract corStruct Object Covariate
recalc.varFunc
Recalculate for varFunc Object
corNatural
General correlation in natural parameterization
fitted.glsStruct
Calculate glsStruct Fitted Values
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.augPred
Plot an augPred Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
recalc
Recalculate Condensed Linear Model Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corCompSymm
Compound Symmetry Correlation Structure
predict.lmList
Predictions from an lmList Object
ranef.lme
Extract lme Random Effects
Names
Names Associated with an Object
corGaus
Gaussian Correlation Structure
coef.lme
Extract lme Coefficients
Dim.corStruct
Dimensions of a corStruct Object
Matrix.pdMat
Assign Matrix to a pdMat Object
getCovariateFormula
Extract Covariates Formula
varWeights.glsStruct
Variance Weights for glsStruct Object
summary.lmList
Summarize an lmList Object
getData
Extract Data from an Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
compareFits
Compare Fitted Objects
summary.pdMat
Summarize a pdMat Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Covariate
Assign Covariate Values
splitFormula
Split a Formula
update.varFunc
Update varFunc Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
getGroups.corStruct
Extract corStruct Groups
solve.reStruct
Apply Solve to an reStruct Object
as.matrix.pdMat
Matrix of a pdMat Object
summary.corStruct
Summarize a corStruct Object
update.modelStruct
Update a modelStruct Object
gls
Fit Linear Model Using Generalized Least Squares
Variogram.corExp
Calculate Semi-variogram for a corExp Object
getData.gls
Extract gls Object Data
getCovariate.data.frame
Extract Data Frame Covariate
asTable
Convert groupedData to a matrix
Variogram.corLin
Calculate Semi-variogram for a corLin Object
varIdent
Constant Variance Function
coef.modelStruct
Extract modelStruct Object Coefficients
comparePred
Compare Predictions
residuals.nlmeStruct
Calculate nlmeStruct Residuals
nlmeObject
Fitted nlme Object
gnlsObject
Fitted gnls Object
corAR1
AR(1) Correlation Structure
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
pooledSD
Extract Pooled Standard Deviation
corCAR1
Continuous AR(1) Correlation Structure
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corLin
Linear Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
varExp
Exponential Variance Function
fdHess
Finite difference Hessian
formula.pdMat
Extract pdMat Formula
corMatrix.corStruct
Matrix of a corStruct Object
simulate.lme
Simulate results from lme models
quinModel
Model function for the Quinidine data
corRatio
Rational Quadratic Correlation Structure
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
corExp
Exponential Correlation Structure
glsStruct
Generalized Least Squares Structure
lmeScale
Scale for lme Optimization
getResponse
Extract Response Variable from an Object
logDet
Extract the Logarithm of the Determinant
nlmeStruct
Nonlinear Mixed-Effects Structure
logLik.corStruct
Extract corStruct Log-Likelihood
model.matrix.reStruct
reStruct Model Matrix
plot.ACF
Plot an ACF Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdFactor
Square-Root Factor of a Positive-Definite Matrix
logDet.reStruct
Extract reStruct Log-Determinants
logLik.reStruct
Calculate reStruct Log-Likelihood
print.summary.pdMat
Print a summary.pdMat Object
formula.pdBlocked
Extract pdBlocked Formula
needUpdate
Check if Update is Needed
lmeStruct
Linear Mixed-Effects Structure
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Coef
Assign Values to Coefficients
isBalanced
Check a Design for Balance
predict.gls
Predictions from a gls Object
logLik.varFunc
Extract varFunc logLik
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
ranef.lmList
Extract lmList Random Effects
logLik.lme
Log-Likelihood of an lme Object
isInitialized
Check if Object is Initialized
predict.lme
Predictions from an lme Object
intervals.lme
Confidence Intervals on lme Parameters
residuals.lmeStruct
Calculate lmeStruct Residuals
gnlsControl
Control Values for gnls Fit
lmeControl
Control Values for lme Fit
nlme.nlsList
NLME fit from nlsList Object
getData.lmList
Extract lmList Object Data
getVarCov
Extract variance-covariance matrix
gnls
Fit Nonlinear Model Using Generalized Least Squares
pdIdent
Multiple of the Identity Positive-Definite Matrix
plot.nmGroupedData
Plot an nmGroupedData Object
Names.formula
Extract Names from a formula
Initialize.glsStruct
Initialize a glsStruct Object
Names.reStruct
Names of an reStruct Object
Covariate.varFunc
Assign varFunc Covariate
varFixed
Fixed Variance Function
varPower
Power Variance Function
varWeights.lmeStruct
Variance Weights for lmeStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
getGroups.lme
Extract lme Object Groups
corMatrix
Extract Correlation Matrix
coef.lmList
Extract lmList Coefficients
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
nlme
Nonlinear Mixed-Effects Models
fixed.effects
Extract Fixed Effects
reStruct
Random Effects Structure
formula.reStruct
Extract reStruct Object Formula
summary.nlsList
Summarize an nlsList Object
getGroupsFormula
Extract Grouping Formula
plot.ranef.lme
Plot a ranef.lme Object
groupedData
Construct a groupedData Object
plot.lmList
Plot an lmList Object
nlsList.selfStart
nlsList Fit from a selfStart Function
lme
Linear Mixed-Effects Models
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
glsControl
Control Values for gls Fit
summary.lme
Summarize an lme Object
gsummary
Summarize by Groups
corSymm
General Correlation Structure
logDet.pdMat
Extract Log-Determinant from a pdMat Object
print.varFunc
Print a varFunc Object
pdBlocked
Positive-Definite Block Diagonal Matrix
intervals.lmList
Confidence Intervals on lmList Coefficients
lmList
List of lm Objects with a Common Model
corSpher
Spherical Correlation Structure
recalc.corStruct
Recalculate for corStruct Object
getData.lme
Extract lme Object Data
varWeights
Extract Variance Function Weights
getCovariate
Extract Covariate from an Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
fitted.lme
Extract lme Fitted Values
varConstPower
Constant Plus Power Variance Function
balancedGrouped
Create a groupedData object from a matrix
pairs.lmList
Pairs Plot of an lmList Object
coef.corStruct
Coefficients of a corStruct Object
coef.varFunc
varFunc Object Coefficients
residuals.gnlsStruct
Calculate gnlsStruct Residuals
lme.groupedData
LME fit from groupedData Object
fixef.lmList
Extract lmList Fixed Effects
pdMat
Positive-Definite Matrix
getResponseFormula
Extract Formula Specifying Response Variable
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
lmList.groupedData
lmList Fit from a groupedData Object
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.nffGroupedData
Plot an nffGroupedData Object
predict.gnls
Predictions from a gnls Object
intervals
Confidence Intervals on Coefficients
plot.compareFits
Plot a compareFits Object
pairs.compareFits
Pairs Plot of compareFits Object
logDet.corStruct
Extract corStruct Log-Determinant
lmeObject
Fitted lme Object
pdLogChol
General Positive-Definite Matrix
intervals.gls
Confidence Intervals on gls Parameters
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdClasses
Positive-Definite Matrix Classes
pdSymm
General Positive-Definite Matrix
plot.Variogram
Plot a Variogram Object
predict.nlme
Predictions from an nlme Object
plot.ranef.lmList
Plot a ranef.lmList Object
pairs.lme
Pairs Plot of an lme Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
pdDiag
Diagonal Positive-Definite Matrix
logLik.gnls
Log-Likelihood of a gnls Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
plot.lme
Plot an lme or nls object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
plot.gls
Plot a gls Object
lme.lmList
LME fit from lmList Object
nlsList
List of nls Objects with a Common Model
corSpatial
Spatial Correlation Structure
pdConstruct
Construct pdMat Objects
plot.nfnGroupedData
Plot an nfnGroupedData Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
nlmeControl
Control Values for nlme Fit
Glucose
Glucose levels over time
Wheat2
Wheat Yield Trials
Machines
Productivity Scores for Machines and Workers
Cefamandole
Pharmacokinetics of Cefamandole
Oxide
Variability in Semiconductor Manufacturing
Wafer
Modeling of Analog MOS Circuits
Dialyzer
High-Flux Hemodialyzer
MathAchieve
Mathematics achievement scores
Tetracycline1
Pharmacokinetics of tetracycline
Glucose2
Glucose Levels Following Alcohol Ingestion
IGF
Radioimmunoassay of IGF-I Protein
RatPupWeight
The weight of rat pups
Ovary
Counts of Ovarian Follicles
Orthodont
Growth curve data on an orthdontic measurement
ergoStool
Ergometrics experiment with stool types
Meat
Tenderness of meat
MathAchSchool
School demographic data for MathAchieve
PBG
Effect of Phenylbiguanide on Blood Pressure
Tetracycline2
Pharmacokinetics of tetracycline
BodyWeight
Rat weight over time for different diets
Quinidine
Quinidine Kinetics
Fatigue
Cracks caused by metal fatigue
Muscle
Contraction of heart muscle sections
Gasoline
Refinery yield of gasoline
Milk
Protein content of cows' milk
Rail
Evaluation of Stress in Railway Rails
Nitrendipene
Assay of nitrendipene
Phenobarb
Phenobarbitol Kinetics
Assay
Bioassay on Cell Culture Plate
Oats
Split-plot Experiment on Varieties of Oats
Wheat
Yields by growing conditions
Spruce
Growth of Spruce Trees
bdf
Language scores
Earthquake
Earthquake Intensity
Gun
Methods for firing naval guns
Remifentanil
Pharmacokinetics of remifentanil
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Pixel
X-ray pixel intensities over time
Soybean
Growth of soybean plants
Relaxin
Assay for Relaxin
Oxboys
Heights of Boys in Oxford