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