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nlme (version 3.1-90)
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
3.1-90
License
GPL (>=2)
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-90)
Search all functions
BodyWeight
Rat weight over time for different diets
Spruce
Growth of Spruce Trees
[.pdMat
Subscript a pdMat Object
bdf
Language scores
Assay
Bioassay on Cell Culture Plate
VarCorr
Extract variance and correlation components
asTable
Convert groupedData to a matrix
Covariate.varFunc
Assign varFunc Covariate
Names.pdMat
Names of a pdMat Object
Wafer
Modeling of Analog MOS Circuits
Initialize.reStruct
Initialize reStruct Object
allCoef
Extract Coefficients from a Set of Objects
Dim.corStruct
Dimensions of a corStruct Object
Glucose
Glucose levels over time
Initialize.lmeStruct
Initialize an lmeStruct Object
Nitrendipene
Assay of nitrendipene
getData.gls
Extract gls Object Data
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Gun
Methods for firing naval guns
Initialize.glsStruct
Initialize a glsStruct Object
LDEsysMat
Generate system matrix for LDEs
Matrix.reStruct
Assign reStruct Matrices
ACF.lme
Autocorrelation Function for lme Residuals
corSpher
Spherical Correlation Structure
as.matrix.pdMat
Matrix of a pdMat Object
Covariate
Assign Covariate Values
balancedGrouped
Create a groupedData object from a matrix
IGF
Radioimmunoassay of IGF-I Protein
corGaus
Gaussian Correlation Structure
Soybean
Growth of soybean plants
BIC.logLik
BIC of a logLik Object
collapse
Collapse According to Groups
as.matrix.reStruct
Matrices of an reStruct Object
Initialize
Initialize Object
corClasses
Correlation Structure Classes
ACF
Autocorrelation Function
corNatural
General correlation in natural parameterization
Dim.corSpatial
Dimensions of a corSpatial Object
asOneFormula
Combine Formulas of a Set of Objects
Tetracycline1
Pharmacokinetics of tetracycline
getCovariateFormula
Extract Covariates Formula
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
Initialize.varFunc
Initialize varFunc Object
Fatigue
Cracks caused by metal fatigue
fixef.lmList
Extract lmList Fixed Effects
corMatrix.corStruct
Matrix of a corStruct Object
corAR1
AR(1) Correlation Structure
corSymm
General Correlation Structure
Names.formula
Extract Names from a formula
Names.pdBlocked
Names of a pdBlocked Object
MathAchSchool
School demographic data for MathAchieve
Relaxin
Assay for Relaxin
Matrix.pdMat
Assign Matrix to a pdMat Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Dim.pdMat
Dimensions of a pdMat Object
Names
Names Associated with an Object
Phenobarb
Phenobarbitol Kinetics
Wheat2
Wheat Yield Trials
corFactor
Factor of a Correlation Matrix
Earthquake
Earthquake Intensity
getGroups.data.frame
Extract Groups from a Data Frame
Matrix
Assign Matrix Values
Wheat
Yields by growing conditions
coef.corStruct
Coefficients of a corStruct Object
coef.varFunc
varFunc Object Coefficients
Names.reStruct
Names of an reStruct Object
MathAchieve
Mathematics achievement scores
Oxide
Variability in Semiconductor Manufacturing
Oxboys
Heights of Boys in Oxford
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Dialyzer
High-Flux Hemodialyzer
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Variogram.default
Calculate Semi-variogram
fitted.glsStruct
Calculate glsStruct Fitted Values
corARMA
ARMA(p,q) Correlation Structure
formula.reStruct
Extract reStruct Object Formula
coef.pdMat
pdMat Object Coefficients
corMatrix
Extract Correlation Matrix
getData
Extract Data from an Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getCovariate
Extract Covariate from an Object
corLin
Linear Correlation Structure
getResponseFormula
Extract Formula Specifying Response Variable
intervals.lmList
Confidence Intervals on lmList Coefficients
getCovariate.varFunc
Extract varFunc Covariate
getGroups.lme
Extract lme Object Groups
pdNatural
General Positive-Definite Matrix in Natural Parametrization
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
compareFits
Compare Fitted Objects
Quinidine
Quinidine Kinetics
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getCovariate.corStruct
Extract corStruct Object Covariate
gnlsControl
Control Values for gnls Fit
logDet.corStruct
Extract corStruct Log-Determinant
gnlsStruct
Generalized Nonlinear Least Squares Structure
lmList
List of lm Objects with a Common Model
coef.lme
Extract lme Coefficients
ergoStool
Ergometrics experiment with stool types
intervals
Confidence Intervals on Coefficients
glsObject
Fitted gls Object
logLik.lme
Log-Likelihood of an lme Object
lme.groupedData
LME fit from groupedData Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
recalc.reStruct
Recalculate for an reStruct Object
collapse.groupedData
Collapse a groupedData Object
gls
Fit Linear Model Using Generalized Least Squares
glsControl
Control Values for gls Fit
getData.lmList
Extract lmList Object Data
lme
Linear Mixed-Effects Models
gnls
Fit Nonlinear Model Using Generalized Least Squares
fitted.lme
Extract lme Fitted Values
pdFactor
Square-Root Factor of a Positive-Definite Matrix
fdHess
Finite difference Hessian
fitted.lmeStruct
Calculate lmeStruct Fitted Values
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
phenoModel
Model function for the Phenobarb data
fitted.lmList
Extract lmList Fitted Values
getGroups.gls
Extract gls Object Groups
coef.modelStruct
Extract modelStruct Object Coefficients
qqnorm.gls
Normal Plot of Residuals from a gls Object
fixed.effects
Extract Fixed Effects
corRatio
Rational Quadratic Correlation Structure
gnlsObject
Fitted gnls Object
lmeObject
Fitted lme Object
plot.nffGroupedData
Plot an nffGroupedData Object
augPred
Augmented Predictions
corExp
Exponential Correlation Structure
varIdent
Constant Variance Function
logDet
Extract the Logarithm of the Determinant
getData.lme
Extract lme Object Data
logLik.gnls
Log-Likelihood of a gnls Object
isInitialized
Check if Object is Initialized
nlmeObject
Fitted nlme Object
lmList.groupedData
lmList Fit from a groupedData Object
lmeScale
Scale for lme Optimization
pairs.lmList
Pairs Plot of an lmList Object
plot.gls
Plot a gls Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
pdClasses
Positive-Definite Matrix Classes
nlsList
List of nls Objects with a Common Model
logDet.pdMat
Extract Log-Determinant from a pdMat Object
getGroups.lmList
Extract lmList Object Groups
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
Initialize.corStruct
Initialize corStruct Object
plot.compareFits
Plot a compareFits Object
pairs.lme
Pairs Plot of an lme Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdMat
Positive-Definite Matrix
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
varFixed
Fixed Variance Function
recalc.modelStruct
Recalculate for a modelStruct Object
intervals.gls
Confidence Intervals on gls Parameters
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
pdIdent
Multiple of the Identity Positive-Definite Matrix
lmeControl
Control Values for lme Fit
pdConstruct
Construct pdMat Objects
logLik.lmList
Log-Likelihood of an lmList Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
summary.gls
Summarize a gls Object
nlmeControl
Control Values for nlme Fit
plot.nfnGroupedData
Plot an nfnGroupedData Object
logDet.reStruct
Extract reStruct Log-Determinants
logLik.corStruct
Extract corStruct Log-Likelihood
varFunc
Variance Function Structure
ranef.lmList
Extract lmList Random Effects
summary.varFunc
Summarize varFunc Object
residuals.lme
Extract lme Residuals
pooledSD
Extract Pooled Standard Deviation
random.effects
Extract Random Effects
intervals.lme
Confidence Intervals on lme Parameters
varWeights.lmeStruct
Variance Weights for lmeStruct Object
predict.lmList
Predictions from an lmList Object
PBG
Effect of Phenylbiguanide on Blood Pressure
solve.reStruct
Apply Solve to an reStruct Object
plot.ranef.lme
Plot a ranef.lme Object
residuals.lmList
Extract lmList Residuals
plot.ranef.lmList
Plot a ranef.lmList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
varClasses
Variance Function Classes
nlme.nlsList
NLME fit from nlsList Object
summary.nlsList
Summarize an nlsList Object
plot.ACF
Plot an ACF Object
ranef.lme
Extract lme Random Effects
nlsList.selfStart
nlsList Fit from a selfStart Function
plot.augPred
Plot an augPred Object
varPower
Power Variance Function
logLik.glsStruct
Log-Likelihood of a glsStruct Object
summary.corStruct
Summarize a corStruct Object
plot.nmGroupedData
Plot an nmGroupedData Object
recalc.corStruct
Recalculate for corStruct Object
summary.pdMat
Summarize a pdMat Object
getGroups.corStruct
Extract corStruct Groups
residuals.lmeStruct
Calculate lmeStruct Residuals
summary.lmList
Summarize an lmList Object
Oats
Split-plot Experiment on Varieties of Oats
formula.pdBlocked
Extract pdBlocked Formula
recalc.varFunc
Recalculate for varFunc Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
nlmeStruct
Nonlinear Mixed-Effects Structure
varConstPower
Constant Plus Power Variance Function
glsStruct
Generalized Least Squares Structure
predict.lme
Predictions from an lme Object
summary.modelStruct
Summarize a modelStruct Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Rail
Evaluation of Stress in Railway Rails
corSpatial
Spatial Correlation Structure
BIC
Bayesian Information Criterion
gapply
Apply a Function by Groups
getResponse
Extract Response Variable from an Object
lmeStruct
Linear Mixed-Effects Structure
Gasoline
Refinery yield of gasoline
Glucose2
Glucose Levels Following Alcohol Ingestion
corCompSymm
Compound Symmetry Correlation Structure
formula.pdMat
Extract pdMat Formula
getVarCov
Extract variance-covariance matrix
pdDiag
Diagonal Positive-Definite Matrix
plot.Variogram
Plot a Variogram Object
RatPupWeight
The weight of rat pups
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
comparePred
Compare Predictions
getGroups
Extract Grouping Factors from an Object
lme.lmList
LME fit from lmList Object
getGroupsFormula
Extract Grouping Formula
predict.gls
Predictions from a gls Object
print.summary.pdMat
Print a summary.pdMat Object
simulate.lme
Simulate results from lme models
varExp
Exponential Variance Function
logLik.reStruct
Calculate reStruct Log-Likelihood
logLik.varFunc
Extract varFunc logLik
nlme
Nonlinear Mixed-Effects Models
pdBlocked
Positive-Definite Block Diagonal Matrix
pdSymm
General Positive-Definite Matrix
plot.lmList
Plot an lmList Object
Cefamandole
Pharmacokinetics of Cefamandole
varComb
Combination of Variance Functions
pairs.compareFits
Pairs Plot of compareFits Object
recalc
Recalculate Condensed Linear Model Object
plot.lme
Plot an lme or nls object
print.varFunc
Print a varFunc Object
varWeights
Extract Variance Function Weights
reStruct
Random Effects Structure
plot.intervals.lmList
Plot lmList Confidence Intervals
groupedData
Construct a groupedData Object
splitFormula
Split a Formula
residuals.nlmeStruct
Calculate nlmeStruct Residuals
Variogram
Calculate Semi-variogram
ACF.gls
Autocorrelation Function for gls Residuals
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Dim
Extract Dimensions from an Object
Milk
Protein content of cows' milk
Meat
Tenderness of meat
Machines
Productivity Scores for Machines and Workers
Pixel
X-ray pixel intensities over time
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Ovary
Counts of Ovarian Follicles
Remifentanil
Pharmacokinetics of remifentanil
getGroups.varFunc
Extract varFunc Groups
anova.gls
Compare Likelihoods of Fitted Objects
coef.gnls
Extract gnls Coefficients
getCovariate.data.frame
Extract Data Frame Covariate
corCAR1
Continuous AR(1) Correlation Structure
needUpdate
Check if Update is Needed
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
predict.gnls
Predictions from a gnls Object
summary.lme
Summarize an lme Object
corFactor.corStruct
Factor of a corStruct Object Matrix
varWeights.glsStruct
Variance Weights for glsStruct Object
Coef
Assign Values to Coefficients
Tetracycline2
Pharmacokinetics of tetracycline
as.matrix.corStruct
Matrix of a corStruct Object
coef.reStruct
reStruct Object Coefficients
gsummary
Summarize by Groups
model.matrix.reStruct
reStruct Model Matrix
predict.nlme
Predictions from an nlme Object
residuals.gls
Extract gls Residuals
residuals.glsStruct
Calculate glsStruct Residuals
update.modelStruct
Update a modelStruct Object
quinModel
Model function for the Quinidine data
Orthodont
Growth curve data on an orthdontic measurement
anova.lme
Compare Likelihoods of Fitted Objects
isBalanced
Check a Design for Balance
pdLogChol
General Positive-Definite Matrix
update.varFunc
Update varFunc Object
coef.lmList
Extract lmList Coefficients
Muscle
Contraction of heart muscle sections