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nlme (version 3.1-86)
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
81,705
Version
3.1-86
License
GPL (>=2)
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2025
Functions in nlme (3.1-86)
Search all functions
ACF
Autocorrelation Function
BIC.logLik
BIC of a logLik Object
Oats
Split-plot Experiment on Varieties of Oats
getResponseFormula
Extract Formula Specifying Response Variable
corFactor.corStruct
Factor of a corStruct Object Matrix
Variogram.default
Calculate Semi-variogram
Dialyzer
High-Flux Hemodialyzer
Gun
Methods for firing naval guns
Covariate
Assign Covariate Values
Ovary
Counts of Ovarian Follicles
Covariate.varFunc
Assign varFunc Covariate
Orthodont
Growth curve data on an orthdontic measurement
coef.pdMat
pdMat Object Coefficients
Coef
Assign Values to Coefficients
collapse
Collapse According to Groups
IGF
Radioimmunoassay of IGF-I Protein
Soybean
Growth of soybean plants
Glucose
Glucose levels over time
getGroups.corStruct
Extract corStruct Groups
getGroups
Extract Grouping Factors from an Object
coef.modelStruct
Extract modelStruct Object Coefficients
Tetracycline1
Pharmacokinetics of tetracycline
glsControl
Control Values for gls Fit
random.effects
Extract Random Effects
Initialize.varFunc
Initialize varFunc Object
Cefamandole
Pharmacokinetics of Cefamandole
BodyWeight
Rat weight over time for different diets
Fatigue
Cracks caused by metal fatigue
getGroups.gls
Extract gls Object Groups
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
plot.augPred
Plot an augPred Object
varFixed
Fixed Variance Function
Remifentanil
Pharmacokinetics of remifentanil
Dim.pdMat
Dimensions of a pdMat Object
Earthquake
Earthquake Intensity
corExp
Exponential Correlation Structure
Gasoline
Refinery yield of gasoline
recalc.reStruct
Recalculate for an reStruct Object
isBalanced
Check a Design for Balance
logDet
Extract the Logarithm of the Determinant
lmeScale
Scale for lme Optimization
getGroupsFormula
Extract Grouping Formula
Initialize.reStruct
Initialize reStruct Object
lmList
List of lm Objects with a Common Model
intervals
Confidence Intervals on Coefficients
logDet.reStruct
Extract reStruct Log-Determinants
gnlsStruct
Generalized Nonlinear Least Squares Structure
residuals.lme
Extract lme Residuals
fixef.lmList
Extract lmList Fixed Effects
glsStruct
Generalized Least Squares Structure
getGroups.lme
Extract lme Object Groups
ACF.gls
Autocorrelation Function for gls Residuals
logLik.varFunc
Extract varFunc logLik
as.matrix.pdMat
Matrix of a pdMat Object
Oxide
Variability in Semiconductor Manufacturing
bdf
Language scores
residuals.glsStruct
Calculate glsStruct Residuals
lmeStruct
Linear Mixed-Effects Structure
corClasses
Correlation Structure Classes
update.varFunc
Update varFunc Object
asTable
Convert groupedData to a matrix
plot.lmList
Plot an lmList Object
Initialize.corStruct
Initialize corStruct Object
varWeights
Extract Variance Function Weights
plot.gls
Plot a gls Object
recalc
Recalculate Condensed Linear Model Object
summary.pdMat
Summarize a pdMat Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
fitted.lmList
Extract lmList Fitted Values
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
getGroups.data.frame
Extract Groups from a Data Frame
pairs.compareFits
Pairs Plot of compareFits Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
varComb
Combination of Variance Functions
[.pdMat
Subscript a pdMat Object
balancedGrouped
Create a groupedData object from a matrix
Names.reStruct
Names of an reStruct Object
varFunc
Variance Function Structure
varClasses
Variance Function Classes
getCovariateFormula
Extract Covariates Formula
splitFormula
Split a Formula
getData
Extract Data from an Object
Muscle
Contraction of heart muscle sections
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
plot.compareFits
Plot a compareFits Object
recalc.corStruct
Recalculate for corStruct Object
Tetracycline2
Pharmacokinetics of tetracycline
getData.lmList
Extract lmList Object Data
Nitrendipene
Assay of nitrendipene
isInitialized
Check if Object is Initialized
intervals.gls
Confidence Intervals on gls Parameters
logLik.lmList
Log-Likelihood of an lmList Object
ranef.lmList
Extract lmList Random Effects
corFactor
Factor of a Correlation Matrix
varPower
Power Variance Function
MathAchieve
Mathematics achievement scores
getResponse
Extract Response Variable from an Object
predict.gnls
Predictions from a gnls Object
summary.corStruct
Summarize a corStruct Object
summary.modelStruct
Summarize a modelStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
corSymm
General Correlation Structure
getGroups.lmList
Extract lmList Object Groups
Initialize
Initialize Object
getCovariate
Extract Covariate from an Object
Initialize.lmeStruct
Initialize an lmeStruct Object
summary.lme
Summarize an lme Object
pdMat
Positive-Definite Matrix
formula.pdMat
Extract pdMat Formula
coef.gnls
Extract gnls Coefficients
corAR1
AR(1) Correlation Structure
coef.varFunc
varFunc Object Coefficients
Oxboys
Heights of Boys in Oxford
pdLogChol
General Positive-Definite Matrix
recalc.varFunc
Recalculate for varFunc Object
Dim.corStruct
Dimensions of a corStruct Object
Dim
Extract Dimensions from an Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
formula.reStruct
Extract reStruct Object Formula
formula.pdBlocked
Extract pdBlocked Formula
intervals.lmList
Confidence Intervals on lmList Coefficients
varWeights.lmeStruct
Variance Weights for lmeStruct Object
lmeObject
Fitted lme Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
phenoModel
Model function for the Phenobarb data
getGroups.varFunc
Extract varFunc Groups
residuals.gls
Extract gls Residuals
fitted.glsStruct
Calculate glsStruct Fitted Values
BIC
Bayesian Information Criterion
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
model.matrix.reStruct
reStruct Model Matrix
pooledSD
Extract Pooled Standard Deviation
summary.varFunc
Summarize varFunc Object
plot.ranef.lme
Plot a ranef.lme Object
corMatrix.corStruct
Matrix of a corStruct Object
plot.ACF
Plot an ACF Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
gsummary
Summarize by Groups
fdHess
Finite difference Hessian
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
varIdent
Constant Variance Function
Variogram.corLin
Calculate Semi-variogram for a corLin Object
RatPupWeight
The weight of rat pups
gnls
Fit Nonlinear Model Using Generalized Least Squares
corSpatial
Spatial Correlation Structure
gnlsObject
Fitted gnls Object
lmeControl
Control Values for lme Fit
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
summary.lmList
Summarize an lmList Object
logDet.corStruct
Extract corStruct Log-Determinant
plot.nfnGroupedData
Plot an nfnGroupedData Object
getData.lme
Extract lme Object Data
fixed.effects
Extract Fixed Effects
nlmeStruct
Nonlinear Mixed-Effects Structure
plot.intervals.lmList
Plot lmList Confidence Intervals
update.modelStruct
Update a modelStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
Pixel
X-ray pixel intensities over time
simulate.lme
Simulate results from lme models
glsObject
Fitted gls Object
predict.gls
Predictions from a gls Object
corGaus
Gaussian Correlation Structure
plot.ranef.lmList
Plot a ranef.lmList Object
getVarCov
Extract variance-covariance matrix
coef.lmList
Extract lmList Coefficients
Phenobarb
Phenobarbitol Kinetics
varConstPower
Constant Plus Power Variance Function
VarCorr
Extract variance and correlation components
Variogram
Calculate Semi-variogram
nlmeObject
Fitted nlme Object
predict.lme
Predictions from an lme Object
Dim.corSpatial
Dimensions of a corSpatial Object
ergoStool
Ergometrics experiment with stool types
nlsList
List of nls Objects with a Common Model
quinModel
Model function for the Quinidine data
logLik.reStruct
Calculate reStruct Log-Likelihood
compareFits
Compare Fitted Objects
Rail
Evaluation of Stress in Railway Rails
logLik.glsStruct
Log-Likelihood of a glsStruct Object
ranef.lme
Extract lme Random Effects
getCovariate.varFunc
Extract varFunc Covariate
PBG
Effect of Phenylbiguanide on Blood Pressure
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Names.pdMat
Names of a pdMat Object
coef.corStruct
Coefficients of a corStruct Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
varExp
Exponential Variance Function
predict.nlme
Predictions from an nlme Object
ACF.lme
Autocorrelation Function for lme Residuals
Assay
Bioassay on Cell Culture Plate
lmList.groupedData
lmList Fit from a groupedData Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
lme.lmList
LME fit from lmList Object
nlmeControl
Control Values for nlme Fit
gapply
Apply a Function by Groups
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
LDEsysMat
Generate system matrix for LDEs
print.summary.pdMat
Print a summary.pdMat Object
corLin
Linear Correlation Structure
collapse.groupedData
Collapse a groupedData Object
residuals.lmList
Extract lmList Residuals
coef.reStruct
reStruct Object Coefficients
pdSymm
General Positive-Definite Matrix
needUpdate
Check if Update is Needed
groupedData
Construct a groupedData Object
plot.nmGroupedData
Plot an nmGroupedData Object
Glucose2
Glucose Levels Following Alcohol Ingestion
reStruct
Random Effects Structure
plot.nffGroupedData
Plot an nffGroupedData Object
solve.reStruct
Apply Solve to an reStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
Wafer
Modeling of Analog MOS Circuits
Meat
Tenderness of meat
Matrix.reStruct
Assign reStruct Matrices
logLik.corStruct
Extract corStruct Log-Likelihood
pdClasses
Positive-Definite Matrix Classes
lme
Linear Mixed-Effects Models
print.varFunc
Print a varFunc Object
Names.formula
Extract Names from a formula
corRatio
Rational Quadratic Correlation Structure
residuals.lmeStruct
Calculate lmeStruct Residuals
corARMA
ARMA(p,q) Correlation Structure
pdDiag
Diagonal Positive-Definite Matrix
Wheat2
Wheat Yield Trials
allCoef
Extract Coefficients from a Set of Objects
MathAchSchool
School demographic data for MathAchieve
augPred
Augmented Predictions
pdIdent
Multiple of the Identity Positive-Definite Matrix
summary.nlsList
Summarize an nlsList Object
asOneFormula
Combine Formulas of a Set of Objects
plot.lme
Plot an lme or nls object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.Variogram
Plot a Variogram Object
Milk
Protein content of cows' milk
Initialize.glsStruct
Initialize a glsStruct Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
lme.groupedData
LME fit from groupedData Object
logLik.lme
Log-Likelihood of an lme Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
gls
Fit Linear Model Using Generalized Least Squares
pdConstruct
Construct pdMat Objects
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
coef.lme
Extract lme Coefficients
corCompSymm
Compound Symmetry Correlation Structure
Matrix
Assign Matrix Values
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
getCovariate.corStruct
Extract corStruct Object Covariate
pairs.lme
Pairs Plot of an lme Object
as.matrix.reStruct
Matrices of an reStruct Object
corNatural
General correlation in natural parameterization
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pairs.lmList
Pairs Plot of an lmList Object
getData.gls
Extract gls Object Data
nlsList.selfStart
nlsList Fit from a selfStart Function
Quinidine
Quinidine Kinetics
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corSpher
Spherical Correlation Structure
Matrix.pdMat
Assign Matrix to a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
Spruce
Growth of Spruce Trees
pdConstruct.pdBlocked
Construct pdBlocked Objects
nlme.nlsList
NLME fit from nlsList Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
summary.gls
Summarize a gls Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
getCovariate.data.frame
Extract Data Frame Covariate
nlme
Nonlinear Mixed-Effects Models
pdBlocked
Positive-Definite Block Diagonal Matrix
fitted.lme
Extract lme Fitted Values
intervals.lme
Confidence Intervals on lme Parameters
comparePred
Compare Predictions
predict.lmList
Predictions from an lmList Object
corMatrix
Extract Correlation Matrix
corCAR1
Continuous AR(1) Correlation Structure
anova.lme
Compare Likelihoods of Fitted Objects
Relaxin
Assay for Relaxin
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
gnlsControl
Control Values for gnls Fit
anova.gls
Compare Likelihoods of Fitted Objects
Wheat
Yields by growing conditions
Machines
Productivity Scores for Machines and Workers
as.matrix.corStruct
Matrix of a corStruct Object
Names
Names Associated with an Object