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nlme (version 3.1-167)
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
80,915
Version
3.1-167
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
January 27th, 2025
Functions in nlme (3.1-167)
Search all functions
Gasoline
Refinery yield of gasoline
Dim.pdMat
Dimensions of a pdMat Object
Fatigue
Cracks caused by metal fatigue
Earthquake
Earthquake Intensity
Glucose
Glucose levels over time
Dialyzer
High-Flux Hemodialyzer
[.pdMat
Subscript a pdMat Object
Dim.corSpatial
Dimensions of a corSpatial Object
Dim.corStruct
Dimensions of a corStruct Object
Dim
Extract Dimensions from an Object
Initialize.lmeStruct
Initialize an lmeStruct Object
Initialize.corStruct
Initialize corStruct Object
Initialize.reStruct
Initialize reStruct Object
Machines
Productivity Scores for Machines and Workers
Glucose2
Glucose Levels Following Alcohol Ingestion
Gun
Methods for firing naval guns
Initialize
Initialize Object
MathAchSchool
School demographic data for MathAchieve
MathAchieve
Mathematics achievement scores
Matrix.reStruct
Assign reStruct Matrices
IGF
Radioimmunoassay of IGF-I Protein
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Initialize.varFunc
Initialize varFunc Object
Muscle
Contraction of heart muscle sections
Matrix
Assign Matrix Values
Names.pdMat
Names of a pdMat Object
Oxide
Variability in Semiconductor Manufacturing
Names.reStruct
Names of an reStruct Object
Oxboys
Heights of Boys in Oxford
Initialize.glsStruct
Initialize a glsStruct Object
Spruce
Growth of Spruce Trees
RatPupWeight
The weight of rat pups
Oats
Split-plot Experiment on Varieties of Oats
Meat
Tenderness of meat
Milk
Protein content of cows' milk
LDEsysMat
Generate system matrix for LDEs
Names.formula
Extract Names from a formula
Names.pdBlocked
Names of a pdBlocked Object
Tetracycline1
Pharmacokinetics of tetracycline
Soybean
Growth of soybean plants
Nitrendipene
Assay of nitrendipene
Names
Names Associated with an Object
Rail
Evaluation of Stress in Railway Rails
VarCorr
Extract variance and correlation components
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Ovary
Counts of Ovarian Follicles
Orthodont
Growth curve data on an orthdontic measurement
PBG
Effect of Phenylbiguanide on Blood Pressure
Relaxin
Assay for Relaxin
Phenobarb
Phenobarbitol Kinetics
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Remifentanil
Pharmacokinetics of Remifentanil
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Tetracycline2
Pharmacokinetics of tetracycline
Variogram
Calculate Semi-variogram
Wafer
Modeling of Analog MOS Circuits
as.matrix.pdMat
Matrix of a pdMat Object
Pixel
X-ray pixel intensities over time
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
balancedGrouped
Create a groupedData object from a matrix
Variogram.default
Calculate Semi-variogram
augPred
Augmented Predictions
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
asOneFormula
Combine Formulas of a Set of Objects
anova.gls
Compare Likelihoods of Fitted Objects
coef.modelStruct
Extract modelStruct Object Coefficients
coef.varFunc
varFunc Object Coefficients
as.matrix.reStruct
Matrices of an reStruct Object
collapse
Collapse According to Groups
Wheat
Yields by growing conditions
Variogram.corLin
Calculate Semi-variogram for a corLin Object
allCoef
Extract Coefficients from a Set of Objects
coef.lme
Extract lme Coefficients
Wheat2
Wheat Yield Trials
asTable
Convert groupedData to a matrix
corClasses
Correlation Structure Classes
corCompSymm
Compound Symmetry Correlation Structure
Quinidine
Quinidine Kinetics
collapse.groupedData
Collapse a groupedData Object
corExp
Exponential Correlation Structure
compareFits
Compare Fitted Objects
corFactor
Factor of a Correlation Matrix
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
bdf
Language scores
corNatural
General correlation in natural parameterization
corCAR1
Continuous AR(1) Correlation Structure
fitted.lmList
Extract lmList Fitted Values
corGaus
Gaussian Correlation Structure
ergoStool
Ergometrics experiment with stool types
corARMA
ARMA(p,q) Correlation Structure
fdHess
Finite difference Hessian
corFactor.corStruct
Factor of a corStruct Object Matrix
fixef.lmList
Extract lmList Fixed Effects
corSpatial
Spatial Correlation Structure
coef.corStruct
Coefficients of a corStruct Object
fixed.effects
Extract Fixed Effects
formula.pdBlocked
Extract pdBlocked Formula
corRatio
Rational Quadratic Correlation Structure
coef.reStruct
reStruct Object Coefficients
fitted.lme
Extract lme Fitted Values
getCovariateFormula
Extract Covariates Formula
coef.pdMat
pdMat Object Coefficients
getData
Extract Data from an Object
getCovariate.data.frame
Extract Data Frame Covariate
getGroups.corStruct
Extract corStruct Groups
getCovariate.varFunc
Extract varFunc Covariate
gapply
Apply a Function by Groups
getGroups.data.frame
Extract Groups from a Data Frame
formula.pdMat
Extract pdMat Formula
formula.reStruct
Extract reStruct Object Formula
getGroups.gls
Extract gls Object Groups
getGroups.lme
Extract lme Object Groups
glsStruct
Generalized Least Squares Structure
gnlsObject
Fitted gnls Object
getGroups.varFunc
Extract varFunc Groups
gnls
Fit Nonlinear Model Using Generalized Least Squares
getGroups.lmList
Extract lmList Object Groups
gls-internal
Auxiliary functions used by gls
gnlsControl
Control Values for gnls Fit
corLin
Linear Correlation Structure
glsControl
Control Values for gls Fit
glsObject
Fitted gls Object
coef.gnls
Extract gnls Coefficients
isBalanced
Check a Design for Balance
corAR1
AR(1) Correlation Structure
gsummary
Summarize by Groups
intervals.lme
Confidence Intervals on lme Parameters
comparePred
Compare Predictions
intervals
Confidence Intervals on Coefficients
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
gls
Fit Linear Model Using Generalized Least Squares
lmList
List of lm Objects with a Common Model
corSpher
Spherical Correlation Structure
coef.lmList
Extract lmList Coefficients
isInitialized
Check if Object is Initialized
corMatrix.corStruct
Matrix of a corStruct Object
corSymm
General Correlation Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
corMatrix
Extract Correlation Matrix
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
lmeStruct
Linear Mixed-Effects Structure
logDet
Extract the Logarithm of the Determinant
lmList.groupedData
lmList Fit from a groupedData Object
lme
Linear Mixed-Effects Models
getData.gls
Extract gls Object Data
getResponse
Extract Response Variable from an Object
getGroupsFormula
Extract Grouping Formula
getData.lmList
Extract lmList Object Data
getCovariate
Extract Covariate from an Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
getData.lme
Extract lme Object Data
getGroups
Extract Grouping Factors from an Object
logLik.lmList
Log-Likelihood of an lmList Object
logLik.lme
Log-Likelihood of an lme Object
getCovariate.corStruct
Extract corStruct Object Covariate
lme.groupedData
LME fit from groupedData Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
logDet.reStruct
Extract reStruct Log-Determinants
lme.lmList
LME fit from lmList Object
getResponseFormula
Extract Formula Specifying Response Variable
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
groupedData
Construct a groupedData Object
intervals.gls
Confidence Intervals on gls Parameters
intervals.lmList
Confidence Intervals on lmList Coefficients
getVarCov
Extract variance-covariance matrix
logLik.corStruct
Extract corStruct Log-Likelihood
nlme-deprecated
Deprecated Functions in Package
nlme
model.matrix.reStruct
reStruct Model Matrix
pdBlocked
Positive-Definite Block Diagonal Matrix
needUpdate
Check if Update is Needed
nlmeObject
Fitted nlme Object
nlmeControl
Control Values for nlme Fit
pdClasses
Positive-Definite Matrix Classes
logLik.reStruct
Calculate reStruct Log-Likelihood
logDet.corStruct
Extract corStruct Log-Determinant
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
nlme
Nonlinear Mixed-Effects Models
lmeObject
Fitted lme Object
logLik.varFunc
Extract varFunc logLik
lmeControl
Specifying Control Values for lme Fit
pdConstruct
Construct pdMat Objects
nlme.nlsList
NLME fit from nlsList Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.gnls
Log-Likelihood of a gnls Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pairs.lmList
Pairs Plot of an lmList Object
nlmeStruct
Nonlinear Mixed-Effects Structure
logLik.glsStruct
Log-Likelihood of a glsStruct Object
pdLogChol
General Positive-Definite Matrix
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdDiag
Diagonal Positive-Definite Matrix
nlsList
List of nls Objects with a Common Model
pdMat
Positive-Definite Matrix
pairs.lme
Pairs Plot of an lme Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pairs.compareFits
Pairs Plot of compareFits Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.ACF
Plot an ACF Object
nlsList.selfStart
nlsList Fit from a selfStart Function
plot.Variogram
Plot a Variogram Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
plot.lme
Plot an lme or nls object
pdSymm
General Positive-Definite Matrix
plot.compareFits
Plot a compareFits Object
plot.lmList
Plot an lmList Object
plot.augPred
Plot an augPred Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
phenoModel
Model function for the Phenobarb data
plot.nffGroupedData
Plot an nffGroupedData Object
plot.gls
Plot a gls Object
plot.intervals.lmList
Plot lmList Confidence Intervals
predict.gls
Predictions from a gls Object
plot.nmGroupedData
Plot an nmGroupedData Object
plot.ranef.lme
Plot a ranef.lme Object
predict.gnls
Predictions from a gnls Object
print.summary.pdMat
Print a summary.pdMat Object
predict.nlme
Predictions from an nlme Object
predict.lmList
Predictions from an lmList Object
ranef.lme
Extract lme Random Effects
print.varFunc
Print a varFunc Object
recalc
Recalculate Condensed Linear Model Object
pooledSD
Extract Pooled Standard Deviation
plot.ranef.lmList
Plot a ranef.lmList Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
reStruct
Random Effects Structure
qqnorm.gls
Normal Plot of Residuals from a gls Object
residuals.lmeStruct
Calculate lmeStruct Residuals
quinModel
Model function for the Quinidine data
residuals.gls
Extract gls Residuals
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.glsStruct
Calculate glsStruct Residuals
recalc.varFunc
Recalculate for varFunc Object
ranef.lmList
Extract lmList Random Effects
residuals.lme
Extract lme Residuals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
residuals.lmList
Extract lmList Residuals
random.effects
Extract Random Effects
predict.lme
Predictions from an lme Object
summary.modelStruct
Summarize a modelStruct Object
summary.corStruct
Summarize a corStruct Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
summary.nlsList
Summarize an nlsList Object
summary.lmList
Summarize an lmList Object
simulate.lme
Simulate Results from
lme
Models
recalc.corStruct
Recalculate for corStruct Object
recalc.reStruct
Recalculate for an reStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
recalc.modelStruct
Recalculate for a modelStruct Object
solve.reStruct
Apply Solve to an reStruct Object
varExp
Exponential Variance Function
varFixed
Fixed Variance Function
update.varFunc
Update varFunc Object
update.modelStruct
Update a modelStruct Object
varComb
Combination of Variance Functions
summary.pdMat
Summarize a pdMat Object
varClasses
Variance Function Classes
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
summary.lme
Summarize an lme Object
varConstProp
Constant Plus Proportion Variance Function
summary.varFunc
Summarize "varFunc" Object
varWeights
Extract Variance Function Weights
varConstPower
Constant Plus Power Variance Function
splitFormula
Split a Formula
varPower
Power Variance Function
varFunc
Variance Function Structure
varIdent
Constant Variance Function
ACF.lme
Autocorrelation Function for lme Residuals
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
BodyWeight
Rat weight over time for different diets
Cefamandole
Pharmacokinetics of Cefamandole
ACF
Autocorrelation Function
Assay
Bioassay on Cell Culture Plate
Coef
Assign Values to Coefficients
Covariate
Assign Covariate Values
Covariate.varFunc
Assign varFunc Covariate
ACF.gls
Autocorrelation Function for gls Residuals