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nlme (version 3.1-163)
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
147,147
Version
3.1-163
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
August 9th, 2023
Functions in nlme (3.1-163)
Search all functions
Gasoline
Refinery yield of gasoline
BodyWeight
Rat weight over time for different diets
Fatigue
Cracks caused by metal fatigue
[.pdMat
Subscript a pdMat Object
Glucose
Glucose levels over time
IGF
Radioimmunoassay of IGF-I Protein
Initialize.glsStruct
Initialize a glsStruct Object
Initialize.corStruct
Initialize corStruct Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Dialyzer
High-Flux Hemodialyzer
Covariate.varFunc
Assign varFunc Covariate
Dim
Extract Dimensions from an Object
Initialize
Initialize Object
Earthquake
Earthquake Intensity
Initialize.varFunc
Initialize varFunc Object
Dim.corSpatial
Dimensions of a corSpatial Object
Dim.pdMat
Dimensions of a pdMat Object
Muscle
Contraction of heart muscle sections
Names.formula
Extract Names from a formula
Initialize.lmeStruct
Initialize an lmeStruct Object
LDEsysMat
Generate system matrix for LDEs
Dim.corStruct
Dimensions of a corStruct Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Names.pdBlocked
Names of a pdBlocked Object
RatPupWeight
The weight of rat pups
MathAchieve
Mathematics achievement scores
Rail
Evaluation of Stress in Railway Rails
Gun
Methods for firing naval guns
Machines
Productivity Scores for Machines and Workers
Tetracycline1
Pharmacokinetics of tetracycline
Tetracycline2
Pharmacokinetics of tetracycline
Names
Names Associated with an Object
Matrix
Assign Matrix Values
Names.pdMat
Names of a pdMat Object
Matrix.reStruct
Assign reStruct Matrices
MathAchSchool
School demographic data for MathAchieve
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Ovary
Counts of Ovarian Follicles
Orthodont
Growth curve data on an orthdontic measurement
Pixel
X-ray pixel intensities over time
Variogram.default
Calculate Semi-variogram
Quinidine
Quinidine Kinetics
Oxboys
Heights of Boys in Oxford
Initialize.reStruct
Initialize reStruct Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Names.reStruct
Names of an reStruct Object
Nitrendipene
Assay of nitrendipene
Spruce
Growth of Spruce Trees
Soybean
Growth of soybean plants
Variogram
Calculate Semi-variogram
PBG
Effect of Phenylbiguanide on Blood Pressure
Oats
Split-plot Experiment on Varieties of Oats
VarCorr
Extract variance and correlation components
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Phenobarb
Phenobarbitol Kinetics
Wheat
Yields by growing conditions
Oxide
Variability in Semiconductor Manufacturing
Meat
Tenderness of meat
as.matrix.pdMat
Matrix of a pdMat Object
Wheat2
Wheat Yield Trials
Relaxin
Assay for Relaxin
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Remifentanil
Pharmacokinetics of Remifentanil
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
augPred
Augmented Predictions
Wafer
Modeling of Analog MOS Circuits
bdf
Language scores
comparePred
Compare Predictions
Milk
Protein content of cows' milk
as.matrix.reStruct
Matrices of an reStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
coef.corStruct
Coefficients of a corStruct Object
allCoef
Extract Coefficients from a Set of Objects
coef.varFunc
varFunc Object Coefficients
balancedGrouped
Create a groupedData object from a matrix
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
anova.lme
Compare Likelihoods of Fitted Objects
anova.gls
Compare Likelihoods of Fitted Objects
coef.gnls
Extract gnls Coefficients
corARMA
ARMA(p,q) Correlation Structure
as.matrix.corStruct
Matrix of a corStruct Object
coef.pdMat
pdMat Object Coefficients
coef.reStruct
reStruct Object Coefficients
collapse
Collapse According to Groups
asOneFormula
Combine Formulas of a Set of Objects
corFactor.corStruct
Factor of a corStruct Object Matrix
coef.lmList
Extract lmList Coefficients
corGaus
Gaussian Correlation Structure
asTable
Convert groupedData to a matrix
corLin
Linear Correlation Structure
corMatrix
Extract Correlation Matrix
collapse.groupedData
Collapse a groupedData Object
corSpher
Spherical Correlation Structure
coef.lme
Extract lme Coefficients
coef.modelStruct
Extract modelStruct Object Coefficients
corMatrix.corStruct
Matrix of a corStruct Object
corCAR1
Continuous AR(1) Correlation Structure
corSymm
General Correlation Structure
corAR1
AR(1) Correlation Structure
ergoStool
Ergometrics experiment with stool types
fdHess
Finite difference Hessian
formula.pdBlocked
Extract pdBlocked Formula
corClasses
Correlation Structure Classes
corRatio
Rational Quadratic Correlation Structure
corSpatial
Spatial Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
formula.pdMat
Extract pdMat Formula
corCompSymm
Compound Symmetry Correlation Structure
compareFits
Compare Fitted Objects
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
glsObject
Fitted gls Object
getGroups.corStruct
Extract corStruct Groups
glsControl
Control Values for gls Fit
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corNatural
General correlation in natural parameterization
getGroups.data.frame
Extract Groups from a Data Frame
getCovariate.data.frame
Extract Data Frame Covariate
gnlsStruct
Generalized Nonlinear Least Squares Structure
corExp
Exponential Correlation Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getCovariate.varFunc
Extract varFunc Covariate
corFactor
Factor of a Correlation Matrix
fitted.lmList
Extract lmList Fitted Values
getData
Extract Data from an Object
fixed.effects
Extract Fixed Effects
getGroupsFormula
Extract Grouping Formula
getCovariateFormula
Extract Covariates Formula
fitted.lme
Extract lme Fitted Values
getResponseFormula
Extract Formula Specifying Response Variable
fixef.lmList
Extract lmList Fixed Effects
logDet.reStruct
Extract reStruct Log-Determinants
groupedData
Construct a groupedData Object
logLik.corStruct
Extract corStruct Log-Likelihood
nlmeControl
Control Values for nlme Fit
getCovariate
Extract Covariate from an Object
nlsList.selfStart
nlsList Fit from a selfStart Function
nlmeObject
Fitted nlme Object
getCovariate.corStruct
Extract corStruct Object Covariate
getData.gls
Extract gls Object Data
getGroups.lme
Extract lme Object Groups
getVarCov
Extract variance-covariance matrix
intervals.gls
Confidence Intervals on gls Parameters
pairs.compareFits
Pairs Plot of compareFits Object
getGroups.varFunc
Extract varFunc Groups
formula.reStruct
Extract reStruct Object Formula
getData.lmList
Extract lmList Object Data
intervals.lmList
Confidence Intervals on lmList Coefficients
getResponse
Extract Response Variable from an Object
gapply
Apply a Function by Groups
gnlsControl
Control Values for gnls Fit
gnlsObject
Fitted gnls Object
intervals.lme
Confidence Intervals on lme Parameters
pdSymm
General Positive-Definite Matrix
isBalanced
Check a Design for Balance
phenoModel
Model function for the Phenobarb data
logDet.corStruct
Extract corStruct Log-Determinant
getData.lme
Extract lme Object Data
plot.ACF
Plot an ACF Object
getGroups
Extract Grouping Factors from an Object
glsStruct
Generalized Least Squares Structure
gsummary
Summarize by Groups
getGroups.gls
Extract gls Object Groups
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.lme
Log-Likelihood of an lme Object
lme.groupedData
LME fit from groupedData Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
getGroups.lmList
Extract lmList Object Groups
isInitialized
Check if Object is Initialized
lme.lmList
LME fit from lmList Object
intervals
Confidence Intervals on Coefficients
plot.Variogram
Plot a Variogram Object
gls-internal
Auxiliary functions used by gls
gls
Fit Linear Model Using Generalized Least Squares
lmeControl
Specifying Control Values for lme Fit
lmList
List of lm Objects with a Common Model
lmList.groupedData
lmList Fit from a groupedData Object
lmeStruct
Linear Mixed-Effects Structure
lmeObject
Fitted lme Object
nlme
Nonlinear Mixed-Effects Models
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
nlmeStruct
Nonlinear Mixed-Effects Structure
logDet
Extract the Logarithm of the Determinant
lme
Linear Mixed-Effects Models
logLik.varFunc
Extract varFunc logLik
logLik.reStruct
Calculate reStruct Log-Likelihood
nlme.nlsList
NLME fit from nlsList Object
logLik.lmList
Log-Likelihood of an lmList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
logLik.glsStruct
Log-Likelihood of a glsStruct Object
pdConstruct
Construct pdMat Objects
logLik.gnls
Log-Likelihood of a gnls Object
model.matrix.reStruct
reStruct Model Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
needUpdate
Check if Update is Needed
plot.ranef.lme
Plot a ranef.lme Object
nlsList
List of nls Objects with a Common Model
plot.nffGroupedData
Plot an nffGroupedData Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pooledSD
Extract Pooled Standard Deviation
random.effects
Extract Random Effects
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdMat
Positive-Definite Matrix
pdConstruct.pdBlocked
Construct pdBlocked Objects
ranef.lmList
Extract lmList Random Effects
nlme-deprecated
Deprecated Functions in Package
nlme
residuals.glsStruct
Calculate glsStruct Residuals
residuals.gnlsStruct
Calculate gnlsStruct Residuals
pairs.lmList
Pairs Plot of an lmList Object
pdBlocked
Positive-Definite Block Diagonal Matrix
pdClasses
Positive-Definite Matrix Classes
plot.nfnGroupedData
Plot an nfnGroupedData Object
predict.gls
Predictions from a gls Object
predict.lmList
Predictions from an lmList Object
plot.compareFits
Plot a compareFits Object
pairs.lme
Pairs Plot of an lme Object
plot.augPred
Plot an augPred Object
predict.gnls
Predictions from a gnls Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
print.varFunc
Print a varFunc Object
plot.gls
Plot a gls Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
predict.lme
Predictions from an lme Object
plot.intervals.lmList
Plot lmList Confidence Intervals
ranef.lme
Extract lme Random Effects
plot.ranef.lmList
Plot a ranef.lmList Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.nmGroupedData
Plot an nmGroupedData Object
quinModel
Model function for the Quinidine data
simulate.lme
Simulate Results from
lme
Models
qqnorm.gls
Normal Plot of Residuals from a gls Object
reStruct
Random Effects Structure
pdDiag
Diagonal Positive-Definite Matrix
recalc.varFunc
Recalculate for varFunc Object
residuals.lme
Extract lme Residuals
pdIdent
Multiple of the Identity Positive-Definite Matrix
residuals.lmList
Extract lmList Residuals
summary.varFunc
Summarize "varFunc" Object
summary.pdMat
Summarize a pdMat Object
residuals.gls
Extract gls Residuals
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
pdLogChol
General Positive-Definite Matrix
solve.reStruct
Apply Solve to an reStruct Object
splitFormula
Split a Formula
residuals.lmeStruct
Calculate lmeStruct Residuals
update.modelStruct
Update a modelStruct Object
predict.nlme
Predictions from an nlme Object
plot.lmList
Plot an lmList Object
plot.lme
Plot an lme or nls object
summary.lmList
Summarize an lmList Object
summary.lme
Summarize an lme Object
varFunc
Variance Function Structure
varClasses
Variance Function Classes
update.varFunc
Update varFunc Object
print.summary.pdMat
Print a summary.pdMat Object
recalc
Recalculate Condensed Linear Model Object
recalc.corStruct
Recalculate for corStruct Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
recalc.reStruct
Recalculate for an reStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
varIdent
Constant Variance Function
summary.corStruct
Summarize a corStruct Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
varConstPower
Constant Plus Power Variance Function
varWeights
Extract Variance Function Weights
varPower
Power Variance Function
varConstProp
Constant Plus Proportion Variance Function
summary.modelStruct
Summarize a modelStruct Object
varComb
Combination of Variance Functions
summary.nlsList
Summarize an nlsList Object
varWeights.glsStruct
Variance Weights for glsStruct Object
varFixed
Fixed Variance Function
varExp
Exponential Variance Function
varWeights.lmeStruct
Variance Weights for lmeStruct Object
Coef
Assign Values to Coefficients
ACF
Autocorrelation Function
Assay
Bioassay on Cell Culture Plate
Covariate
Assign Covariate Values
Cefamandole
Pharmacokinetics of Cefamandole
ACF.gls
Autocorrelation Function for gls Residuals
ACF.lme
Autocorrelation Function for lme Residuals