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nlme (version 3.1-166)
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
3.1-166
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
August 14th, 2024
Functions in nlme (3.1-166)
Search all functions
Cefamandole
Pharmacokinetics of Cefamandole
ACF
Autocorrelation Function
ACF.gls
Autocorrelation Function for gls Residuals
ACF.lme
Autocorrelation Function for lme Residuals
Covariate
Assign Covariate Values
BodyWeight
Rat weight over time for different diets
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Dim.corStruct
Dimensions of a corStruct Object
Coef
Assign Values to Coefficients
Fatigue
Cracks caused by metal fatigue
Dim
Extract Dimensions from an Object
[.pdMat
Subscript a pdMat Object
Earthquake
Earthquake Intensity
Glucose
Glucose levels over time
Dim.pdMat
Dimensions of a pdMat Object
Dim.corSpatial
Dimensions of a corSpatial Object
Dialyzer
High-Flux Hemodialyzer
Glucose2
Glucose Levels Following Alcohol Ingestion
Initialize.corStruct
Initialize corStruct Object
Gasoline
Refinery yield of gasoline
Initialize.glsStruct
Initialize a glsStruct Object
MathAchieve
Mathematics achievement scores
Machines
Productivity Scores for Machines and Workers
MathAchSchool
School demographic data for MathAchieve
Gun
Methods for firing naval guns
IGF
Radioimmunoassay of IGF-I Protein
Meat
Tenderness of meat
Milk
Protein content of cows' milk
Initialize
Initialize Object
Initialize.reStruct
Initialize reStruct Object
Names
Names Associated with an Object
Oxboys
Heights of Boys in Oxford
Oxide
Variability in Semiconductor Manufacturing
Initialize.lmeStruct
Initialize an lmeStruct Object
Muscle
Contraction of heart muscle sections
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Ovary
Counts of Ovarian Follicles
RatPupWeight
The weight of rat pups
Quinidine
Quinidine Kinetics
Names.formula
Extract Names from a formula
Orthodont
Growth curve data on an orthdontic measurement
Names.pdMat
Names of a pdMat Object
Matrix
Assign Matrix Values
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Names.reStruct
Names of an reStruct Object
Soybean
Growth of soybean plants
Pixel
X-ray pixel intensities over time
Rail
Evaluation of Stress in Railway Rails
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Spruce
Growth of Spruce Trees
LDEsysMat
Generate system matrix for LDEs
Tetracycline1
Pharmacokinetics of tetracycline
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Tetracycline2
Pharmacokinetics of tetracycline
Variogram.default
Calculate Semi-variogram
Wafer
Modeling of Analog MOS Circuits
Phenobarb
Phenobarbitol Kinetics
Names.pdBlocked
Names of a pdBlocked Object
Initialize.varFunc
Initialize varFunc Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
anova.lme
Compare Likelihoods of Fitted Objects
asTable
Convert groupedData to a matrix
asOneFormula
Combine Formulas of a Set of Objects
as.matrix.corStruct
Matrix of a corStruct Object
PBG
Effect of Phenylbiguanide on Blood Pressure
Variogram.corLin
Calculate Semi-variogram for a corLin Object
coef.corStruct
Coefficients of a corStruct Object
augPred
Augmented Predictions
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Matrix.reStruct
Assign reStruct Matrices
allCoef
Extract Coefficients from a Set of Objects
Remifentanil
Pharmacokinetics of Remifentanil
VarCorr
Extract variance and correlation components
bdf
Language scores
Nitrendipene
Assay of nitrendipene
Relaxin
Assay for Relaxin
coef.lmList
Extract lmList Coefficients
balancedGrouped
Create a groupedData object from a matrix
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Wheat
Yields by growing conditions
coef.pdMat
pdMat Object Coefficients
coef.gnls
Extract gnls Coefficients
Oats
Split-plot Experiment on Varieties of Oats
anova.gls
Compare Likelihoods of Fitted Objects
Wheat2
Wheat Yield Trials
as.matrix.reStruct
Matrices of an reStruct Object
coef.lme
Extract lme Coefficients
comparePred
Compare Predictions
coef.modelStruct
Extract modelStruct Object Coefficients
as.matrix.pdMat
Matrix of a pdMat Object
Variogram
Calculate Semi-variogram
coef.reStruct
reStruct Object Coefficients
corSpatial
Spatial Correlation Structure
corRatio
Rational Quadratic Correlation Structure
corCompSymm
Compound Symmetry Correlation Structure
corAR1
AR(1) Correlation Structure
corClasses
Correlation Structure Classes
coef.varFunc
varFunc Object Coefficients
collapse
Collapse According to Groups
fdHess
Finite difference Hessian
corLin
Linear Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
compareFits
Compare Fitted Objects
collapse.groupedData
Collapse a groupedData Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
ergoStool
Ergometrics experiment with stool types
fixef.lmList
Extract lmList Fixed Effects
getCovariate
Extract Covariate from an Object
corMatrix
Extract Correlation Matrix
fixed.effects
Extract Fixed Effects
getData.gls
Extract gls Object Data
corFactor.corStruct
Factor of a corStruct Object Matrix
corCAR1
Continuous AR(1) Correlation Structure
corARMA
ARMA(p,q) Correlation Structure
corExp
Exponential Correlation Structure
formula.pdBlocked
Extract pdBlocked Formula
corSymm
General Correlation Structure
corGaus
Gaussian Correlation Structure
corSpher
Spherical Correlation Structure
getData.lmList
Extract lmList Object Data
corFactor
Factor of a Correlation Matrix
getCovariate.corStruct
Extract corStruct Object Covariate
getGroups.gls
Extract gls Object Groups
getGroups.lmList
Extract lmList Object Groups
getData.lme
Extract lme Object Data
formula.pdMat
Extract pdMat Formula
getGroups
Extract Grouping Factors from an Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
gapply
Apply a Function by Groups
fitted.lme
Extract lme Fitted Values
getResponse
Extract Response Variable from an Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getGroupsFormula
Extract Grouping Formula
fitted.lmList
Extract lmList Fitted Values
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
formula.reStruct
Extract reStruct Object Formula
getCovariateFormula
Extract Covariates Formula
getGroups.corStruct
Extract corStruct Groups
corNatural
General correlation in natural parameterization
fitted.glsStruct
Calculate glsStruct Fitted Values
corMatrix.corStruct
Matrix of a corStruct Object
getVarCov
Extract variance-covariance matrix
getResponseFormula
Extract Formula Specifying Response Variable
getGroups.data.frame
Extract Groups from a Data Frame
glsStruct
Generalized Least Squares Structure
gls
Fit Linear Model Using Generalized Least Squares
getCovariate.varFunc
Extract varFunc Covariate
gnls
Fit Nonlinear Model Using Generalized Least Squares
getCovariate.data.frame
Extract Data Frame Covariate
gls-internal
Auxiliary functions used by gls
getGroups.lme
Extract lme Object Groups
getData
Extract Data from an Object
intervals.lmList
Confidence Intervals on lmList Coefficients
glsControl
Control Values for gls Fit
gnlsControl
Control Values for gnls Fit
getGroups.varFunc
Extract varFunc Groups
gnlsObject
Fitted gnls Object
intervals
Confidence Intervals on Coefficients
glsObject
Fitted gls Object
intervals.lme
Confidence Intervals on lme Parameters
isInitialized
Check if Object is Initialized
intervals.gls
Confidence Intervals on gls Parameters
gsummary
Summarize by Groups
isBalanced
Check a Design for Balance
lmList
List of lm Objects with a Common Model
gnlsStruct
Generalized Nonlinear Least Squares Structure
logDet.corStruct
Extract corStruct Log-Determinant
groupedData
Construct a groupedData Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
lmList.groupedData
lmList Fit from a groupedData Object
lmeStruct
Linear Mixed-Effects Structure
lme.groupedData
LME fit from groupedData Object
lme
Linear Mixed-Effects Models
logDet
Extract the Logarithm of the Determinant
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logLik.lme
Log-Likelihood of an lme Object
logLik.gnls
Log-Likelihood of a gnls Object
logDet.reStruct
Extract reStruct Log-Determinants
lmeControl
Specifying Control Values for lme Fit
logLik.varFunc
Extract varFunc logLik
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
lmeObject
Fitted lme Object
logLik.lmList
Log-Likelihood of an lmList Object
model.matrix.reStruct
reStruct Model Matrix
lme.lmList
LME fit from lmList Object
logLik.corStruct
Extract corStruct Log-Likelihood
nlmeObject
Fitted nlme Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
nlme-deprecated
Deprecated Functions in Package
nlme
nlmeStruct
Nonlinear Mixed-Effects Structure
nlme.nlsList
NLME fit from nlsList Object
nlsList
List of nls Objects with a Common Model
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
nlme
Nonlinear Mixed-Effects Models
pairs.compareFits
Pairs Plot of compareFits Object
nlmeControl
Control Values for nlme Fit
needUpdate
Check if Update is Needed
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
nlsList.selfStart
nlsList Fit from a selfStart Function
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdDiag
Diagonal Positive-Definite Matrix
pairs.lmList
Pairs Plot of an lmList Object
pdConstruct
Construct pdMat Objects
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pairs.lme
Pairs Plot of an lme Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdMat
Positive-Definite Matrix
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdClasses
Positive-Definite Matrix Classes
pdBlocked
Positive-Definite Block Diagonal Matrix
pdLogChol
General Positive-Definite Matrix
phenoModel
Model function for the Phenobarb data
pdSymm
General Positive-Definite Matrix
pdIdent
Multiple of the Identity Positive-Definite Matrix
plot.compareFits
Plot a compareFits Object
plot.augPred
Plot an augPred Object
plot.lmList
Plot an lmList Object
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.nffGroupedData
Plot an nffGroupedData Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.gls
Plot a gls Object
plot.ACF
Plot an ACF Object
plot.Variogram
Plot a Variogram Object
plot.lme
Plot an lme or nls object
plot.nmGroupedData
Plot an nmGroupedData Object
print.summary.pdMat
Print a summary.pdMat Object
plot.ranef.lme
Plot a ranef.lme Object
predict.gnls
Predictions from a gnls Object
predict.lmList
Predictions from an lmList Object
pooledSD
Extract Pooled Standard Deviation
predict.gls
Predictions from a gls Object
predict.nlme
Predictions from an nlme Object
predict.lme
Predictions from an lme Object
plot.ranef.lmList
Plot a ranef.lmList Object
ranef.lme
Extract lme Random Effects
print.varFunc
Print a varFunc Object
recalc
Recalculate Condensed Linear Model Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
reStruct
Random Effects Structure
quinModel
Model function for the Quinidine data
recalc.corStruct
Recalculate for corStruct Object
ranef.lmList
Extract lmList Random Effects
random.effects
Extract Random Effects
recalc.varFunc
Recalculate for varFunc Object
residuals.lmList
Extract lmList Residuals
recalc.modelStruct
Recalculate for a modelStruct Object
residuals.lmeStruct
Calculate lmeStruct Residuals
residuals.gls
Extract gls Residuals
residuals.lme
Extract lme Residuals
recalc.reStruct
Recalculate for an reStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
summary.corStruct
Summarize a corStruct Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
summary.modelStruct
Summarize a modelStruct Object
simulate.lme
Simulate Results from
lme
Models
splitFormula
Split a Formula
summary.lmList
Summarize an lmList Object
solve.reStruct
Apply Solve to an reStruct Object
summary.lme
Summarize an lme Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
summary.nlsList
Summarize an nlsList Object
varClasses
Variance Function Classes
update.modelStruct
Update a modelStruct Object
varConstPower
Constant Plus Power Variance Function
varComb
Combination of Variance Functions
varExp
Exponential Variance Function
varConstProp
Constant Plus Proportion Variance Function
varFixed
Fixed Variance Function
summary.pdMat
Summarize a pdMat Object
summary.varFunc
Summarize "varFunc" Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varPower
Power Variance Function
varWeights
Extract Variance Function Weights
varWeights.glsStruct
Variance Weights for glsStruct Object
varFunc
Variance Function Structure
varIdent
Constant Variance Function
update.varFunc
Update varFunc Object
Covariate.varFunc
Assign varFunc Covariate
Assay
Bioassay on Cell Culture Plate