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nlme (version 3.1-18)
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)
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Install
install.packages('nlme')
Monthly Downloads
83,497
Version
3.1-18
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
October 7th, 2001
Functions in nlme (3.1-18)
Search functions
AIC.logLik
AIC of a logLik Object
BIC
Bayesian Information Criterion
MEEM
EM iterations for mixed-effects
Matrix
Assign Matrix Values
as.matrix.corStruct
Matrix of a corStruct Object
Names.pdMat
Names of a pdMat Object
as.matrix.pdMat
Matrix of a pdMat Object
contr.SAS
Contrast Matrices
corMatrix.corStruct
Matrix of a corStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
coef.gnls
Extract gnls Coefficients
anova.gls
Compare Likelihoods of Fitted Objects
isInitialized.reStruct
Check if an reStruct Object is Initialized
coef.modelStruct
Extract modelStruct Object Coefficients
predict.gls
Predictions from a gls Object
ACF
Autocorrelation Function
print.corStruct
Print a corStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
Coef
Assign Values to Coefficients
varIdent
Constant Variance Function
formula.nlsList
Extract nlsList Object Formula
Dim.pdMat
Dimensions of a pdMat Object
update.groupedData
Update a groupedData Object
Dim
Extract Dimensions from an Object
Names.pdBlocked
Names of a pdBlocked Object
[.pdMat
Subscript a pdMat Object
allCoef
Extract Coefficients from a Set of Objects
ACF.lme
Autocorrelation Function for lme Residuals
BIC.logLik
BIC of a logLik Object
Dim.corStruct
Dimensions of a corStruct Object
asOneFormula
Combine Formulas of a Set of Objects
AIC.lme
Akaike Information Criterion
print.modelStruct
Print a modelStruct Object
print.summary.pdMat
Print a summary.pdMat Object
Names.formula
Extract Names from a formula
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
as.matrix.reStruct
Matrices of an reStruct Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Names
Names Associated with an Object
Covariate
Assign Covariate Values
formula.lmList
Extract lmList Object Formula
VarCorr
Extract variance and correlation components
update.gls
Update a gls Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
ACF.gls
Autocorrelation Function for gls Residuals
formula.corStruct
Extract corStruct Object Formula
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
varWeights.glsStruct
Variance Weights for glsStruct Object
initialize
Initialize Object
Matrix.reStruct
Assign reStruct Matrices
intervals.lmList
Confidence Intervals on lmList Coefficients
initialize.varFunc
Initialize varFunc Object
coef.lme
Extract lme Coefficients
recalc.corStruct
Recalculate for corStruct Object
print.varFunc
Print a varFunc Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varWeights
Extract Variance Function Weights
reStruct
Random Effects Structure
update.lme
Update an lme Object
print.summary.varFunc
Print a summary.varFunc Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
coef.varFunc
varFunc Object Coefficients
recalc.reStruct
Recalculate for an reStruct Object
MEestimate
Estimate mixed-effects parameters
formula.nls
Extract Model Formula from nls Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
formula.pdMat
Extract pdMat Formula
update.modelStruct
Update a modelStruct Object
residuals.lme
Extract lme Residuals
varConstPower
Constant Plus Power Variance Function
corAR1
AR(1) Correlation Structure
varExp
Exponential Variance Function
corSymm
General Correlation Structure
coef.gls
Extract gls Coefficients
MEdims
Calculate dimensions in mixed-effects
coef.corStruct
Coefficients of a corStruct Object
getGroups.varFunc
Extract varFunc Groups
varFixed
Fixed Variance Function
coef.lmList
Extract lmList Coefficients
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
update.varFunc
Update varFunc Object
residuals.gls
Extract gls Residuals
update.nlsList
Update an nlsList Object
summary.pdMat
Summarize a pdMat Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
corNatural
General correlation in natural parameterization
logDet.pdMat
Extract Log-Determinant from a pdMat Object
update.gnls
Update a gnls Object
Covariate.varFunc
Assign varFunc Covariate
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
coef.pdIdent
pdIdent Object Coefficients
gls
Fit Linear Model Using Generalized Least Squares
Variogram
Calculate Semi-variogram
varComb
Combination of Variance Functions
corExp
Exponential Correlation Structure
formula.varFunc
Extract varFunc Formula
qqnorm.gls
Normal Plot of Residuals from a gls Object
Names.reStruct
Names of an reStruct Object
formula.reStruct
Extract reStruct Object Formula
formula.lme
Extract lme Object Formula
fixed.effects.lme
Extract lme Fixed Effects
pruneLevels
Prune Factor Levels
summary.corStruct
Summarize a corStruct Object
corARMA
ARMA(p,q) Correlation Structure
getResponse.lme
Extract lme Object Response
coef.pdMat
pdMat Object Coefficients
AIC
Akaike Information Criterion
gnls
Fit Nonlinear Model Using Generalized Least Squares
corFactor.corStruct
Factor of a corStruct Object Matrix
corFactor
Factor of a Correlation Matrix
corCompSymm
Compound Symmetry Correlation Structure
corCAR1
Continuous AR(1) Correlation Structure
coef.pdDiag
pdDiag Object Coefficients
Matrix.pdMat
Assign Matrix to a pdMat Object
formula.modelStruct
Extract modelStruct Object Formula
plot.nffGroupedData
Plot an nffGroupedData Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
groupedData
Construct a groupedData Object
print.gls
Print a gls Object
random.effects.lmList
Extract lmList Random Effects
formula.gls
Extract gls Object Formula
formula.gnls
Extract gnls Object Formula
recalc
Recalculate Condensed Linear Model Object
predict.nlme
Predictions from an nlme Object
getCovariate
Extract Covariate from an Object
fixed.effects
Extract Fixed Effects
Variogram.corExp
Calculate Semi-variogram for a corExp Object
getData
Extract Data from an Object
getData.gls
Extract gls Object Data
anova.lme
Compare Likelihoods of Fitted Objects
summary.lme
Summarize an lme Object
gsummary
Summarize by Groups
getResponse.lmList
Extract lmList Object Response
print.anova.lme
Print an anova.lme Object
getGroups
Extract Grouping Factors from an Object
plot.compareFits
Plot a compareFits Object
isInitialized
Check if Object is Initialized
MEdecomp
Decompose a mixed-effects model
print.summary.gls
Print a summary.gls Object
recalc.varFunc
Recalculate for varFunc Object
collapse.groupedData
Collapse a groupedData Object
print.summary.modelStruct
Print a summary.modelStruct Object
summary.gls
Summarize a gls Object
update.nlme
Update an nlme Object
predict.lmList
Predictions from an lmList Object
solve.reStruct
Apply Solve to an reStruct Object
varClasses
Variance Function Classes
print.lmList
Print an lmList Object
predict.lme
Predictions from an lme Object
Dim.corSpatial
Dimensions of a corSpatial Object
plot.Variogram
Plot a Variogram Object
random.effects
Extract Random Effects
plot.augPred
Plot an augPred Object
print.groupedData
Print a groupedData Object
simulate.lme
simulate lme models
pooledSD
Extract Pooled Standard Deviation
pairs.lmList
Pairs Plot of an lmList Object
initialize.lmeStruct
Initialize an lmeStruct Object
logDet.reStruct
Extract reStruct Log-Determinants
collapse
Collapse According to Groups
lmeStruct
Linear Mixed-Effects Structure
needUpdate
Check if Update is Needed
summary.lmList
Summarize an lmList Object
random.effects.lme
Extract lme Random Effects
gapply
Apply a Function by Groups
corRatio
Rational Quadratic Correlation Structure
intervals.lme
Confidence Intervals on lme Parameters
logLik.glsStruct
Log-Likelihood of a glsStruct Object
residuals.lmList
Extract lmList Residuals
plot.ranef.lme
Plot a ranef.lme Object
pdClasses
Positive-Definite Matrix Classes
intervals.gls
Confidence Intervals on gls Parameters
pdNatural
General Positive-Definite Matrix in Natural Parametrization
glsObject
Fitted gls Object
residuals.gnls
Extract gnls Residuals
varPower
Power Variance Function
pdBlocked
Positive-Definite Block Diagonal Matrix
update.lmList
Update an lmList Object
logDet.corStruct
Extract corStruct Log-Determinant
logDet
Extract the Logarithm of the Determinant
isBalanced
Check a Design for Balance
lmeControl
Control Values for lme Fit
logLik.varFunc
Extract varFunc logLik
getCovariate.corStruct
Extract corStruct Object Covariate
getCovariate.varFunc
Extract varFunc Covariate
print.reStruct
Print an reStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdMat
Positive-Definite Matrix
getResponse.data.frame
Extract Response from a Data Frame
lme.groupedData
LME fit from groupedData Object
nlsList.selfStart
nlsList Fit from a selfStart Function
splitFormula
Split a Formula
recalc.modelStruct
Recalculate for a modelStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
lme
Linear Mixed-Effects Models
varFunc
Variance Function Structure
fixed.effects.lmList
Extract lmList Fixed Effects
lmeObject
Fitted lme Object
coef.reStruct
reStruct Object Coefficients
compareFits
Compare Fitted Objects
gnlsControl
Control Values for gnls Fit
nlme
Nonlinear Mixed-Effects Models
balancedGrouped
Create a groupedData object from a matrix
summary.nlsList
Summarize an nlsList Object
print.summary.lme
Print a summary.lme Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
print.summary.lmList
Print a summary.lmList Object
plot.nmGroupedData
Plot an nmGroupedData Object
residuals.lmeStruct
Calculate lmeStruct Residuals
Variogram.default
Calculate Semi-variogram
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdSymm
General Positive-Definite Matrix
nlsList
List of nls Objects with a Common Model
print.lme
Print an lme Object
initialize.glsStruct
Initialize a glsStruct Object
nlme.nlsList
NLME fit from nlsList Object
plot.intervals.lmList
Plot lmList Confidence Intervals
getData.lme
Extract lme Object Data
formula.nlme
Extract nlme Object Formula
fdHess
Finite difference Hessian
getResponse.gls
Extract gls Object Response
getGroups.lme
Extract lme Object Groups
getResponseFormula
Extract Formula Specifying Response Variable
glsStruct
Generalized Least Squares Structure
lme.lmList
LME fit from lmList Object
fitted.lmList
Extract lmList Fitted Values
getGroupsFormula
Extract Grouping Formula
pdLogChol
General Positive-Definite Matrix
fitted.gnls
Extract gnls Fitted Values
initialize.corStruct
Initialize corStruct Object
glsControl
Control Values for gls Fit
corGaus
Gaussian Correlation Structure
print.summary.corStruct
Print a summary.corStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
corLin
Linear Correlation Structure
gnlsStruct
Generalized Nonlinear Least Squares Structure
lmList.groupedData
lmList Fit from a groupedData Object
coef.pdCompSymm
pdCompSymm Object Coefficients
initialize.reStruct
Initialize reStruct Object
print.pdMat
Print a pdMat Object
getData.lmList
Extract lmList Object Data
summary.varFunc
Summarize varFunc Object
plot.ACF
Plot an ACF Object
lmeScale
Scale for lme Optimization
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
comparePred
Compare Predictions
formula.pdBlocked
Extract pdBlocked Formula
pairs.compareFits
Pairs Plot of compareFits Object
formula.groupedData
Extract groupedData Formula
pdConstruct
Construct pdMat Objects
plot.lmList
Plot an lmList Object
lmList
List of lm Objects with a Common Model
fitted.glsStruct
Calculate glsStruct Fitted Values
fitted.lme
Extract lme Fitted Values
intervals
Confidence Intervals on Coefficients
logLik.gnls
Log-Likelihood of a gnls Object
summary.modelStruct
Summarize a modelStruct Object
plot.ranef.lmList
Plot a ranef.lmList Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
asTable
Convert groupedData to a matrix
getResponse
Extract Response Variable from an Object
nlmeStruct
Nonlinear Mixed-Effects Structure
corClasses
Correlation Structure Classes
gnlsObject
Fitted gnls Object
predict.gnls
Predictions from a gnls Object
getCovariateFormula
Extract Covariates Formula
corSpher
Spherical Correlation Structure
getGroups.lmList
Extract lmList Object Groups
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corMatrix
Extract Correlation Matrix
getGroups.corStruct
Extract corStruct Groups
getCovariate.data.frame
Extract Data Frame Covariate
corSpatial
Spatial Correlation Structure
getGroups.gls
Extract gls Object Groups
augPred
Augmented Predictions
fitted.gls
Extract gls Fitted Values
model.matrix.reStruct
reStruct Model Matrix
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
pdFactor
Square-Root Factor of a Positive-Definite Matrix
logLik.lm
Extract Log-Likelihood from an lm Object
logLik.lme
Log-Likelihood of an lme Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdDiag
Diagonal Positive-Definite Matrix
pdConstruct.pdBlocked
Construct pdBlocked Objects
logLik.gls
Log-Likelihood of a gls Object
logLik.corStruct
Extract corStruct Log-Likelihood
logLik.lmList
Log-Likelihood of an lmList Object
nlmeObject
Fitted nlme Object
pairs.lme
Pairs Plot of an lme Object
nlmeControl
Control Values for nlme Fit
plot.gls
Plot a gls Object
plot.lme
Plot an lme Object
Meat
Tenderness of meat
MathAchSchool
School demographic data for MathAchieve
Oxboys
Heights of Boys in Oxford
Cefamandole
Pharmacokinetics of Cefamandole
Wheat
Yields by growing conditions
Remifentanil
Pharmacokinetics of remifentanil
Tetracycline1
Pharmacokinetics of tetracycline
Gasoline
Refinery yield of gasoline
Ovary
Counts of Ovarian Follicles
Wafer
Modeling of Analog MOS Circuits
Glucose
Glucose levels over time
Quinidine
Quinidine Kinetics
Pixel
X-ray pixel intensities over time
Oxide
Variability in Semiconductor Manufacturing
Tetracycline2
Pharmacokinetics of tetracycline
Earthquake
Earthquake Intensity
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Wheat2
Wheat Yield Trials
Dialyzer
High-Flux Hemodialyzer
Muscle
Contraction of heart muscle sections
Spruce
Growth of Spruce Trees
Gun
Methods for firing naval guns
Relaxin
Assay for Relaxin
bdf
Language scores
Oats
Split-plot Experiment on Varieties of Oats
IGF
Radioimmunoassay of IGF-I Protein
PBG
Effect of Phenylbiguanide on Blood Pressure
BodyWeight
Rat weight over time for different diets
Soybean
Growth of soybean plants
Glucose2
Glucose Levels Following Alcohol Ingestion
Assay
Bioassay on Cell Culture Plate
Fatigue
Cracks caused by metal fatigue
RatPupWeight
The weight of rat pups
Orthodont
Growth curve data on an orthdontic measurement
Milk
Protein content of cows' milk
MathAchieve
Mathematics achievement scores
ergoStool
Ergometrics experiment with stool types
Rail
Evaluation of Stress in Railway Rails
Nitrendipene
Assay of nitrendipene
Phenobarb
Phenobarbitol Kinetics
Machines
Productivity Scores for Machines and Workers