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nlme (version 3.1-39)
Linear and nonlinear mixed effects models
Description
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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Install
install.packages('nlme')
Monthly Downloads
83,497
Version
3.1-39
License
GPL version 2 or later
Maintainer
Douglas Bates
Last Published
March 25th, 2003
Functions in nlme (3.1-39)
Search functions
Dim.corSpatial
Dimensions of a corSpatial Object
Dim
Extract Dimensions from an Object
corFactor
Factor of a Correlation Matrix
ACF.gls
Autocorrelation Function for gls Residuals
Coef
Assign Values to Coefficients
Variogram.corLin
Calculate Semi-variogram for a corLin Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
MEEM
EM iterations for mixed-effects
Initialize
Initialize Object
coef.pdMat
pdMat Object Coefficients
Initialize.varFunc
Initialize varFunc Object
formula.gnls
Extract gnls Object Formula
as.matrix.pdMat
Matrix of a pdMat Object
corARMA
ARMA(p,q) Correlation Structure
lmList.groupedData
lmList Fit from a groupedData Object
coef.gls
Extract gls Coefficients
coef.gnls
Extract gnls Coefficients
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
asTable
Convert groupedData to a matrix
coef.pdDiag
pdDiag Object Coefficients
Initialize.reStruct
Initialize reStruct Object
fixef.lme
Extract lme Fixed Effects
collapse.groupedData
Collapse a groupedData Object
Names.reStruct
Names of an reStruct Object
formula.varFunc
Extract varFunc Formula
collapse
Collapse According to Groups
Names.formula
Extract Names from a formula
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
lmeScale
Scale for lme Optimization
coef.modelStruct
Extract modelStruct Object Coefficients
balancedGrouped
Create a groupedData object from a matrix
ACF
Autocorrelation Function
Names.pdMat
Names of a pdMat Object
logDet.reStruct
Extract reStruct Log-Determinants
Matrix.reStruct
Assign reStruct Matrices
BIC
Bayesian Information Criterion
corMatrix.corStruct
Matrix of a corStruct Object
corCAR1
Continuous AR(1) Correlation Structure
coef.varFunc
varFunc Object Coefficients
corRatio
Rational Quadratic Correlation Structure
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
anova.lme
Compare Likelihoods of Fitted Objects
VarCorr
Extract variance and correlation components
fixed.effects
Extract Fixed Effects
gnlsStruct
Generalized Nonlinear Least Squares Structure
gls
Fit Linear Model Using Generalized Least Squares
getGroups.data.frame
Extract Groups from a Data Frame
phenoModel
Model function for the Phenobarb data
ACF.lme
Autocorrelation Function for lme Residuals
formula.nlsList
Extract nlsList Object Formula
corClasses
Correlation Structure Classes
plot.Variogram
Plot a Variogram Object
formula.nlme
Extract nlme Object Formula
Dim.corStruct
Dimensions of a corStruct Object
formula.groupedData
Extract groupedData Formula
getGroupsFormula
Extract Grouping Formula
BIC.logLik
BIC of a logLik Object
getGroups.varFunc
Extract varFunc Groups
lmList
List of lm Objects with a Common Model
corAR1
AR(1) Correlation Structure
augPred
Augmented Predictions
corGaus
Gaussian Correlation Structure
coef.reStruct
reStruct Object Coefficients
print.reStruct
Print an reStruct Object
lmeControl
Control Values for lme Fit
corLin
Linear Correlation Structure
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logDet.corStruct
Extract corStruct Log-Determinant
Variogram
Calculate Semi-variogram
Dim.pdMat
Dimensions of a pdMat Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
pdBlocked
Positive-Definite Block Diagonal Matrix
MEdecomp
Decompose a mixed-effects model
pairs.lmList
Pairs Plot of an lmList Object
getGroups.lmList
Extract lmList Object Groups
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.intervals.lmList
Plot lmList Confidence Intervals
getVarCov
Extract variance-covariance matrix
getResponseFormula
Extract Formula Specifying Response Variable
gnlsControl
Control Values for gnls Fit
summary.nlsList
Summarize an nlsList Object
anova.gls
Compare Likelihoods of Fitted Objects
Variogram.default
Calculate Semi-variogram
print.summary.corStruct
Print a summary.corStruct Object
coef.corStruct
Coefficients of a corStruct Object
getResponse.data.frame
Extract Response from a Data Frame
formula.modelStruct
Extract modelStruct Object Formula
intervals.lmList
Confidence Intervals on lmList Coefficients
formula.gls
Extract gls Object Formula
getGroups.gls
Extract gls Object Groups
getResponse.lme
Extract lme Object Response
pairs.compareFits
Pairs Plot of compareFits Object
model.matrix.reStruct
reStruct Model Matrix
needUpdate
Check if Update is Needed
pdNatural
General Positive-Definite Matrix in Natural Parametrization
print.summary.varFunc
Print a summary.varFunc Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
logDet
Extract the Logarithm of the Determinant
coef.pdIdent
pdIdent Object Coefficients
nlme
Nonlinear Mixed-Effects Models
varClasses
Variance Function Classes
asOneFormula
Combine Formulas of a Set of Objects
formula.lmList
Extract lmList Object Formula
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
as.matrix.corStruct
Matrix of a corStruct Object
Initialize.glsStruct
Initialize a glsStruct Object
glsObject
Fitted gls Object
pdClasses
Positive-Definite Matrix Classes
logLik.gls
Log-Likelihood of a gls Object
random.effects
Extract Random Effects
formula.lme
Extract lme Object Formula
residuals.nlmeStruct
Calculate nlmeStruct Residuals
pdLogChol
General Positive-Definite Matrix
logLik.reStruct
Calculate reStruct Log-Likelihood
corFactor.corStruct
Factor of a corStruct Object Matrix
nlsList
List of nls Objects with a Common Model
plot.nmGroupedData
Plot an nmGroupedData Object
coef.lme
Extract lme Coefficients
predict.gnls
Predictions from a gnls Object
print.summary.gls
Print a summary.gls Object
summary.pdMat
Summarize a pdMat Object
pairs.lme
Pairs Plot of an lme Object
pooledSD
Extract Pooled Standard Deviation
plot.lme
Plot an lme or nls object
getData
Extract Data from an Object
getGroups
Extract Grouping Factors from an Object
corMatrix
Extract Correlation Matrix
Covariate.varFunc
Assign varFunc Covariate
pdDiag
Diagonal Positive-Definite Matrix
summary.gls
Summarize a gls Object
print.summary.pdMat
Print a summary.pdMat Object
pruneLevels
Prune Factor Levels
recalc.corStruct
Recalculate for corStruct Object
plot.augPred
Plot an augPred Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
splitFormula
Split a Formula
formula.corStruct
Extract corStruct Object Formula
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getGroups.lme
Extract lme Object Groups
getCovariate.data.frame
Extract Data Frame Covariate
formula.pdMat
Extract pdMat Formula
fitted.gnls
Extract gnls Fitted Values
fdHess
Finite difference Hessian
gnlsObject
Fitted gnls Object
gsummary
Summarize by Groups
Initialize.lmeStruct
Initialize an lmeStruct Object
getCovariate
Extract Covariate from an Object
intervals.lme
Confidence Intervals on lme Parameters
Initialize.corStruct
Initialize corStruct Object
formula.reStruct
Extract reStruct Object Formula
Matrix
Assign Matrix Values
recalc.reStruct
Recalculate for an reStruct Object
lmeStruct
Linear Mixed-Effects Structure
plot.compareFits
Plot a compareFits Object
Matrix.pdMat
Assign Matrix to a pdMat Object
ranef.lme
Extract lme Random Effects
varWeights
Extract Variance Function Weights
getData.lme
Extract lme Object Data
plot.ranef.lmList
Plot a ranef.lmList Object
update.modelStruct
Update a modelStruct Object
getResponse.lmList
Extract lmList Object Response
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
lme
Linear Mixed-Effects Models
getData.lmList
Extract lmList Object Data
compareFits
Compare Fitted Objects
fixef.lmList
Extract lmList Fixed Effects
isInitialized.reStruct
Check if an reStruct Object is Initialized
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
print.lme
Print an lme Object
varConstPower
Constant Plus Power Variance Function
glsStruct
Generalized Least Squares Structure
ranef.lmList
Extract lmList Random Effects
print.summary.lme
Print a summary.lme Object
predict.gls
Predictions from a gls Object
summary.lme
Summarize an lme Object
nlmeObject
Fitted nlme Object
solve.reStruct
Apply Solve to an reStruct Object
lme.lmList
LME fit from lmList Object
coef.pdCompSymm
pdCompSymm Object Coefficients
quinModel
Model function for the Quinidine data
logLik.corStruct
Extract corStruct Log-Likelihood
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
logLik.varFunc
Extract varFunc logLik
nlme.nlsList
NLME fit from nlsList Object
pdConstruct
Construct pdMat Objects
comparePred
Compare Predictions
recalc.varFunc
Recalculate for varFunc Object
residuals.lme
Extract lme Residuals
update.varFunc
Update varFunc Object
groupedData
Construct a groupedData Object
print.corStruct
Print a corStruct Object
corNatural
General correlation in natural parameterization
pdMat
Positive-Definite Matrix
corSymm
General Correlation Structure
logLik.gnls
Log-Likelihood of a gnls Object
residuals.gls
Extract gls Residuals
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
print.groupedData
Print a groupedData Object
fitted.glsStruct
Calculate glsStruct Fitted Values
print.anova.lme
Print an anova.lme Object
predict.lme
Predictions from an lme Object
varExp
Exponential Variance Function
print.summary.modelStruct
Print a summary.modelStruct Object
residuals.lmList
Extract lmList Residuals
residuals.gnlsStruct
Calculate gnlsStruct Residuals
print.varFunc
Print a varFunc Object
varPower
Power Variance Function
summary.modelStruct
Summarize a modelStruct Object
fitted.lmList
Extract lmList Fitted Values
pdSymm
General Positive-Definite Matrix
plot.nffGroupedData
Plot an nffGroupedData Object
recalc
Recalculate Condensed Linear Model Object
predict.nlme
Predictions from an nlme Object
getCovariate.corStruct
Extract corStruct Object Covariate
glsControl
Control Values for gls Fit
print.summary.lmList
Print a summary.lmList Object
varIdent
Constant Variance Function
isBalanced
Check a Design for Balance
varWeights.lmeStruct
Variance Weights for lmeStruct Object
isInitialized
Check if Object is Initialized
varWeights.glsStruct
Variance Weights for glsStruct Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
summary.corStruct
Summarize a corStruct Object
summary.varFunc
Summarize varFunc Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
nlsList.selfStart
nlsList Fit from a selfStart Function
residuals.glsStruct
Calculate glsStruct Residuals
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Names
Names Associated with an Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getGroups.corStruct
Extract corStruct Groups
getResponse.gls
Extract gls Object Response
getData.gls
Extract gls Object Data
logLik.lme
Log-Likelihood of an lme Object
nlmeStruct
Nonlinear Mixed-Effects Structure
pdConstruct.pdBlocked
Construct pdBlocked Objects
plot.ACF
Plot an ACF Object
predict.lmList
Predictions from an lmList Object
print.modelStruct
Print a modelStruct Object
print.pdMat
Print a pdMat Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
reStruct
Random Effects Structure
allCoef
Extract Coefficients from a Set of Objects
corCompSymm
Compound Symmetry Correlation Structure
summary.lmList
Summarize an lmList Object
fitted.lme
Extract lme Fitted Values
fitted.gls
Extract gls Fitted Values
getResponse
Extract Response Variable from an Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
gapply
Apply a Function by Groups
formula.pdBlocked
Extract pdBlocked Formula
intervals.gls
Confidence Intervals on gls Parameters
gnls
Fit Nonlinear Model Using Generalized Least Squares
logLik.glsStruct
Log-Likelihood of a glsStruct Object
nlmeControl
Control Values for nlme Fit
plot.lmList
Plot an lmList Object
print.lmList
Print an lmList Object
varComb
Combination of Variance Functions
varFunc
Variance Function Structure
simulate.lme
simulate lme models
[.pdMat
Subscript a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
as.matrix.reStruct
Matrices of an reStruct Object
coef.lmList
Extract lmList Coefficients
getCovariate.varFunc
Extract varFunc Covariate
getCovariateFormula
Extract Covariates Formula
lme.groupedData
LME fit from groupedData Object
logLik.lmList
Log-Likelihood of an lmList Object
nlme-internal
Internal nlme functions
print.gls
Print a gls Object
plot.ranef.lme
Plot a ranef.lme Object
varFixed
Fixed Variance Function
residuals.lmeStruct
Calculate lmeStruct Residuals
Covariate
Assign Covariate Values
LDEsysMat
Generate system matrix for LDEs
MEestimate
Estimate mixed-effects parameters
MEdims
Calculate dimensions in mixed-effects
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
contr.SAS
Contrast Matrices
corExp
Exponential Correlation Structure
corSpatial
Spatial Correlation Structure
corSpher
Spherical Correlation Structure
intervals
Confidence Intervals on Coefficients
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
lmeObject
Fitted lme Object
plot.gls
Plot a gls Object
recalc.modelStruct
Recalculate for a modelStruct Object
Glucose
Glucose levels over time
Glucose2
Glucose Levels Following Alcohol Ingestion
Rail
Evaluation of Stress in Railway Rails
Relaxin
Assay for Relaxin
Gun
Methods for firing naval guns
Oxboys
Heights of Boys in Oxford
BodyWeight
Rat weight over time for different diets
PBG
Effect of Phenylbiguanide on Blood Pressure
RatPupWeight
The weight of rat pups
Soybean
Growth of soybean plants
Wheat2
Wheat Yield Trials
Fatigue
Cracks caused by metal fatigue
Ovary
Counts of Ovarian Follicles
Spruce
Growth of Spruce Trees
Quinidine
Quinidine Kinetics
Assay
Bioassay on Cell Culture Plate
Muscle
Contraction of heart muscle sections
Wheat
Yields by growing conditions
bdf
Language scores
Oats
Split-plot Experiment on Varieties of Oats
Nitrendipene
Assay of nitrendipene
Meat
Tenderness of meat
Milk
Protein content of cows' milk
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
MathAchieve
Mathematics achievement scores
Tetracycline2
Pharmacokinetics of tetracycline
Cefamandole
Pharmacokinetics of Cefamandole
Wafer
Modeling of Analog MOS Circuits
Phenobarb
Phenobarbitol Kinetics
Gasoline
Refinery yield of gasoline
ergoStool
Ergometrics experiment with stool types
Earthquake
Earthquake Intensity
Oxide
Variability in Semiconductor Manufacturing
MathAchSchool
School demographic data for MathAchieve
Pixel
X-ray pixel intensities over time
Remifentanil
Pharmacokinetics of remifentanil
Orthodont
Growth curve data on an orthdontic measurement
Tetracycline1
Pharmacokinetics of tetracycline
Machines
Productivity Scores for Machines and Workers
Dialyzer
High-Flux Hemodialyzer
IGF
Radioimmunoassay of IGF-I Protein