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nlme (version 3.1-101)
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
62,596
Version
3.1-101
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
May 6th, 2011
Functions in nlme (3.1-101)
Search all functions
ACF
Autocorrelation Function
Variogram.corLin
Calculate Semi-variogram for a corLin Object
ACF.lme
Autocorrelation Function for lme Residuals
fdHess
Finite difference Hessian
Initialize.reStruct
Initialize reStruct Object
getCovariate.data.frame
Extract Data Frame Covariate
Variogram.corExp
Calculate Semi-variogram for a corExp Object
glsControl
Control Values for gls Fit
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Dialyzer
High-Flux Hemodialyzer
ACF.gls
Autocorrelation Function for gls Residuals
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Assay
Bioassay on Cell Culture Plate
Machines
Productivity Scores for Machines and Workers
Cefamandole
Pharmacokinetics of Cefamandole
Tetracycline2
Pharmacokinetics of tetracycline
Tetracycline1
Pharmacokinetics of tetracycline
Variogram.default
Calculate Semi-variogram
Initialize.corStruct
Initialize corStruct Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
anova.gls
Compare Likelihoods of Fitted Objects
Names.pdBlocked
Names of a pdBlocked Object
coef.lmList
Extract lmList Coefficients
corSpher
Spherical Correlation Structure
BodyWeight
Rat weight over time for different diets
Dim.pdMat
Dimensions of a pdMat Object
Names.formula
Extract Names from a formula
ergoStool
Ergometrics experiment with stool types
corNatural
General correlation in natural parameterization
Muscle
Contraction of heart muscle sections
Initialize.varFunc
Initialize varFunc Object
Wafer
Modeling of Analog MOS Circuits
fitted.lmeStruct
Calculate lmeStruct Fitted Values
Orthodont
Growth curve data on an orthdontic measurement
recalc.corStruct
Recalculate for corStruct Object
getCovariate.corStruct
Extract corStruct Object Covariate
simulate.lme
Simulate results from lme models
Dim
Extract Dimensions from an Object
Relaxin
Assay for Relaxin
Soybean
Growth of soybean plants
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Initialize.glsStruct
Initialize a glsStruct Object
getCovariateFormula
Extract Covariates Formula
Initialize.lmeStruct
Initialize an lmeStruct Object
Gasoline
Refinery yield of gasoline
Matrix.reStruct
Assign reStruct Matrices
isBalanced
Check a Design for Balance
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Names
Names Associated with an Object
Names.reStruct
Names of an reStruct Object
compareFits
Compare Fitted Objects
Dim.corSpatial
Dimensions of a corSpatial Object
Ovary
Counts of Ovarian Follicles
corCompSymm
Compound Symmetry Correlation Structure
corARMA
ARMA(p,q) Correlation Structure
gsummary
Summarize by Groups
lmeObject
Fitted lme Object
getCovariate
Extract Covariate from an Object
corExp
Exponential Correlation Structure
as.matrix.corStruct
Matrix of a corStruct Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
intervals.lmList
Confidence Intervals on lmList Coefficients
lmeControl
Control Values for lme Fit
plot.intervals.lmList
Plot lmList Confidence Intervals
Gun
Methods for firing naval guns
allCoef
Extract Coefficients from a Set of Objects
coef.varFunc
varFunc Object Coefficients
RatPupWeight
The weight of rat pups
gnls
Fit Nonlinear Model Using Generalized Least Squares
getResponseFormula
Extract Formula Specifying Response Variable
lmeStruct
Linear Mixed-Effects Structure
logLik.corStruct
Extract corStruct Log-Likelihood
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getCovariate.varFunc
Extract varFunc Covariate
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
coef.reStruct
reStruct Object Coefficients
needUpdate
Check if Update is Needed
coef.modelStruct
Extract modelStruct Object Coefficients
plot.compareFits
Plot a compareFits Object
logDet.corStruct
Extract corStruct Log-Determinant
LDEsysMat
Generate system matrix for LDEs
corSymm
General Correlation Structure
pdMat
Positive-Definite Matrix
summary.lmList
Summarize an lmList Object
as.matrix.pdMat
Matrix of a pdMat Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
Covariate.varFunc
Assign varFunc Covariate
PBG
Effect of Phenylbiguanide on Blood Pressure
lmList
List of lm Objects with a Common Model
Glucose
Glucose levels over time
Quinidine
Quinidine Kinetics
plot.gls
Plot a gls Object
pdSymm
General Positive-Definite Matrix
Names.pdMat
Names of a pdMat Object
getGroups.corStruct
Extract corStruct Groups
Wheat
Yields by growing conditions
Initialize
Initialize Object
corCAR1
Continuous AR(1) Correlation Structure
bdf
Language scores
[.pdMat
Subscript a pdMat Object
nlsList
List of nls Objects with a Common Model
logDet.reStruct
Extract reStruct Log-Determinants
fitted.glsStruct
Calculate glsStruct Fitted Values
corClasses
Correlation Structure Classes
logLik.glsStruct
Log-Likelihood of a glsStruct Object
predict.gls
Predictions from a gls Object
Rail
Evaluation of Stress in Railway Rails
solve.reStruct
Apply Solve to an reStruct Object
residuals.lmList
Extract lmList Residuals
Oxboys
Heights of Boys in Oxford
Dim.corStruct
Dimensions of a corStruct Object
Spruce
Growth of Spruce Trees
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
coef.gnls
Extract gnls Coefficients
nlmeObject
Fitted nlme Object
recalc.reStruct
Recalculate for an reStruct Object
corGaus
Gaussian Correlation Structure
VarCorr
Extract variance and correlation components
Remifentanil
Pharmacokinetics of remifentanil
Earthquake
Earthquake Intensity
corAR1
AR(1) Correlation Structure
Pixel
X-ray pixel intensities over time
varWeights.glsStruct
Variance Weights for glsStruct Object
coef.lme
Extract lme Coefficients
varClasses
Variance Function Classes
MathAchSchool
School demographic data for MathAchieve
Covariate
Assign Covariate Values
getData
Extract Data from an Object
Fatigue
Cracks caused by metal fatigue
pairs.lmList
Pairs Plot of an lmList Object
getGroupsFormula
Extract Grouping Formula
collapse.groupedData
Collapse a groupedData Object
Coef
Assign Values to Coefficients
augPred
Augmented Predictions
isInitialized
Check if Object is Initialized
coef.pdMat
pdMat Object Coefficients
coef.corStruct
Coefficients of a corStruct Object
varComb
Combination of Variance Functions
varExp
Exponential Variance Function
MathAchieve
Mathematics achievement scores
fitted.lmList
Extract lmList Fitted Values
collapse
Collapse According to Groups
pairs.lme
Pairs Plot of an lme Object
logLik.varFunc
Extract varFunc logLik
plot.lme
Plot an lme or nls object
corFactor
Factor of a Correlation Matrix
gls
Fit Linear Model Using Generalized Least Squares
formula.pdMat
Extract pdMat Formula
glsStruct
Generalized Least Squares Structure
lme.lmList
LME fit from lmList Object
corSpatial
Spatial Correlation Structure
plot.nmGroupedData
Plot an nmGroupedData Object
corLin
Linear Correlation Structure
residuals.lme
Extract lme Residuals
fitted.lme
Extract lme Fitted Values
corRatio
Rational Quadratic Correlation Structure
nlme.nlsList
NLME fit from nlsList Object
random.effects
Extract Random Effects
model.matrix.reStruct
reStruct Model Matrix
getGroups.varFunc
Extract varFunc Groups
varFixed
Fixed Variance Function
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
logLik.lmList
Log-Likelihood of an lmList Object
formula.reStruct
Extract reStruct Object Formula
lmeScale
Scale for lme Optimization
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Matrix
Assign Matrix Values
gapply
Apply a Function by Groups
corMatrix
Extract Correlation Matrix
formula.pdBlocked
Extract pdBlocked Formula
IGF
Radioimmunoassay of IGF-I Protein
nlmeStruct
Nonlinear Mixed-Effects Structure
plot.ACF
Plot an ACF Object
plot.ranef.lme
Plot a ranef.lme Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
corMatrix.corStruct
Matrix of a corStruct Object
varPower
Power Variance Function
logDet.pdMat
Extract Log-Determinant from a pdMat Object
getGroups
Extract Grouping Factors from an Object
comparePred
Compare Predictions
gnlsStruct
Generalized Nonlinear Least Squares Structure
Variogram
Calculate Semi-variogram
getData.gls
Extract gls Object Data
plot.nffGroupedData
Plot an nffGroupedData Object
Phenobarb
Phenobarbitol Kinetics
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
varWeights
Extract Variance Function Weights
pdBlocked
Positive-Definite Block Diagonal Matrix
Nitrendipene
Assay of nitrendipene
pdClasses
Positive-Definite Matrix Classes
intervals.gls
Confidence Intervals on gls Parameters
residuals.nlmeStruct
Calculate nlmeStruct Residuals
as.matrix.reStruct
Matrices of an reStruct Object
predict.gnls
Predictions from a gnls Object
balancedGrouped
Create a groupedData object from a matrix
Oxide
Variability in Semiconductor Manufacturing
ranef.lmList
Extract lmList Random Effects
asTable
Convert groupedData to a matrix
fixed.effects
Extract Fixed Effects
getData.lmList
Extract lmList Object Data
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
nlsList.selfStart
nlsList Fit from a selfStart Function
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
getVarCov
Extract variance-covariance matrix
intervals.lme
Confidence Intervals on lme Parameters
nlme
Nonlinear Mixed-Effects Models
lmList.groupedData
lmList Fit from a groupedData Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
recalc
Recalculate Condensed Linear Model Object
logDet
Extract the Logarithm of the Determinant
splitFormula
Split a Formula
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
recalc.varFunc
Recalculate for varFunc Object
reStruct
Random Effects Structure
nlmeControl
Control Values for nlme Fit
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
residuals.lmeStruct
Calculate lmeStruct Residuals
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
varFunc
Variance Function Structure
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
Wheat2
Wheat Yield Trials
pdLogChol
General Positive-Definite Matrix
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
varWeights.lmeStruct
Variance Weights for lmeStruct Object
glsObject
Fitted gls Object
update.modelStruct
Update a modelStruct Object
summary.lme
Summarize an lme Object
predict.lme
Predictions from an lme Object
gnlsObject
Fitted gnls Object
summary.gls
Summarize a gls Object
fixef.lmList
Extract lmList Fixed Effects
pdConstruct
Construct pdMat Objects
logLik.gnls
Log-Likelihood of a gnls Object
quinModel
Model function for the Quinidine data
summary.varFunc
Summarize varFunc Object
plot.Variogram
Plot a Variogram Object
getResponse
Extract Response Variable from an Object
predict.nlme
Predictions from an nlme Object
phenoModel
Model function for the Phenobarb data
plot.ranef.lmList
Plot a ranef.lmList Object
summary.nlsList
Summarize an nlsList Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
logLik.lme
Log-Likelihood of an lme Object
pooledSD
Extract Pooled Standard Deviation
pdDiag
Diagonal Positive-Definite Matrix
recalc.modelStruct
Recalculate for a modelStruct Object
plot.augPred
Plot an augPred Object
residuals.glsStruct
Calculate glsStruct Residuals
predict.lmList
Predictions from an lmList Object
intervals
Confidence Intervals on Coefficients
getGroups.gls
Extract gls Object Groups
getGroups.lme
Extract lme Object Groups
summary.corStruct
Summarize a corStruct Object
update.varFunc
Update varFunc Object
Matrix.pdMat
Assign Matrix to a pdMat Object
Milk
Protein content of cows' milk
asOneFormula
Combine Formulas of a Set of Objects
ranef.lme
Extract lme Random Effects
summary.pdMat
Summarize a pdMat Object
print.varFunc
Print a varFunc Object
corFactor.corStruct
Factor of a corStruct Object Matrix
getData.lme
Extract lme Object Data
gnlsControl
Control Values for gnls Fit
groupedData
Construct a groupedData Object
pairs.compareFits
Pairs Plot of compareFits Object
plot.lmList
Plot an lmList Object
summary.modelStruct
Summarize a modelStruct Object
getGroups.lmList
Extract lmList Object Groups
varIdent
Constant Variance Function
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Meat
Tenderness of meat
anova.lme
Compare Likelihoods of Fitted Objects
getGroups.data.frame
Extract Groups from a Data Frame
lme
Linear Mixed-Effects Models
lme.groupedData
LME fit from groupedData Object
Oats
Split-plot Experiment on Varieties of Oats
print.summary.pdMat
Print a summary.pdMat Object
residuals.gls
Extract gls Residuals
varConstPower
Constant Plus Power Variance Function