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nlme (version 3.1-102)
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
85,005
Version
3.1-102
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
July 23rd, 2011
Functions in nlme (3.1-102)
Search all functions
coef.reStruct
reStruct Object Coefficients
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
Phenobarb
Phenobarbitol Kinetics
getData.gls
Extract gls Object Data
formula.pdMat
Extract pdMat Formula
Glucose
Glucose levels over time
Dim.corStruct
Dimensions of a corStruct Object
getGroups.corStruct
Extract corStruct Groups
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
coef.lme
Extract lme Coefficients
getGroups
Extract Grouping Factors from an Object
Remifentanil
Pharmacokinetics of remifentanil
Initialize.lmeStruct
Initialize an lmeStruct Object
glsStruct
Generalized Least Squares Structure
RatPupWeight
The weight of rat pups
fdHess
Finite difference Hessian
Machines
Productivity Scores for Machines and Workers
fitted.lmeStruct
Calculate lmeStruct Fitted Values
Orthodont
Growth curve data on an orthdontic measurement
lme.groupedData
LME fit from groupedData Object
anova.lme
Compare Likelihoods of Fitted Objects
getGroups.lmList
Extract lmList Object Groups
Fatigue
Cracks caused by metal fatigue
Earthquake
Earthquake Intensity
Oxboys
Heights of Boys in Oxford
lmList.groupedData
lmList Fit from a groupedData Object
VarCorr
Extract variance and correlation components
[.pdMat
Subscript a pdMat Object
allCoef
Extract Coefficients from a Set of Objects
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
coef.gnls
Extract gnls Coefficients
fitted.lmList
Extract lmList Fitted Values
as.matrix.reStruct
Matrices of an reStruct Object
Dim.corSpatial
Dimensions of a corSpatial Object
corAR1
AR(1) Correlation Structure
corMatrix.corStruct
Matrix of a corStruct Object
ACF.lme
Autocorrelation Function for lme Residuals
Meat
Tenderness of meat
Initialize
Initialize Object
Oxide
Variability in Semiconductor Manufacturing
Initialize.reStruct
Initialize reStruct Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Names.pdBlocked
Names of a pdBlocked Object
MathAchieve
Mathematics achievement scores
comparePred
Compare Predictions
Matrix.reStruct
Assign reStruct Matrices
logLik.corStruct
Extract corStruct Log-Likelihood
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
as.matrix.pdMat
Matrix of a pdMat Object
coef.corStruct
Coefficients of a corStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
coef.pdMat
pdMat Object Coefficients
MathAchSchool
School demographic data for MathAchieve
ACF.gls
Autocorrelation Function for gls Residuals
Assay
Bioassay on Cell Culture Plate
Initialize.varFunc
Initialize varFunc Object
formula.reStruct
Extract reStruct Object Formula
Muscle
Contraction of heart muscle sections
Tetracycline2
Pharmacokinetics of tetracycline
compareFits
Compare Fitted Objects
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Covariate.varFunc
Assign varFunc Covariate
plot.nmGroupedData
Plot an nmGroupedData Object
Dim.pdMat
Dimensions of a pdMat Object
Milk
Protein content of cows' milk
Names.formula
Extract Names from a formula
Rail
Evaluation of Stress in Railway Rails
coef.lmList
Extract lmList Coefficients
Variogram.corExp
Calculate Semi-variogram for a corExp Object
coef.varFunc
varFunc Object Coefficients
Pixel
X-ray pixel intensities over time
Covariate
Assign Covariate Values
Names
Names Associated with an Object
Nitrendipene
Assay of nitrendipene
corSpher
Spherical Correlation Structure
getCovariate
Extract Covariate from an Object
getResponseFormula
Extract Formula Specifying Response Variable
Wafer
Modeling of Analog MOS Circuits
print.summary.pdMat
Print a summary.pdMat Object
getData.lmList
Extract lmList Object Data
Variogram.default
Calculate Semi-variogram
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getData.lme
Extract lme Object Data
groupedData
Construct a groupedData Object
logLik.reStruct
Calculate reStruct Log-Likelihood
Names.pdMat
Names of a pdMat Object
nlmeObject
Fitted nlme Object
intervals
Confidence Intervals on Coefficients
logDet.pdMat
Extract Log-Determinant from a pdMat Object
lme.lmList
LME fit from lmList Object
corSpatial
Spatial Correlation Structure
logDet.reStruct
Extract reStruct Log-Determinants
lme
Linear Mixed-Effects Models
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
gapply
Apply a Function by Groups
getGroups.gls
Extract gls Object Groups
Glucose2
Glucose Levels Following Alcohol Ingestion
Wheat2
Wheat Yield Trials
predict.lme
Predictions from an lme Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
corLin
Linear Correlation Structure
corFactor
Factor of a Correlation Matrix
Cefamandole
Pharmacokinetics of Cefamandole
plot.augPred
Plot an augPred Object
Gasoline
Refinery yield of gasoline
asOneFormula
Combine Formulas of a Set of Objects
nlsList
List of nls Objects with a Common Model
IGF
Radioimmunoassay of IGF-I Protein
Quinidine
Quinidine Kinetics
fitted.lme
Extract lme Fitted Values
Wheat
Yields by growing conditions
BodyWeight
Rat weight over time for different diets
corCAR1
Continuous AR(1) Correlation Structure
Relaxin
Assay for Relaxin
PBG
Effect of Phenylbiguanide on Blood Pressure
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
Names.reStruct
Names of an reStruct Object
recalc.reStruct
Recalculate for an reStruct Object
collapse.groupedData
Collapse a groupedData Object
asTable
Convert groupedData to a matrix
plot.nfnGroupedData
Plot an nfnGroupedData Object
logDet
Extract the Logarithm of the Determinant
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
quinModel
Model function for the Quinidine data
Spruce
Growth of Spruce Trees
corNatural
General correlation in natural parameterization
Tetracycline1
Pharmacokinetics of tetracycline
print.varFunc
Print a varFunc Object
corSymm
General Correlation Structure
Variogram.corLin
Calculate Semi-variogram for a corLin Object
pdBlocked
Positive-Definite Block Diagonal Matrix
intervals.lmList
Confidence Intervals on lmList Coefficients
augPred
Augmented Predictions
getVarCov
Extract variance-covariance matrix
plot.ranef.lmList
Plot a ranef.lmList Object
anova.gls
Compare Likelihoods of Fitted Objects
corFactor.corStruct
Factor of a corStruct Object Matrix
bdf
Language scores
collapse
Collapse According to Groups
Oats
Split-plot Experiment on Varieties of Oats
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
isBalanced
Check a Design for Balance
update.modelStruct
Update a modelStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
getGroups.lme
Extract lme Object Groups
corMatrix
Extract Correlation Matrix
isInitialized
Check if Object is Initialized
glsControl
Control Values for gls Fit
pdClasses
Positive-Definite Matrix Classes
LDEsysMat
Generate system matrix for LDEs
formula.pdBlocked
Extract pdBlocked Formula
logDet.corStruct
Extract corStruct Log-Determinant
pdLogChol
General Positive-Definite Matrix
getCovariate.corStruct
Extract corStruct Object Covariate
logLik.gnls
Log-Likelihood of a gnls Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pairs.compareFits
Pairs Plot of compareFits Object
pdSymm
General Positive-Definite Matrix
pdIdent
Multiple of the Identity Positive-Definite Matrix
corExp
Exponential Correlation Structure
logLik.lme
Log-Likelihood of an lme Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
corGaus
Gaussian Correlation Structure
lmeObject
Fitted lme Object
corARMA
ARMA(p,q) Correlation Structure
plot.lmList
Plot an lmList Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
Coef
Assign Values to Coefficients
balancedGrouped
Create a groupedData object from a matrix
predict.gls
Predictions from a gls Object
as.matrix.corStruct
Matrix of a corStruct Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
plot.intervals.lmList
Plot lmList Confidence Intervals
nlmeControl
Control Values for nlme Fit
Gun
Methods for firing naval guns
reStruct
Random Effects Structure
fixef.lmList
Extract lmList Fixed Effects
pdConstruct.pdBlocked
Construct pdBlocked Objects
residuals.lme
Extract lme Residuals
corCompSymm
Compound Symmetry Correlation Structure
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
summary.lmList
Summarize an lmList Object
ACF
Autocorrelation Function
varExp
Exponential Variance Function
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
ranef.lmList
Extract lmList Random Effects
update.varFunc
Update varFunc Object
summary.nlsList
Summarize an nlsList Object
lmList
List of lm Objects with a Common Model
summary.varFunc
Summarize varFunc Object
corRatio
Rational Quadratic Correlation Structure
getCovariateFormula
Extract Covariates Formula
glsObject
Fitted gls Object
Variogram
Calculate Semi-variogram
ranef.lme
Extract lme Random Effects
nlsList.selfStart
nlsList Fit from a selfStart Function
getCovariate.data.frame
Extract Data Frame Covariate
getCovariate.varFunc
Extract varFunc Covariate
residuals.glsStruct
Calculate glsStruct Residuals
plot.compareFits
Plot a compareFits Object
splitFormula
Split a Formula
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getResponse
Extract Response Variable from an Object
gsummary
Summarize by Groups
coef.modelStruct
Extract modelStruct Object Coefficients
Initialize.glsStruct
Initialize a glsStruct Object
Soybean
Growth of soybean plants
pairs.lme
Pairs Plot of an lme Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
varFunc
Variance Function Structure
qqnorm.gls
Normal Plot of Residuals from a gls Object
summary.lme
Summarize an lme Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
Ovary
Counts of Ovarian Follicles
Initialize.corStruct
Initialize corStruct Object
varClasses
Variance Function Classes
logLik.varFunc
Extract varFunc logLik
gnlsObject
Fitted gnls Object
corClasses
Correlation Structure Classes
summary.modelStruct
Summarize a modelStruct Object
phenoModel
Model function for the Phenobarb data
varIdent
Constant Variance Function
lmeScale
Scale for lme Optimization
fixed.effects
Extract Fixed Effects
plot.lme
Plot an lme or nls object
ergoStool
Ergometrics experiment with stool types
plot.ACF
Plot an ACF Object
nlme
Nonlinear Mixed-Effects Models
varWeights.glsStruct
Variance Weights for glsStruct Object
gnlsControl
Control Values for gnls Fit
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
simulate.lme
Simulate Results from
lme
Models
gnls
Fit Nonlinear Model Using Generalized Least Squares
intervals.lme
Confidence Intervals on lme Parameters
recalc
Recalculate Condensed Linear Model Object
pdDiag
Diagonal Positive-Definite Matrix
varWeights
Extract Variance Function Weights
gls
Fit Linear Model Using Generalized Least Squares
intervals.gls
Confidence Intervals on gls Parameters
residuals.lmList
Extract lmList Residuals
random.effects
Extract Random Effects
lmeControl
Control Values for lme Fit
nlme.nlsList
NLME fit from nlsList Object
needUpdate
Check if Update is Needed
summary.pdMat
Summarize a pdMat Object
pdMat
Positive-Definite Matrix
fitted.glsStruct
Calculate glsStruct Fitted Values
getData
Extract Data from an Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
lmeStruct
Linear Mixed-Effects Structure
pdConstruct
Construct pdMat Objects
recalc.corStruct
Recalculate for corStruct Object
pooledSD
Extract Pooled Standard Deviation
pairs.lmList
Pairs Plot of an lmList Object
plot.ranef.lme
Plot a ranef.lme Object
residuals.gls
Extract gls Residuals
model.matrix.reStruct
reStruct Model Matrix
predict.gnls
Predictions from a gnls Object
nlmeStruct
Nonlinear Mixed-Effects Structure
solve.reStruct
Apply Solve to an reStruct Object
plot.gls
Plot a gls Object
recalc.modelStruct
Recalculate for a modelStruct Object
predict.lmList
Predictions from an lmList Object
summary.corStruct
Summarize a corStruct Object
varConstPower
Constant Plus Power Variance Function
varFixed
Fixed Variance Function
plot.Variogram
Plot a Variogram Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
varComb
Combination of Variance Functions
predict.nlme
Predictions from an nlme Object
summary.gls
Summarize a gls Object
recalc.varFunc
Recalculate for varFunc Object
varPower
Power Variance Function
Matrix
Assign Matrix Values
Dialyzer
High-Flux Hemodialyzer
Dim
Extract Dimensions from an Object
Matrix.pdMat
Assign Matrix to a pdMat Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
getGroupsFormula
Extract Grouping Formula
getGroups.varFunc
Extract varFunc Groups
logLik.lmList
Log-Likelihood of an lmList Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
residuals.lmeStruct
Calculate lmeStruct Residuals
varWeights.lmeStruct
Variance Weights for lmeStruct Object