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nlme (version 3.1-98)
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
3.1-98
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
February 10th, 2011
Functions in nlme (3.1-98)
Search all functions
Initialize.glsStruct
Initialize a glsStruct Object
Tetracycline1
Pharmacokinetics of tetracycline
Matrix.reStruct
Assign reStruct Matrices
pdMat
Positive-Definite Matrix
update.varFunc
Update varFunc Object
BIC
Bayesian Information Criterion
Covariate.varFunc
Assign varFunc Covariate
LDEsysMat
Generate system matrix for LDEs
Tetracycline2
Pharmacokinetics of tetracycline
Variogram.corExp
Calculate Semi-variogram for a corExp Object
allCoef
Extract Coefficients from a Set of Objects
coef.modelStruct
Extract modelStruct Object Coefficients
collapse
Collapse According to Groups
corLin
Linear Correlation Structure
corMatrix.corStruct
Matrix of a corStruct Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
corSpatial
Spatial Correlation Structure
getCovariate
Extract Covariate from an Object
getGroups.lme
Extract lme Object Groups
Names
Names Associated with an Object
plot.lme
Plot an lme or nls object
pooledSD
Extract Pooled Standard Deviation
getCovariate.corStruct
Extract corStruct Object Covariate
MathAchieve
Mathematics achievement scores
varWeights.lmeStruct
Variance Weights for lmeStruct Object
VarCorr
Extract variance and correlation components
Oxide
Variability in Semiconductor Manufacturing
logDet.corStruct
Extract corStruct Log-Determinant
Wafer
Modeling of Analog MOS Circuits
Remifentanil
Pharmacokinetics of remifentanil
logDet.pdMat
Extract Log-Determinant from a pdMat Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
balancedGrouped
Create a groupedData object from a matrix
logLik.gnls
Log-Likelihood of a gnls Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
getGroups.lmList
Extract lmList Object Groups
gnlsObject
Fitted gnls Object
corFactor
Factor of a Correlation Matrix
groupedData
Construct a groupedData Object
pdSymm
General Positive-Definite Matrix
model.matrix.reStruct
reStruct Model Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
gnlsControl
Control Values for gnls Fit
Machines
Productivity Scores for Machines and Workers
Matrix.pdMat
Assign Matrix to a pdMat Object
Names.formula
Extract Names from a formula
intervals
Confidence Intervals on Coefficients
Quinidine
Quinidine Kinetics
plot.gls
Plot a gls Object
plot.intervals.lmList
Plot lmList Confidence Intervals
Soybean
Growth of soybean plants
predict.lmList
Predictions from an lmList Object
gsummary
Summarize by Groups
collapse.groupedData
Collapse a groupedData Object
lme
Linear Mixed-Effects Models
as.matrix.pdMat
Matrix of a pdMat Object
Gasoline
Refinery yield of gasoline
getCovariateFormula
Extract Covariates Formula
anova.lme
Compare Likelihoods of Fitted Objects
comparePred
Compare Predictions
ranef.lmList
Extract lmList Random Effects
pdBlocked
Positive-Definite Block Diagonal Matrix
Fatigue
Cracks caused by metal fatigue
Gun
Methods for firing naval guns
Glucose2
Glucose Levels Following Alcohol Ingestion
recalc.corStruct
Recalculate for corStruct Object
phenoModel
Model function for the Phenobarb data
quinModel
Model function for the Quinidine data
lmeObject
Fitted lme Object
varFixed
Fixed Variance Function
corCompSymm
Compound Symmetry Correlation Structure
Milk
Protein content of cows' milk
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
residuals.gls
Extract gls Residuals
reStruct
Random Effects Structure
fixed.effects
Extract Fixed Effects
corFactor.corStruct
Factor of a corStruct Object Matrix
recalc
Recalculate Condensed Linear Model Object
summary.nlsList
Summarize an nlsList Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
fixef.lmList
Extract lmList Fixed Effects
coef.varFunc
varFunc Object Coefficients
varIdent
Constant Variance Function
corExp
Exponential Correlation Structure
summary.varFunc
Summarize varFunc Object
lmeControl
Control Values for lme Fit
intervals.gls
Confidence Intervals on gls Parameters
coef.reStruct
reStruct Object Coefficients
getResponseFormula
Extract Formula Specifying Response Variable
getGroups
Extract Grouping Factors from an Object
logLik.lmList
Log-Likelihood of an lmList Object
Dim.pdMat
Dimensions of a pdMat Object
Nitrendipene
Assay of nitrendipene
nlme.nlsList
NLME fit from nlsList Object
getCovariate.data.frame
Extract Data Frame Covariate
pairs.lme
Pairs Plot of an lme Object
corAR1
AR(1) Correlation Structure
Dim.corStruct
Dimensions of a corStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
gapply
Apply a Function by Groups
formula.pdMat
Extract pdMat Formula
lme.groupedData
LME fit from groupedData Object
Covariate
Assign Covariate Values
plot.Variogram
Plot a Variogram Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
as.matrix.reStruct
Matrices of an reStruct Object
pairs.compareFits
Pairs Plot of compareFits Object
Initialize.reStruct
Initialize reStruct Object
coef.gnls
Extract gnls Coefficients
anova.gls
Compare Likelihoods of Fitted Objects
fitted.lme
Extract lme Fitted Values
predict.gnls
Predictions from a gnls Object
recalc.modelStruct
Recalculate for a modelStruct Object
pdConstruct
Construct pdMat Objects
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
plot.ACF
Plot an ACF Object
summary.modelStruct
Summarize a modelStruct Object
glsStruct
Generalized Least Squares Structure
logLik.reStruct
Calculate reStruct Log-Likelihood
nlmeControl
Control Values for nlme Fit
print.varFunc
Print a varFunc Object
varPower
Power Variance Function
print.summary.pdMat
Print a summary.pdMat Object
logLik.varFunc
Extract varFunc logLik
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
corClasses
Correlation Structure Classes
corARMA
ARMA(p,q) Correlation Structure
recalc.varFunc
Recalculate for varFunc Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
plot.nffGroupedData
Plot an nffGroupedData Object
lmeStruct
Linear Mixed-Effects Structure
getData.gls
Extract gls Object Data
summary.gls
Summarize a gls Object
getGroups.varFunc
Extract varFunc Groups
getData.lme
Extract lme Object Data
update.modelStruct
Update a modelStruct Object
varExp
Exponential Variance Function
lmList.groupedData
lmList Fit from a groupedData Object
logDet.reStruct
Extract reStruct Log-Determinants
nlmeStruct
Nonlinear Mixed-Effects Structure
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdClasses
Positive-Definite Matrix Classes
Initialize.varFunc
Initialize varFunc Object
Initialize.lmeStruct
Initialize an lmeStruct Object
predict.gls
Predictions from a gls Object
ranef.lme
Extract lme Random Effects
Initialize.corStruct
Initialize corStruct Object
random.effects
Extract Random Effects
getGroupsFormula
Extract Grouping Formula
Glucose
Glucose levels over time
Matrix
Assign Matrix Values
Spruce
Growth of Spruce Trees
corMatrix
Extract Correlation Matrix
ergoStool
Ergometrics experiment with stool types
lmList
List of lm Objects with a Common Model
needUpdate
Check if Update is Needed
MathAchSchool
School demographic data for MathAchieve
Names.reStruct
Names of an reStruct Object
Oats
Split-plot Experiment on Varieties of Oats
fdHess
Finite difference Hessian
pdLogChol
General Positive-Definite Matrix
fitted.glsStruct
Calculate glsStruct Fitted Values
residuals.gnlsStruct
Calculate gnlsStruct Residuals
summary.lme
Summarize an lme Object
getData.lmList
Extract lmList Object Data
lme.lmList
LME fit from lmList Object
intervals.lme
Confidence Intervals on lme Parameters
nlsList
List of nls Objects with a Common Model
residuals.lmList
Extract lmList Residuals
summary.corStruct
Summarize a corStruct Object
varConstPower
Constant Plus Power Variance Function
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
[.pdMat
Subscript a pdMat Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
coef.corStruct
Coefficients of a corStruct Object
corCAR1
Continuous AR(1) Correlation Structure
formula.pdBlocked
Extract pdBlocked Formula
gls
Fit Linear Model Using Generalized Least Squares
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
residuals.lme
Extract lme Residuals
ACF.gls
Autocorrelation Function for gls Residuals
Earthquake
Earthquake Intensity
Orthodont
Growth curve data on an orthdontic measurement
Names.pdBlocked
Names of a pdBlocked Object
Dim
Extract Dimensions from an Object
IGF
Radioimmunoassay of IGF-I Protein
coef.pdMat
pdMat Object Coefficients
as.matrix.corStruct
Matrix of a corStruct Object
Wheat2
Wheat Yield Trials
getData
Extract Data from an Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
nlsList.selfStart
nlsList Fit from a selfStart Function
fitted.lmList
Extract lmList Fitted Values
Variogram
Calculate Semi-variogram
formula.reStruct
Extract reStruct Object Formula
predict.nlme
Predictions from an nlme Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Meat
Tenderness of meat
pairs.lmList
Pairs Plot of an lmList Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
logLik.lme
Log-Likelihood of an lme Object
plot.ranef.lme
Plot a ranef.lme Object
getResponse
Extract Response Variable from an Object
solve.reStruct
Apply Solve to an reStruct Object
varClasses
Variance Function Classes
logLik.corStruct
Extract corStruct Log-Likelihood
plot.ranef.lmList
Plot a ranef.lmList Object
splitFormula
Split a Formula
residuals.nlmeStruct
Calculate nlmeStruct Residuals
BodyWeight
Rat weight over time for different diets
plot.compareFits
Plot a compareFits Object
BIC.logLik
BIC of a logLik Object
Muscle
Contraction of heart muscle sections
varWeights
Extract Variance Function Weights
Names.pdMat
Names of a pdMat Object
corRatio
Rational Quadratic Correlation Structure
isInitialized
Check if Object is Initialized
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
varComb
Combination of Variance Functions
Dialyzer
High-Flux Hemodialyzer
Pixel
X-ray pixel intensities over time
coef.lme
Extract lme Coefficients
corSymm
General Correlation Structure
isBalanced
Check a Design for Balance
getVarCov
Extract variance-covariance matrix
pdDiag
Diagonal Positive-Definite Matrix
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
Rail
Evaluation of Stress in Railway Rails
Phenobarb
Phenobarbitol Kinetics
Wheat
Yields by growing conditions
coef.lmList
Extract lmList Coefficients
bdf
Language scores
corGaus
Gaussian Correlation Structure
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
nlmeObject
Fitted nlme Object
predict.lme
Predictions from an lme Object
plot.lmList
Plot an lmList Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
Assay
Bioassay on Cell Culture Plate
Cefamandole
Pharmacokinetics of Cefamandole
PBG
Effect of Phenylbiguanide on Blood Pressure
Dim.corSpatial
Dimensions of a corSpatial Object
Relaxin
Assay for Relaxin
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.default
Calculate Semi-variogram
corSpher
Spherical Correlation Structure
getGroups.gls
Extract gls Object Groups
corNatural
General correlation in natural parameterization
logDet
Extract the Logarithm of the Determinant
nlme
Nonlinear Mixed-Effects Models
plot.augPred
Plot an augPred Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
recalc.reStruct
Recalculate for an reStruct Object
residuals.lmeStruct
Calculate lmeStruct Residuals
varWeights.glsStruct
Variance Weights for glsStruct Object
ACF.lme
Autocorrelation Function for lme Residuals
Coef
Assign Values to Coefficients
Initialize
Initialize Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
compareFits
Compare Fitted Objects
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getGroups.corStruct
Extract corStruct Groups
glsControl
Control Values for gls Fit
glsObject
Fitted gls Object
intervals.lmList
Confidence Intervals on lmList Coefficients
lmeScale
Scale for lme Optimization
plot.nmGroupedData
Plot an nmGroupedData Object
residuals.glsStruct
Calculate glsStruct Residuals
summary.lmList
Summarize an lmList Object
summary.pdMat
Summarize a pdMat Object
varFunc
Variance Function Structure
RatPupWeight
The weight of rat pups
Oxboys
Heights of Boys in Oxford
ACF
Autocorrelation Function
asTable
Convert groupedData to a matrix
getCovariate.varFunc
Extract varFunc Covariate
Ovary
Counts of Ovarian Follicles
asOneFormula
Combine Formulas of a Set of Objects
augPred
Augmented Predictions
Variogram.corLin
Calculate Semi-variogram for a corLin Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
simulate.lme
Simulate results from lme models
gnlsStruct
Generalized Nonlinear Least Squares Structure