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nlme (version 3.1-89)
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
98,563
Version
3.1-89
License
GPL (>=2)
Maintainer
R-core R-core@R-project.org
Last Published
June 7th, 2008
Functions in nlme (3.1-89)
Search functions
glsObject
Fitted gls Object
Glucose
Glucose levels over time
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Tetracycline2
Pharmacokinetics of tetracycline
Nitrendipene
Assay of nitrendipene
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Relaxin
Assay for Relaxin
coef.gnls
Extract gnls Coefficients
pairs.compareFits
Pairs Plot of compareFits Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Names.pdMat
Names of a pdMat Object
Earthquake
Earthquake Intensity
corAR1
AR(1) Correlation Structure
Milk
Protein content of cows' milk
BIC
Bayesian Information Criterion
coef.varFunc
varFunc Object Coefficients
Covariate.varFunc
Assign varFunc Covariate
balancedGrouped
Create a groupedData object from a matrix
Tetracycline1
Pharmacokinetics of tetracycline
Variogram.corExp
Calculate Semi-variogram for a corExp Object
asTable
Convert groupedData to a matrix
Ovary
Counts of Ovarian Follicles
fixed.effects
Extract Fixed Effects
Initialize
Initialize Object
RatPupWeight
The weight of rat pups
Dim
Extract Dimensions from an Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
getData.lmList
Extract lmList Object Data
Names.reStruct
Names of an reStruct Object
ACF.lme
Autocorrelation Function for lme Residuals
Muscle
Contraction of heart muscle sections
MathAchSchool
School demographic data for MathAchieve
BIC.logLik
BIC of a logLik Object
asOneFormula
Combine Formulas of a Set of Objects
as.matrix.pdMat
Matrix of a pdMat Object
Soybean
Growth of soybean plants
Phenobarb
Phenobarbitol Kinetics
VarCorr
Extract variance and correlation components
collapse.groupedData
Collapse a groupedData Object
pairs.lmList
Pairs Plot of an lmList Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
Wafer
Modeling of Analog MOS Circuits
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
Matrix.reStruct
Assign reStruct Matrices
corMatrix.corStruct
Matrix of a corStruct Object
Coef
Assign Values to Coefficients
glsControl
Control Values for gls Fit
Dim.pdMat
Dimensions of a pdMat Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
getData.gls
Extract gls Object Data
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Wheat
Yields by growing conditions
fdHess
Finite difference Hessian
fitted.glsStruct
Calculate glsStruct Fitted Values
ACF.gls
Autocorrelation Function for gls Residuals
Matrix.pdMat
Assign Matrix to a pdMat Object
Spruce
Growth of Spruce Trees
as.matrix.reStruct
Matrices of an reStruct Object
[.pdMat
Subscript a pdMat Object
Quinidine
Quinidine Kinetics
anova.lme
Compare Likelihoods of Fitted Objects
BodyWeight
Rat weight over time for different diets
Machines
Productivity Scores for Machines and Workers
corRatio
Rational Quadratic Correlation Structure
getCovariateFormula
Extract Covariates Formula
Initialize.reStruct
Initialize reStruct Object
Dim.corSpatial
Dimensions of a corSpatial Object
getGroupsFormula
Extract Grouping Formula
lmeStruct
Linear Mixed-Effects Structure
formula.pdMat
Extract pdMat Formula
pdDiag
Diagonal Positive-Definite Matrix
Gasoline
Refinery yield of gasoline
ACF
Autocorrelation Function
Rail
Evaluation of Stress in Railway Rails
Names.formula
Extract Names from a formula
Wheat2
Wheat Yield Trials
intervals.lme
Confidence Intervals on lme Parameters
formula.reStruct
Extract reStruct Object Formula
getCovariate.corStruct
Extract corStruct Object Covariate
getData
Extract Data from an Object
formula.pdBlocked
Extract pdBlocked Formula
predict.lmList
Predictions from an lmList Object
logLik.lme
Log-Likelihood of an lme Object
fixef.lmList
Extract lmList Fixed Effects
plot.intervals.lmList
Plot lmList Confidence Intervals
fitted.lme
Extract lme Fitted Values
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
intervals.gls
Confidence Intervals on gls Parameters
allCoef
Extract Coefficients from a Set of Objects
ergoStool
Ergometrics experiment with stool types
logLik.glsStruct
Log-Likelihood of a glsStruct Object
Initialize.lmeStruct
Initialize an lmeStruct Object
pdSymm
General Positive-Definite Matrix
getCovariate
Extract Covariate from an Object
nlmeControl
Control Values for nlme Fit
getGroups
Extract Grouping Factors from an Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
bdf
Language scores
needUpdate
Check if Update is Needed
Names
Names Associated with an Object
getResponseFormula
Extract Formula Specifying Response Variable
predict.gls
Predictions from a gls Object
corSymm
General Correlation Structure
getCovariate.data.frame
Extract Data Frame Covariate
model.matrix.reStruct
reStruct Model Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
phenoModel
Model function for the Phenobarb data
PBG
Effect of Phenylbiguanide on Blood Pressure
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
getGroups.data.frame
Extract Groups from a Data Frame
getData.lme
Extract lme Object Data
pdNatural
General Positive-Definite Matrix in Natural Parametrization
plot.lmList
Plot an lmList Object
coef.reStruct
reStruct Object Coefficients
lme.groupedData
LME fit from groupedData Object
lme
Linear Mixed-Effects Models
corFactor.corStruct
Factor of a corStruct Object Matrix
plot.nmGroupedData
Plot an nmGroupedData Object
comparePred
Compare Predictions
logLik.corStruct
Extract corStruct Log-Likelihood
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
pdBlocked
Positive-Definite Block Diagonal Matrix
varWeights
Extract Variance Function Weights
recalc.modelStruct
Recalculate for a modelStruct Object
getResponse
Extract Response Variable from an Object
logLik.gnls
Log-Likelihood of a gnls Object
getGroups.lme
Extract lme Object Groups
pdFactor
Square-Root Factor of a Positive-Definite Matrix
as.matrix.corStruct
Matrix of a corStruct Object
lmeControl
Control Values for lme Fit
plot.lme
Plot an lme or nls object
corFactor
Factor of a Correlation Matrix
corGaus
Gaussian Correlation Structure
summary.pdMat
Summarize a pdMat Object
intervals
Confidence Intervals on Coefficients
logLik.reStruct
Calculate reStruct Log-Likelihood
nlme.nlsList
NLME fit from nlsList Object
isInitialized
Check if Object is Initialized
logDet
Extract the Logarithm of the Determinant
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdClasses
Positive-Definite Matrix Classes
residuals.glsStruct
Calculate glsStruct Residuals
groupedData
Construct a groupedData Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
varConstPower
Constant Plus Power Variance Function
residuals.nlmeStruct
Calculate nlmeStruct Residuals
logDet.reStruct
Extract reStruct Log-Determinants
logLik.varFunc
Extract varFunc logLik
ranef.lmList
Extract lmList Random Effects
recalc
Recalculate Condensed Linear Model Object
plot.augPred
Plot an augPred Object
plot.Variogram
Plot a Variogram Object
ranef.lme
Extract lme Random Effects
recalc.varFunc
Recalculate for varFunc Object
varWeights.glsStruct
Variance Weights for glsStruct Object
solve.reStruct
Apply Solve to an reStruct Object
plot.gls
Plot a gls Object
varFixed
Fixed Variance Function
anova.gls
Compare Likelihoods of Fitted Objects
plot.ranef.lme
Plot a ranef.lme Object
lmeScale
Scale for lme Optimization
getGroups.varFunc
Extract varFunc Groups
pdConstruct
Construct pdMat Objects
pairs.lme
Pairs Plot of an lme Object
varIdent
Constant Variance Function
corSpatial
Spatial Correlation Structure
recalc.corStruct
Recalculate for corStruct Object
summary.nlsList
Summarize an nlsList Object
pdLogChol
General Positive-Definite Matrix
varPower
Power Variance Function
getCovariate.varFunc
Extract varFunc Covariate
corCompSymm
Compound Symmetry Correlation Structure
glsStruct
Generalized Least Squares Structure
gnlsObject
Fitted gnls Object
pdMat
Positive-Definite Matrix
nlmeObject
Fitted nlme Object
lmList
List of lm Objects with a Common Model
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
print.varFunc
Print a varFunc Object
predict.lme
Predictions from an lme Object
varClasses
Variance Function Classes
coef.pdMat
pdMat Object Coefficients
residuals.lmeStruct
Calculate lmeStruct Residuals
varComb
Combination of Variance Functions
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.lme
Extract lme Residuals
reStruct
Random Effects Structure
lme.lmList
LME fit from lmList Object
summary.modelStruct
Summarize a modelStruct Object
quinModel
Model function for the Quinidine data
logDet.corStruct
Extract corStruct Log-Determinant
nlmeStruct
Nonlinear Mixed-Effects Structure
varFunc
Variance Function Structure
summary.varFunc
Summarize varFunc Object
plot.compareFits
Plot a compareFits Object
getGroups.corStruct
Extract corStruct Groups
simulate.lme
Simulate results from lme models
summary.lme
Summarize an lme Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
plot.ACF
Plot an ACF Object
residuals.gls
Extract gls Residuals
print.summary.pdMat
Print a summary.pdMat Object
summary.gls
Summarize a gls Object
splitFormula
Split a Formula
Dim.corStruct
Dimensions of a corStruct Object
corExp
Exponential Correlation Structure
Oxide
Variability in Semiconductor Manufacturing
corMatrix
Extract Correlation Matrix
corClasses
Correlation Structure Classes
lmList.groupedData
lmList Fit from a groupedData Object
fitted.lmList
Extract lmList Fitted Values
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
update.modelStruct
Update a modelStruct Object
Assay
Bioassay on Cell Culture Plate
Cefamandole
Pharmacokinetics of Cefamandole
Remifentanil
Pharmacokinetics of remifentanil
Variogram.default
Calculate Semi-variogram
Initialize.glsStruct
Initialize a glsStruct Object
Gun
Methods for firing naval guns
Fatigue
Cracks caused by metal fatigue
Names.pdBlocked
Names of a pdBlocked Object
Initialize.corStruct
Initialize corStruct Object
Meat
Tenderness of meat
Oxboys
Heights of Boys in Oxford
augPred
Augmented Predictions
corARMA
ARMA(p,q) Correlation Structure
coef.corStruct
Coefficients of a corStruct Object
coef.lmList
Extract lmList Coefficients
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
collapse
Collapse According to Groups
compareFits
Compare Fitted Objects
corNatural
General correlation in natural parameterization
gnls
Fit Nonlinear Model Using Generalized Least Squares
gapply
Apply a Function by Groups
getGroups.gls
Extract gls Object Groups
isBalanced
Check a Design for Balance
intervals.lmList
Confidence Intervals on lmList Coefficients
logLik.lmList
Log-Likelihood of an lmList Object
predict.nlme
Predictions from an nlme Object
recalc.reStruct
Recalculate for an reStruct Object
nlme
Nonlinear Mixed-Effects Models
predict.gnls
Predictions from a gnls Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
random.effects
Extract Random Effects
Dialyzer
High-Flux Hemodialyzer
plot.ranef.lmList
Plot a ranef.lmList Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Pixel
X-ray pixel intensities over time
coef.modelStruct
Extract modelStruct Object Coefficients
MathAchieve
Mathematics achievement scores
Oats
Split-plot Experiment on Varieties of Oats
logDet.pdMat
Extract Log-Determinant from a pdMat Object
Orthodont
Growth curve data on an orthdontic measurement
update.varFunc
Update varFunc Object
coef.lme
Extract lme Coefficients
corLin
Linear Correlation Structure
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
corSpher
Spherical Correlation Structure
gls
Fit Linear Model Using Generalized Least Squares
lmeObject
Fitted lme Object
nlsList
List of nls Objects with a Common Model
summary.lmList
Summarize an lmList Object
summary.corStruct
Summarize a corStruct Object
gsummary
Summarize by Groups
residuals.lmList
Extract lmList Residuals
varExp
Exponential Variance Function
gnlsControl
Control Values for gnls Fit
LDEsysMat
Generate system matrix for LDEs
fitted.lmeStruct
Calculate lmeStruct Fitted Values
Initialize.varFunc
Initialize varFunc Object
Covariate
Assign Covariate Values
plot.nfnGroupedData
Plot an nfnGroupedData Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram
Calculate Semi-variogram
corCAR1
Continuous AR(1) Correlation Structure
getGroups.lmList
Extract lmList Object Groups
pooledSD
Extract Pooled Standard Deviation
IGF
Radioimmunoassay of IGF-I Protein
nlsList.selfStart
nlsList Fit from a selfStart Function
Glucose2
Glucose Levels Following Alcohol Ingestion
Matrix
Assign Matrix Values
getVarCov
Extract variance-covariance matrix