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nlme (version 3.1-100)
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
3.1-100
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
March 12th, 2011
Functions in nlme (3.1-100)
Search all functions
Tetracycline2
Pharmacokinetics of tetracycline
pdClasses
Positive-Definite Matrix Classes
plot.intervals.lmList
Plot lmList Confidence Intervals
ACF.lme
Autocorrelation Function for lme Residuals
as.matrix.corStruct
Matrix of a corStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
predict.lme
Predictions from an lme Object
residuals.lmeStruct
Calculate lmeStruct Residuals
Dialyzer
High-Flux Hemodialyzer
Assay
Bioassay on Cell Culture Plate
corCompSymm
Compound Symmetry Correlation Structure
Names.reStruct
Names of an reStruct Object
MathAchSchool
School demographic data for MathAchieve
Initialize.glsStruct
Initialize a glsStruct Object
as.matrix.reStruct
Matrices of an reStruct Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
VarCorr
Extract variance and correlation components
Muscle
Contraction of heart muscle sections
Names.pdMat
Names of a pdMat Object
IGF
Radioimmunoassay of IGF-I Protein
getGroups.lmList
Extract lmList Object Groups
Milk
Protein content of cows' milk
getVarCov
Extract variance-covariance matrix
getResponseFormula
Extract Formula Specifying Response Variable
Matrix.pdMat
Assign Matrix to a pdMat Object
lme.lmList
LME fit from lmList Object
lmList
List of lm Objects with a Common Model
nlmeObject
Fitted nlme Object
Nitrendipene
Assay of nitrendipene
coef.varFunc
varFunc Object Coefficients
Wheat2
Wheat Yield Trials
augPred
Augmented Predictions
pdConstruct.pdBlocked
Construct pdBlocked Objects
corCAR1
Continuous AR(1) Correlation Structure
corNatural
General correlation in natural parameterization
fitted.lme
Extract lme Fitted Values
Relaxin
Assay for Relaxin
lme
Linear Mixed-Effects Models
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Dim.pdMat
Dimensions of a pdMat Object
glsControl
Control Values for gls Fit
ergoStool
Ergometrics experiment with stool types
getCovariate.corStruct
Extract corStruct Object Covariate
BodyWeight
Rat weight over time for different diets
gnlsControl
Control Values for gnls Fit
plot.ranef.lme
Plot a ranef.lme Object
getResponse
Extract Response Variable from an Object
lme.groupedData
LME fit from groupedData Object
getCovariateFormula
Extract Covariates Formula
coef.lme
Extract lme Coefficients
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
recalc.corStruct
Recalculate for corStruct Object
summary.gls
Summarize a gls Object
getGroups
Extract Grouping Factors from an Object
getGroups.data.frame
Extract Groups from a Data Frame
Dim
Extract Dimensions from an Object
recalc
Recalculate Condensed Linear Model Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
solve.reStruct
Apply Solve to an reStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
fixed.effects
Extract Fixed Effects
Ovary
Counts of Ovarian Follicles
Glucose2
Glucose Levels Following Alcohol Ingestion
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
Spruce
Growth of Spruce Trees
fixef.lmList
Extract lmList Fixed Effects
Oxide
Variability in Semiconductor Manufacturing
PBG
Effect of Phenylbiguanide on Blood Pressure
coef.modelStruct
Extract modelStruct Object Coefficients
asOneFormula
Combine Formulas of a Set of Objects
Names.formula
Extract Names from a formula
update.modelStruct
Update a modelStruct Object
ACF
Autocorrelation Function
Initialize.varFunc
Initialize varFunc Object
Gasoline
Refinery yield of gasoline
predict.gnls
Predictions from a gnls Object
pdBlocked
Positive-Definite Block Diagonal Matrix
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
Meat
Tenderness of meat
pdNatural
General Positive-Definite Matrix in Natural Parametrization
residuals.lme
Extract lme Residuals
pdIdent
Multiple of the Identity Positive-Definite Matrix
varConstPower
Constant Plus Power Variance Function
Coef
Assign Values to Coefficients
Wafer
Modeling of Analog MOS Circuits
print.varFunc
Print a varFunc Object
plot.ranef.lmList
Plot a ranef.lmList Object
Initialize.reStruct
Initialize reStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
residuals.gls
Extract gls Residuals
Pixel
X-ray pixel intensities over time
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Orthodont
Growth curve data on an orthdontic measurement
Tetracycline1
Pharmacokinetics of tetracycline
logLik.reStruct
Calculate reStruct Log-Likelihood
Initialize.lmeStruct
Initialize an lmeStruct Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
LDEsysMat
Generate system matrix for LDEs
anova.gls
Compare Likelihoods of Fitted Objects
Glucose
Glucose levels over time
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
plot.compareFits
Plot a compareFits Object
plot.augPred
Plot an augPred Object
Gun
Methods for firing naval guns
pairs.lme
Pairs Plot of an lme Object
coef.corStruct
Coefficients of a corStruct Object
Machines
Productivity Scores for Machines and Workers
lmeScale
Scale for lme Optimization
Rail
Evaluation of Stress in Railway Rails
Phenobarb
Phenobarbitol Kinetics
coef.reStruct
reStruct Object Coefficients
Soybean
Growth of soybean plants
as.matrix.pdMat
Matrix of a pdMat Object
Remifentanil
Pharmacokinetics of remifentanil
pdMat
Positive-Definite Matrix
Matrix
Assign Matrix Values
varFixed
Fixed Variance Function
Variogram.corLin
Calculate Semi-variogram for a corLin Object
MathAchieve
Mathematics achievement scores
plot.nmGroupedData
Plot an nmGroupedData Object
asTable
Convert groupedData to a matrix
fitted.glsStruct
Calculate glsStruct Fitted Values
Cefamandole
Pharmacokinetics of Cefamandole
allCoef
Extract Coefficients from a Set of Objects
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
collapse
Collapse According to Groups
corClasses
Correlation Structure Classes
corRatio
Rational Quadratic Correlation Structure
fitted.lmList
Extract lmList Fitted Values
anova.lme
Compare Likelihoods of Fitted Objects
coef.pdMat
pdMat Object Coefficients
collapse.groupedData
Collapse a groupedData Object
comparePred
Compare Predictions
glsStruct
Generalized Least Squares Structure
corExp
Exponential Correlation Structure
RatPupWeight
The weight of rat pups
balancedGrouped
Create a groupedData object from a matrix
summary.varFunc
Summarize varFunc Object
getCovariate.data.frame
Extract Data Frame Covariate
bdf
Language scores
Dim.corStruct
Dimensions of a corStruct Object
corMatrix
Extract Correlation Matrix
getGroups.varFunc
Extract varFunc Groups
corFactor.corStruct
Factor of a corStruct Object Matrix
corARMA
ARMA(p,q) Correlation Structure
Names
Names Associated with an Object
corSpatial
Spatial Correlation Structure
coef.lmList
Extract lmList Coefficients
corLin
Linear Correlation Structure
getGroups.corStruct
Extract corStruct Groups
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
ACF.gls
Autocorrelation Function for gls Residuals
gls
Fit Linear Model Using Generalized Least Squares
Oxboys
Heights of Boys in Oxford
nlme
Nonlinear Mixed-Effects Models
getGroups.gls
Extract gls Object Groups
Quinidine
Quinidine Kinetics
groupedData
Construct a groupedData Object
predict.lmList
Predictions from an lmList Object
fdHess
Finite difference Hessian
Initialize
Initialize Object
getData.lme
Extract lme Object Data
lmList.groupedData
lmList Fit from a groupedData Object
corSymm
General Correlation Structure
getData
Extract Data from an Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
getData.lmList
Extract lmList Object Data
compareFits
Compare Fitted Objects
gapply
Apply a Function by Groups
intervals.lmList
Confidence Intervals on lmList Coefficients
gnlsObject
Fitted gnls Object
summary.lme
Summarize an lme Object
Dim.corSpatial
Dimensions of a corSpatial Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
nlmeStruct
Nonlinear Mixed-Effects Structure
intervals.gls
Confidence Intervals on gls Parameters
nlsList
List of nls Objects with a Common Model
varWeights.glsStruct
Variance Weights for glsStruct Object
pairs.lmList
Pairs Plot of an lmList Object
Names.pdBlocked
Names of a pdBlocked Object
summary.corStruct
Summarize a corStruct Object
ranef.lme
Extract lme Random Effects
gnlsStruct
Generalized Nonlinear Least Squares Structure
intervals
Confidence Intervals on Coefficients
corMatrix.corStruct
Matrix of a corStruct Object
Initialize.corStruct
Initialize corStruct Object
gsummary
Summarize by Groups
Variogram.default
Calculate Semi-variogram
varWeights
Extract Variance Function Weights
isInitialized
Check if Object is Initialized
pooledSD
Extract Pooled Standard Deviation
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
plot.lmList
Plot an lmList Object
recalc.varFunc
Recalculate for varFunc Object
quinModel
Model function for the Quinidine data
pdConstruct
Construct pdMat Objects
summary.nlsList
Summarize an nlsList Object
getData.gls
Extract gls Object Data
nlmeControl
Control Values for nlme Fit
pairs.compareFits
Pairs Plot of compareFits Object
getCovariate
Extract Covariate from an Object
formula.reStruct
Extract reStruct Object Formula
pdSymm
General Positive-Definite Matrix
glsObject
Fitted gls Object
phenoModel
Model function for the Phenobarb data
lmeControl
Control Values for lme Fit
intervals.lme
Confidence Intervals on lme Parameters
varClasses
Variance Function Classes
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
logLik.varFunc
Extract varFunc logLik
splitFormula
Split a Formula
logDet.pdMat
Extract Log-Determinant from a pdMat Object
summary.lmList
Summarize an lmList Object
needUpdate
Check if Update is Needed
logLik.gnls
Log-Likelihood of a gnls Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
recalc.reStruct
Recalculate for an reStruct Object
varIdent
Constant Variance Function
nlsList.selfStart
nlsList Fit from a selfStart Function
Wheat
Yields by growing conditions
plot.Variogram
Plot a Variogram Object
plot.lme
Plot an lme or nls object
Variogram
Calculate Semi-variogram
simulate.lme
Simulate results from lme models
recalc.modelStruct
Recalculate for a modelStruct Object
coef.gnls
Extract gnls Coefficients
plot.ACF
Plot an ACF Object
nlme.nlsList
NLME fit from nlsList Object
varComb
Combination of Variance Functions
update.varFunc
Update varFunc Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
corGaus
Gaussian Correlation Structure
varExp
Exponential Variance Function
pdFactor
Square-Root Factor of a Positive-Definite Matrix
corAR1
AR(1) Correlation Structure
varPower
Power Variance Function
predict.nlme
Predictions from an nlme Object
Earthquake
Earthquake Intensity
random.effects
Extract Random Effects
Covariate.varFunc
Assign varFunc Covariate
Oats
Split-plot Experiment on Varieties of Oats
formula.pdBlocked
Extract pdBlocked Formula
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Fatigue
Cracks caused by metal fatigue
getGroups.lme
Extract lme Object Groups
logLik.corStruct
Extract corStruct Log-Likelihood
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
lmeObject
Fitted lme Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
[.pdMat
Subscript a pdMat Object
Matrix.reStruct
Assign reStruct Matrices
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
pdLogChol
General Positive-Definite Matrix
predict.gls
Predictions from a gls Object
corSpher
Spherical Correlation Structure
getCovariate.varFunc
Extract varFunc Covariate
formula.pdMat
Extract pdMat Formula
residuals.lmList
Extract lmList Residuals
getGroupsFormula
Extract Grouping Formula
isBalanced
Check a Design for Balance
reStruct
Random Effects Structure
residuals.gnlsStruct
Calculate gnlsStruct Residuals
print.summary.pdMat
Print a summary.pdMat Object
summary.modelStruct
Summarize a modelStruct Object
lmeStruct
Linear Mixed-Effects Structure
logDet.corStruct
Extract corStruct Log-Determinant
logDet.reStruct
Extract reStruct Log-Determinants
logLik.lme
Log-Likelihood of an lme Object
pdDiag
Diagonal Positive-Definite Matrix
plot.gls
Plot a gls Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
Covariate
Assign Covariate Values
corFactor
Factor of a Correlation Matrix
logLik.glsStruct
Log-Likelihood of a glsStruct Object
model.matrix.reStruct
reStruct Model Matrix
logDet
Extract the Logarithm of the Determinant
qqnorm.gls
Normal Plot of Residuals from a gls Object
ranef.lmList
Extract lmList Random Effects
summary.pdMat
Summarize a pdMat Object
varFunc
Variance Function Structure