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nlme (version 3.1-113)
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
149,202
Version
3.1-113
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
November 17th, 2013
Functions in nlme (3.1-113)
Search all functions
Dim.corSpatial
Dimensions of a corSpatial Object
Oats
Split-plot Experiment on Varieties of Oats
Matrix.pdMat
Assign Matrix to a pdMat Object
Relaxin
Assay for Relaxin
coef.pdMat
pdMat Object Coefficients
Pixel
X-ray pixel intensities over time
comparePred
Compare Predictions
as.matrix.corStruct
Matrix of a corStruct Object
coef.lme
Extract lme Coefficients
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corFactor.corStruct
Factor of a corStruct Object Matrix
gapply
Apply a Function by Groups
coef.varFunc
varFunc Object Coefficients
corSpher
Spherical Correlation Structure
gls-internal
Auxiliary functions used by gls
getCovariate.data.frame
Extract Data Frame Covariate
gnlsStruct
Generalized Nonlinear Least Squares Structure
logLik.corStruct
Extract corStruct Log-Likelihood
formula.pdBlocked
Extract pdBlocked Formula
Glucose2
Glucose Levels Following Alcohol Ingestion
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
getGroups.varFunc
Extract varFunc Groups
logDet.corStruct
Extract corStruct Log-Determinant
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
glsStruct
Generalized Least Squares Structure
glsObject
Fitted gls Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
coef.corStruct
Coefficients of a corStruct Object
getCovariate
Extract Covariate from an Object
corRatio
Rational Quadratic Correlation Structure
logLik.lmList
Log-Likelihood of an lmList Object
fitted.lme
Extract lme Fitted Values
pdSymm
General Positive-Definite Matrix
formula.pdMat
Extract pdMat Formula
reStruct
Random Effects Structure
getGroups
Extract Grouping Factors from an Object
intervals.lmList
Confidence Intervals on lmList Coefficients
logLik.gnls
Log-Likelihood of a gnls Object
pdConstruct
Construct pdMat Objects
pdDiag
Diagonal Positive-Definite Matrix
pairs.compareFits
Pairs Plot of compareFits Object
Dim.corStruct
Dimensions of a corStruct Object
Initialize.corStruct
Initialize corStruct Object
plot.ranef.lme
Plot a ranef.lme Object
predict.nlme
Predictions from an nlme Object
predict.lmList
Predictions from an lmList Object
Names.pdMat
Names of a pdMat Object
Matrix
Assign Matrix Values
Gun
Methods for firing naval guns
Quinidine
Quinidine Kinetics
Phenobarb
Phenobarbitol Kinetics
ACF
Autocorrelation Function
Muscle
Contraction of heart muscle sections
Initialize.reStruct
Initialize reStruct Object
varWeights
Extract Variance Function Weights
Spruce
Growth of Spruce Trees
Cefamandole
Pharmacokinetics of Cefamandole
varWeights.lmeStruct
Variance Weights for lmeStruct Object
Names.pdBlocked
Names of a pdBlocked Object
Wafer
Modeling of Analog MOS Circuits
pdFactor
Square-Root Factor of a Positive-Definite Matrix
RatPupWeight
The weight of rat pups
corClasses
Correlation Structure Classes
lmList
List of lm Objects with a Common Model
Covariate.varFunc
Assign varFunc Covariate
Names
Names Associated with an Object
corSymm
General Correlation Structure
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
IGF
Radioimmunoassay of IGF-I Protein
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Matrix.reStruct
Assign reStruct Matrices
getGroups.lme
Extract lme Object Groups
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
corLin
Linear Correlation Structure
pooledSD
Extract Pooled Standard Deviation
anova.gls
Compare Likelihoods of Fitted Objects
summary.pdMat
Summarize a pdMat Object
Dim.pdMat
Dimensions of a pdMat Object
logLik.reStruct
Calculate reStruct Log-Likelihood
collapse.groupedData
Collapse a groupedData Object
getData
Extract Data from an Object
pdBlocked
Positive-Definite Block Diagonal Matrix
Meat
Tenderness of meat
recalc.corStruct
Recalculate for corStruct Object
corGaus
Gaussian Correlation Structure
nlme.nlsList
NLME fit from nlsList Object
Fatigue
Cracks caused by metal fatigue
pdMat
Positive-Definite Matrix
getResponseFormula
Extract Formula Specifying Response Variable
Initialize.glsStruct
Initialize a glsStruct Object
lme.lmList
LME fit from lmList Object
lmeObject
Fitted lme Object
coef.gnls
Extract gnls Coefficients
corSpatial
Spatial Correlation Structure
lmeScale
Scale for lme Optimization
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
Gasoline
Refinery yield of gasoline
Variogram.corLin
Calculate Semi-variogram for a corLin Object
recalc.modelStruct
Recalculate for a modelStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
model.matrix.reStruct
reStruct Model Matrix
varComb
Combination of Variance Functions
coef.lmList
Extract lmList Coefficients
getData.lme
Extract lme Object Data
varClasses
Variance Function Classes
corARMA
ARMA(p,q) Correlation Structure
gsummary
Summarize by Groups
lmList.groupedData
lmList Fit from a groupedData Object
pdClasses
Positive-Definite Matrix Classes
plot.compareFits
Plot a compareFits Object
nlmeControl
Control Values for nlme Fit
getCovariate.corStruct
Extract corStruct Object Covariate
plot.intervals.lmList
Plot lmList Confidence Intervals
logLik.glsStruct
Log-Likelihood of a glsStruct Object
predict.gnls
Predictions from a gnls Object
plot.Variogram
Plot a Variogram Object
logLik.lme
Log-Likelihood of an lme Object
plot.gls
Plot a gls Object
residuals.gls
Extract gls Residuals
Glucose
Glucose levels over time
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
ACF.gls
Autocorrelation Function for gls Residuals
quinModel
Model function for the Quinidine data
Names.formula
Extract Names from a formula
update.modelStruct
Update a modelStruct Object
print.varFunc
Print a varFunc Object
varConstPower
Constant Plus Power Variance Function
residuals.lme
Extract lme Residuals
update.varFunc
Update varFunc Object
VarCorr
Extract variance and correlation components
ranef.lmList
Extract lmList Random Effects
Orthodont
Growth curve data on an orthdontic measurement
print.summary.pdMat
Print a summary.pdMat Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
as.matrix.pdMat
Matrix of a pdMat Object
getVarCov
Extract variance-covariance matrix
balancedGrouped
Create a groupedData object from a matrix
Initialize.varFunc
Initialize varFunc Object
corExp
Exponential Correlation Structure
ergoStool
Ergometrics experiment with stool types
lme
Linear Mixed-Effects Models
getCovariateFormula
Extract Covariates Formula
fitted.lmList
Extract lmList Fitted Values
logDet.reStruct
Extract reStruct Log-Determinants
fixef.lmList
Extract lmList Fixed Effects
needUpdate
Check if Update is Needed
plot.augPred
Plot an augPred Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
getResponse
Extract Response Variable from an Object
corFactor
Factor of a Correlation Matrix
predict.lme
Predictions from an lme Object
nlmeObject
Fitted nlme Object
plot.nmGroupedData
Plot an nmGroupedData Object
recalc
Recalculate Condensed Linear Model Object
random.effects
Extract Random Effects
ranef.lme
Extract lme Random Effects
varPower
Power Variance Function
pdNatural
General Positive-Definite Matrix in Natural Parametrization
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
residuals.nlmeStruct
Calculate nlmeStruct Residuals
recalc.reStruct
Recalculate for an reStruct Object
summary.gls
Summarize a gls Object
varIdent
Constant Variance Function
Dim
Extract Dimensions from an Object
LDEsysMat
Generate system matrix for LDEs
Ovary
Counts of Ovarian Follicles
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
anova.lme
Compare Likelihoods of Fitted Objects
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corNatural
General correlation in natural parameterization
intervals.gls
Confidence Intervals on gls Parameters
isInitialized
Check if Object is Initialized
BodyWeight
Rat weight over time for different diets
logLik.varFunc
Extract varFunc logLik
nlme
Nonlinear Mixed-Effects Models
nlmeStruct
Nonlinear Mixed-Effects Structure
phenoModel
Model function for the Phenobarb data
Earthquake
Earthquake Intensity
Oxboys
Heights of Boys in Oxford
[.pdMat
Subscript a pdMat Object
varFixed
Fixed Variance Function
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
as.matrix.reStruct
Matrices of an reStruct Object
pairs.lme
Pairs Plot of an lme Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
ACF.lme
Autocorrelation Function for lme Residuals
plot.lme
Plot an lme or nls object
Assay
Bioassay on Cell Culture Plate
Coef
Assign Values to Coefficients
simulate.lme
Simulate Results from
lme
Models
Initialize
Initialize Object
Nitrendipene
Assay of nitrendipene
Soybean
Growth of soybean plants
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Tetracycline1
Pharmacokinetics of tetracycline
Variogram
Calculate Semi-variogram
corMatrix
Extract Correlation Matrix
fitted.lmeStruct
Calculate lmeStruct Fitted Values
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
gls
Fit Linear Model Using Generalized Least Squares
glsControl
Control Values for gls Fit
intervals.lme
Confidence Intervals on lme Parameters
lmeControl
Control Values for lme Fit
pdLogChol
General Positive-Definite Matrix
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
Machines
Productivity Scores for Machines and Workers
Names.reStruct
Names of an reStruct Object
Oxide
Variability in Semiconductor Manufacturing
getData.lmList
Extract lmList Object Data
gnlsControl
Control Values for gnls Fit
getCovariate.varFunc
Extract varFunc Covariate
Tetracycline2
Pharmacokinetics of tetracycline
allCoef
Extract Coefficients from a Set of Objects
Rail
Evaluation of Stress in Railway Rails
formula.reStruct
Extract reStruct Object Formula
coef.reStruct
reStruct Object Coefficients
getData.gls
Extract gls Object Data
pairs.lmList
Pairs Plot of an lmList Object
plot.ACF
Plot an ACF Object
fdHess
Finite difference Hessian
corCAR1
Continuous AR(1) Correlation Structure
groupedData
Construct a groupedData Object
logDet
Extract the Logarithm of the Determinant
varFunc
Variance Function Structure
MathAchSchool
School demographic data for MathAchieve
asOneFormula
Combine Formulas of a Set of Objects
coef.modelStruct
Extract modelStruct Object Coefficients
corMatrix.corStruct
Matrix of a corStruct Object
getGroups.lmList
Extract lmList Object Groups
getGroupsFormula
Extract Grouping Formula
nlsList
List of nls Objects with a Common Model
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
residuals.lmeStruct
Calculate lmeStruct Residuals
varWeights.glsStruct
Variance Weights for glsStruct Object
summary.corStruct
Summarize a corStruct Object
solve.reStruct
Apply Solve to an reStruct Object
summary.lmList
Summarize an lmList Object
augPred
Augmented Predictions
compareFits
Compare Fitted Objects
corAR1
AR(1) Correlation Structure
corCompSymm
Compound Symmetry Correlation Structure
lme.groupedData
LME fit from groupedData Object
getGroups.corStruct
Extract corStruct Groups
plot.lmList
Plot an lmList Object
summary.lme
Summarize an lme Object
residuals.glsStruct
Calculate glsStruct Residuals
summary.varFunc
Summarize varFunc Object
Milk
Protein content of cows' milk
Wheat2
Wheat Yield Trials
Variogram.default
Calculate Semi-variogram
fitted.glsStruct
Calculate glsStruct Fitted Values
getGroups.gls
Extract gls Object Groups
gnls
Fit Nonlinear Model Using Generalized Least Squares
plot.nfnGroupedData
Plot an nfnGroupedData Object
predict.gls
Predictions from a gls Object
summary.modelStruct
Summarize a modelStruct Object
summary.nlsList
Summarize an nlsList Object
MathAchieve
Mathematics achievement scores
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Dialyzer
High-Flux Hemodialyzer
Initialize.lmeStruct
Initialize an lmeStruct Object
Remifentanil
Pharmacokinetics of remifentanil
PBG
Effect of Phenylbiguanide on Blood Pressure
asTable
Convert groupedData to a matrix
bdf
Language scores
gnlsObject
Fitted gnls Object
intervals
Confidence Intervals on Coefficients
lmeStruct
Linear Mixed-Effects Structure
isBalanced
Check a Design for Balance
recalc.varFunc
Recalculate for varFunc Object
residuals.lmList
Extract lmList Residuals
splitFormula
Split a Formula
fixed.effects
Extract Fixed Effects
varExp
Exponential Variance Function
Covariate
Assign Covariate Values
Wheat
Yields by growing conditions
collapse
Collapse According to Groups
nlsList.selfStart
nlsList Fit from a selfStart Function
plot.ranef.lmList
Plot a ranef.lmList Object
plot.nffGroupedData
Plot an nffGroupedData Object