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nlme (version 3.1-114)
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
139,641
Version
3.1-114
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
March 8th, 2014
Functions in nlme (3.1-114)
Search all functions
Orthodont
Growth curve data on an orthdontic measurement
Dialyzer
High-Flux Hemodialyzer
Tetracycline1
Pharmacokinetics of tetracycline
collapse
Collapse According to Groups
coef.reStruct
reStruct Object Coefficients
Covariate
Assign Covariate Values
Initialize
Initialize Object
LDEsysMat
Generate system matrix for LDEs
RatPupWeight
The weight of rat pups
corGaus
Gaussian Correlation Structure
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
bdf
Language scores
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
glsControl
Control Values for gls Fit
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
comparePred
Compare Predictions
intervals.lmList
Confidence Intervals on lmList Coefficients
logDet.corStruct
Extract corStruct Log-Determinant
lme.lmList
LME fit from lmList Object
plot.nffGroupedData
Plot an nffGroupedData Object
predict.gnls
Predictions from a gnls Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
needUpdate
Check if Update is Needed
quinModel
Model function for the Quinidine data
residuals.lmList
Extract lmList Residuals
Dim
Extract Dimensions from an Object
Initialize.reStruct
Initialize reStruct Object
asOneFormula
Combine Formulas of a Set of Objects
getCovariateFormula
Extract Covariates Formula
lmList.groupedData
lmList Fit from a groupedData Object
plot.ranef.lmList
Plot a ranef.lmList Object
recalc.modelStruct
Recalculate for a modelStruct Object
varFunc
Variance Function Structure
as.matrix.reStruct
Matrices of an reStruct Object
Names.reStruct
Names of an reStruct Object
Fatigue
Cracks caused by metal fatigue
fitted.lmeStruct
Calculate lmeStruct Fitted Values
Muscle
Contraction of heart muscle sections
Initialize.varFunc
Initialize varFunc Object
getGroups
Extract Grouping Factors from an Object
Matrix
Assign Matrix Values
Meat
Tenderness of meat
gls
Fit Linear Model Using Generalized Least Squares
Assay
Bioassay on Cell Culture Plate
fixef.lmList
Extract lmList Fixed Effects
Names.pdMat
Names of a pdMat Object
Cefamandole
Pharmacokinetics of Cefamandole
Variogram
Calculate Semi-variogram
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
ACF.lme
Autocorrelation Function for lme Residuals
MathAchSchool
School demographic data for MathAchieve
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
as.matrix.pdMat
Matrix of a pdMat Object
Initialize.glsStruct
Initialize a glsStruct Object
Milk
Protein content of cows' milk
glsObject
Fitted gls Object
fitted.lme
Extract lme Fitted Values
getData.lmList
Extract lmList Object Data
pairs.lmList
Pairs Plot of an lmList Object
update.modelStruct
Update a modelStruct Object
Gun
Methods for firing naval guns
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
coef.lmList
Extract lmList Coefficients
Names.formula
Extract Names from a formula
Variogram.default
Calculate Semi-variogram
Dim.pdMat
Dimensions of a pdMat Object
lme.groupedData
LME fit from groupedData Object
Quinidine
Quinidine Kinetics
corLin
Linear Correlation Structure
fdHess
Finite difference Hessian
corMatrix
Extract Correlation Matrix
Oxboys
Heights of Boys in Oxford
anova.gls
Compare Likelihoods of Fitted Objects
Wheat2
Wheat Yield Trials
pdLogChol
General Positive-Definite Matrix
Machines
Productivity Scores for Machines and Workers
coef.varFunc
varFunc Object Coefficients
balancedGrouped
Create a groupedData object from a matrix
varIdent
Constant Variance Function
pairs.lme
Pairs Plot of an lme Object
corSpatial
Spatial Correlation Structure
getCovariate
Extract Covariate from an Object
logLik.lmList
Log-Likelihood of an lmList Object
groupedData
Construct a groupedData Object
formula.pdBlocked
Extract pdBlocked Formula
gsummary
Summarize by Groups
nlmeStruct
Nonlinear Mixed-Effects Structure
corMatrix.corStruct
Matrix of a corStruct Object
pdMat
Positive-Definite Matrix
Spruce
Growth of Spruce Trees
predict.nlme
Predictions from an nlme Object
phenoModel
Model function for the Phenobarb data
asTable
Convert groupedData to a matrix
model.matrix.reStruct
reStruct Model Matrix
varConstPower
Constant Plus Power Variance Function
pdIdent
Multiple of the Identity Positive-Definite Matrix
reStruct
Random Effects Structure
varComb
Combination of Variance Functions
coef.modelStruct
Extract modelStruct Object Coefficients
pdBlocked
Positive-Definite Block Diagonal Matrix
summary.nlsList
Summarize an nlsList Object
getResponseFormula
Extract Formula Specifying Response Variable
predict.lme
Predictions from an lme Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
plot.ACF
Plot an ACF Object
getGroups.gls
Extract gls Object Groups
residuals.lme
Extract lme Residuals
plot.gls
Plot a gls Object
update.varFunc
Update varFunc Object
lmList
List of lm Objects with a Common Model
getResponse
Extract Response Variable from an Object
gls-internal
Auxiliary functions used by gls
logLik.lme
Log-Likelihood of an lme Object
lmeStruct
Linear Mixed-Effects Structure
simulate.lme
Simulate Results from
lme
Models
Initialize.corStruct
Initialize corStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
logDet
Extract the Logarithm of the Determinant
pdFactor
Square-Root Factor of a Positive-Definite Matrix
allCoef
Extract Coefficients from a Set of Objects
pdNatural
General Positive-Definite Matrix in Natural Parametrization
corSpher
Spherical Correlation Structure
plot.nfnGroupedData
Plot an nfnGroupedData Object
getData
Extract Data from an Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
summary.varFunc
Summarize varFunc Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
nlme.nlsList
NLME fit from nlsList Object
plot.lmList
Plot an lmList Object
Covariate.varFunc
Assign varFunc Covariate
residuals.nlmeStruct
Calculate nlmeStruct Residuals
plot.ranef.lme
Plot a ranef.lme Object
Matrix.pdMat
Assign Matrix to a pdMat Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
[.pdMat
Subscript a pdMat Object
Gasoline
Refinery yield of gasoline
residuals.lmeStruct
Calculate lmeStruct Residuals
corAR1
AR(1) Correlation Structure
print.summary.pdMat
Print a summary.pdMat Object
Names
Names Associated with an Object
Matrix.reStruct
Assign reStruct Matrices
summary.lmList
Summarize an lmList Object
corRatio
Rational Quadratic Correlation Structure
getGroups.corStruct
Extract corStruct Groups
coef.gnls
Extract gnls Coefficients
glsStruct
Generalized Least Squares Structure
corCompSymm
Compound Symmetry Correlation Structure
logDet.reStruct
Extract reStruct Log-Determinants
varFixed
Fixed Variance Function
getCovariate.data.frame
Extract Data Frame Covariate
formula.reStruct
Extract reStruct Object Formula
pdConstruct
Construct pdMat Objects
Initialize.lmeStruct
Initialize an lmeStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
predict.gls
Predictions from a gls Object
getData.lme
Extract lme Object Data
plot.Variogram
Plot a Variogram Object
getGroups.lme
Extract lme Object Groups
logLik.reStruct
Calculate reStruct Log-Likelihood
residuals.gls
Extract gls Residuals
nlme
Nonlinear Mixed-Effects Models
recalc.varFunc
Recalculate for varFunc Object
random.effects
Extract Random Effects
splitFormula
Split a Formula
logLik.corStruct
Extract corStruct Log-Likelihood
Dim.corStruct
Dimensions of a corStruct Object
Tetracycline2
Pharmacokinetics of tetracycline
corClasses
Correlation Structure Classes
coef.corStruct
Coefficients of a corStruct Object
fitted.lmList
Extract lmList Fitted Values
getGroupsFormula
Extract Grouping Formula
getData.gls
Extract gls Object Data
pdDiag
Diagonal Positive-Definite Matrix
ranef.lmList
Extract lmList Random Effects
summary.gls
Summarize a gls Object
varClasses
Variance Function Classes
qqnorm.gls
Normal Plot of Residuals from a gls Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
varExp
Exponential Variance Function
corCAR1
Continuous AR(1) Correlation Structure
Oats
Split-plot Experiment on Varieties of Oats
ACF
Autocorrelation Function
gapply
Apply a Function by Groups
PBG
Effect of Phenylbiguanide on Blood Pressure
MathAchieve
Mathematics achievement scores
formula.pdMat
Extract pdMat Formula
collapse.groupedData
Collapse a groupedData Object
compareFits
Compare Fitted Objects
intervals.lme
Confidence Intervals on lme Parameters
anova.lme
Compare Likelihoods of Fitted Objects
fitted.glsStruct
Calculate glsStruct Fitted Values
Oxide
Variability in Semiconductor Manufacturing
corFactor
Factor of a Correlation Matrix
logLik.gnls
Log-Likelihood of a gnls Object
residuals.glsStruct
Calculate glsStruct Residuals
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
nlmeObject
Fitted nlme Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
logLik.varFunc
Extract varFunc logLik
recalc.reStruct
Recalculate for an reStruct Object
Rail
Evaluation of Stress in Railway Rails
lme
Linear Mixed-Effects Models
Ovary
Counts of Ovarian Follicles
summary.corStruct
Summarize a corStruct Object
predict.lmList
Predictions from an lmList Object
nlmeControl
Control Values for nlme Fit
coef.lme
Extract lme Coefficients
pooledSD
Extract Pooled Standard Deviation
varWeights
Extract Variance Function Weights
varPower
Power Variance Function
pairs.compareFits
Pairs Plot of compareFits Object
Pixel
X-ray pixel intensities over time
print.varFunc
Print a varFunc Object
Wheat
Yields by growing conditions
Wafer
Modeling of Analog MOS Circuits
corFactor.corStruct
Factor of a corStruct Object Matrix
ACF.gls
Autocorrelation Function for gls Residuals
getCovariate.corStruct
Extract corStruct Object Covariate
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
ranef.lme
Extract lme Random Effects
gnlsControl
Control Values for gnls Fit
corExp
Exponential Correlation Structure
Dim.corSpatial
Dimensions of a corSpatial Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
as.matrix.corStruct
Matrix of a corStruct Object
intervals
Confidence Intervals on Coefficients
lmeObject
Fitted lme Object
coef.pdMat
pdMat Object Coefficients
logLik.glsStruct
Log-Likelihood of a glsStruct Object
recalc.corStruct
Recalculate for corStruct Object
corNatural
General correlation in natural parameterization
summary.lme
Summarize an lme Object
isBalanced
Check a Design for Balance
solve.reStruct
Apply Solve to an reStruct Object
summary.modelStruct
Summarize a modelStruct Object
nlsList
List of nls Objects with a Common Model
Glucose
Glucose levels over time
Phenobarb
Phenobarbitol Kinetics
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Nitrendipene
Assay of nitrendipene
Names.pdBlocked
Names of a pdBlocked Object
corARMA
ARMA(p,q) Correlation Structure
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Coef
Assign Values to Coefficients
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Remifentanil
Pharmacokinetics of remifentanil
fixed.effects
Extract Fixed Effects
getGroups.lmList
Extract lmList Object Groups
plot.compareFits
Plot a compareFits Object
isInitialized
Check if Object is Initialized
gnlsObject
Fitted gnls Object
pdClasses
Positive-Definite Matrix Classes
lmeControl
Control Values for lme Fit
summary.pdMat
Summarize a pdMat Object
nlsList.selfStart
nlsList Fit from a selfStart Function
plot.lme
Plot an lme or nls object
recalc
Recalculate Condensed Linear Model Object
plot.augPred
Plot an augPred Object
Relaxin
Assay for Relaxin
getGroups.varFunc
Extract varFunc Groups
lmeScale
Scale for lme Optimization
IGF
Radioimmunoassay of IGF-I Protein
Glucose2
Glucose Levels Following Alcohol Ingestion
varWeights.glsStruct
Variance Weights for glsStruct Object
BodyWeight
Rat weight over time for different diets
VarCorr
Extract variance and correlation components
plot.intervals.lmList
Plot lmList Confidence Intervals
Earthquake
Earthquake Intensity
augPred
Augmented Predictions
varWeights.lmeStruct
Variance Weights for lmeStruct Object
Soybean
Growth of soybean plants
pdSymm
General Positive-Definite Matrix
intervals.gls
Confidence Intervals on gls Parameters
plot.nmGroupedData
Plot an nmGroupedData Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
getCovariate.varFunc
Extract varFunc Covariate
getVarCov
Extract variance-covariance matrix
ergoStool
Ergometrics experiment with stool types
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
Variogram.corExp
Calculate Semi-variogram for a corExp Object
corSymm
General Correlation Structure
logDet.pdMat
Extract Log-Determinant from a pdMat Object