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nlme (version 3.1-95)
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
3.1-95
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
October 5th, 2009
Functions in nlme (3.1-95)
Search all functions
Muscle
Contraction of heart muscle sections
coef.modelStruct
Extract modelStruct Object Coefficients
Dim.corSpatial
Dimensions of a corSpatial Object
intervals.lmList
Confidence Intervals on lmList Coefficients
Glucose2
Glucose Levels Following Alcohol Ingestion
Meat
Tenderness of meat
Names.pdBlocked
Names of a pdBlocked Object
Names.reStruct
Names of an reStruct Object
ACF
Autocorrelation Function
coef.varFunc
varFunc Object Coefficients
fdHess
Finite difference Hessian
VarCorr
Extract variance and correlation components
logDet.reStruct
Extract reStruct Log-Determinants
fitted.lmList
Extract lmList Fitted Values
gapply
Apply a Function by Groups
MathAchSchool
School demographic data for MathAchieve
lmeStruct
Linear Mixed-Effects Structure
lmList
List of lm Objects with a Common Model
Wheat
Yields by growing conditions
Initialize
Initialize Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
getGroups
Extract Grouping Factors from an Object
BIC
Bayesian Information Criterion
formula.reStruct
Extract reStruct Object Formula
gnlsObject
Fitted gnls Object
recalc
Recalculate Condensed Linear Model Object
nlsList
List of nls Objects with a Common Model
pdNatural
General Positive-Definite Matrix in Natural Parametrization
Assay
Bioassay on Cell Culture Plate
update.varFunc
Update varFunc Object
coef.corStruct
Coefficients of a corStruct Object
coef.reStruct
reStruct Object Coefficients
[.pdMat
Subscript a pdMat Object
summary.lme
Summarize an lme Object
plot.gls
Plot a gls Object
Spruce
Growth of Spruce Trees
predict.gnls
Predictions from a gnls Object
BodyWeight
Rat weight over time for different diets
varClasses
Variance Function Classes
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Fatigue
Cracks caused by metal fatigue
Covariate
Assign Covariate Values
summary.varFunc
Summarize varFunc Object
fitted.glsStruct
Calculate glsStruct Fitted Values
Cefamandole
Pharmacokinetics of Cefamandole
Matrix.reStruct
Assign reStruct Matrices
Initialize.lmeStruct
Initialize an lmeStruct Object
Quinidine
Quinidine Kinetics
Orthodont
Growth curve data on an orthdontic measurement
Initialize.varFunc
Initialize varFunc Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
print.varFunc
Print a varFunc Object
Initialize.reStruct
Initialize reStruct Object
Gasoline
Refinery yield of gasoline
Coef
Assign Values to Coefficients
Dim
Extract Dimensions from an Object
corARMA
ARMA(p,q) Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
allCoef
Extract Coefficients from a Set of Objects
intervals.gls
Confidence Intervals on gls Parameters
balancedGrouped
Create a groupedData object from a matrix
augPred
Augmented Predictions
Names
Names Associated with an Object
Tetracycline1
Pharmacokinetics of tetracycline
corCAR1
Continuous AR(1) Correlation Structure
Oxide
Variability in Semiconductor Manufacturing
lme
Linear Mixed-Effects Models
getCovariate.data.frame
Extract Data Frame Covariate
getGroups.data.frame
Extract Groups from a Data Frame
Gun
Methods for firing naval guns
Phenobarb
Phenobarbitol Kinetics
Matrix.pdMat
Assign Matrix to a pdMat Object
collapse.groupedData
Collapse a groupedData Object
glsControl
Control Values for gls Fit
as.matrix.reStruct
Matrices of an reStruct Object
lmList.groupedData
lmList Fit from a groupedData Object
lmeScale
Scale for lme Optimization
logLik.varFunc
Extract varFunc logLik
Wafer
Modeling of Analog MOS Circuits
gnls
Fit Nonlinear Model Using Generalized Least Squares
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
gsummary
Summarize by Groups
corCompSymm
Compound Symmetry Correlation Structure
corRatio
Rational Quadratic Correlation Structure
ergoStool
Ergometrics experiment with stool types
Soybean
Growth of soybean plants
corSymm
General Correlation Structure
logLik.lme
Log-Likelihood of an lme Object
logLik.lmList
Log-Likelihood of an lmList Object
varExp
Exponential Variance Function
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Variogram.default
Calculate Semi-variogram
MathAchieve
Mathematics achievement scores
coef.lme
Extract lme Coefficients
corNatural
General correlation in natural parameterization
Initialize.glsStruct
Initialize a glsStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
coef.pdMat
pdMat Object Coefficients
getCovariate.corStruct
Extract corStruct Object Covariate
logLik.reStruct
Calculate reStruct Log-Likelihood
plot.lme
Plot an lme or nls object
RatPupWeight
The weight of rat pups
coef.gnls
Extract gnls Coefficients
predict.lmList
Predictions from an lmList Object
ranef.lme
Extract lme Random Effects
summary.corStruct
Summarize a corStruct Object
Names.pdMat
Names of a pdMat Object
pdLogChol
General Positive-Definite Matrix
anova.lme
Compare Likelihoods of Fitted Objects
Ovary
Counts of Ovarian Follicles
corLin
Linear Correlation Structure
solve.reStruct
Apply Solve to an reStruct Object
corSpher
Spherical Correlation Structure
getResponse
Extract Response Variable from an Object
Wheat2
Wheat Yield Trials
pdConstruct.pdBlocked
Construct pdBlocked Objects
residuals.gls
Extract gls Residuals
logDet.pdMat
Extract Log-Determinant from a pdMat Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdSymm
General Positive-Definite Matrix
splitFormula
Split a Formula
pdBlocked
Positive-Definite Block Diagonal Matrix
qqnorm.gls
Normal Plot of Residuals from a gls Object
quinModel
Model function for the Quinidine data
glsObject
Fitted gls Object
corClasses
Correlation Structure Classes
isInitialized
Check if Object is Initialized
corFactor
Factor of a Correlation Matrix
nlme.nlsList
NLME fit from nlsList Object
pdClasses
Positive-Definite Matrix Classes
corExp
Exponential Correlation Structure
getData.lmList
Extract lmList Object Data
getResponseFormula
Extract Formula Specifying Response Variable
pooledSD
Extract Pooled Standard Deviation
corGaus
Gaussian Correlation Structure
intervals
Confidence Intervals on Coefficients
varIdent
Constant Variance Function
pdMat
Positive-Definite Matrix
logDet.corStruct
Extract corStruct Log-Determinant
corMatrix
Extract Correlation Matrix
pdIdent
Multiple of the Identity Positive-Definite Matrix
getGroups.varFunc
Extract varFunc Groups
fitted.lme
Extract lme Fitted Values
logDet
Extract the Logarithm of the Determinant
plot.Variogram
Plot a Variogram Object
getVarCov
Extract variance-covariance matrix
plot.ranef.lme
Plot a ranef.lme Object
random.effects
Extract Random Effects
nlme
Nonlinear Mixed-Effects Models
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
anova.gls
Compare Likelihoods of Fitted Objects
ranef.lmList
Extract lmList Random Effects
pairs.compareFits
Pairs Plot of compareFits Object
residuals.lmeStruct
Calculate lmeStruct Residuals
needUpdate
Check if Update is Needed
plot.nmGroupedData
Plot an nmGroupedData Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
summary.pdMat
Summarize a pdMat Object
phenoModel
Model function for the Phenobarb data
plot.ACF
Plot an ACF Object
recalc.varFunc
Recalculate for varFunc Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
varWeights.lmeStruct
Variance Weights for lmeStruct Object
update.modelStruct
Update a modelStruct Object
varConstPower
Constant Plus Power Variance Function
Names.formula
Extract Names from a formula
Variogram
Calculate Semi-variogram
as.matrix.pdMat
Matrix of a pdMat Object
bdf
Language scores
Earthquake
Earthquake Intensity
ACF.gls
Autocorrelation Function for gls Residuals
Nitrendipene
Assay of nitrendipene
getData
Extract Data from an Object
Machines
Productivity Scores for Machines and Workers
glsStruct
Generalized Least Squares Structure
fixed.effects
Extract Fixed Effects
getCovariateFormula
Extract Covariates Formula
Dialyzer
High-Flux Hemodialyzer
isBalanced
Check a Design for Balance
Dim.corStruct
Dimensions of a corStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
coef.lmList
Extract lmList Coefficients
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
comparePred
Compare Predictions
Milk
Protein content of cows' milk
Glucose
Glucose levels over time
corSpatial
Spatial Correlation Structure
fixef.lmList
Extract lmList Fixed Effects
Rail
Evaluation of Stress in Railway Rails
corFactor.corStruct
Factor of a corStruct Object Matrix
nlmeStruct
Nonlinear Mixed-Effects Structure
Remifentanil
Pharmacokinetics of remifentanil
asOneFormula
Combine Formulas of a Set of Objects
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
nlmeObject
Fitted nlme Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
plot.ranef.lmList
Plot a ranef.lmList Object
getCovariate.varFunc
Extract varFunc Covariate
getGroups.gls
Extract gls Object Groups
getCovariate
Extract Covariate from an Object
gls
Fit Linear Model Using Generalized Least Squares
residuals.gnlsStruct
Calculate gnlsStruct Residuals
summary.nlsList
Summarize an nlsList Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
getGroups.lmList
Extract lmList Object Groups
residuals.nlmeStruct
Calculate nlmeStruct Residuals
formula.pdBlocked
Extract pdBlocked Formula
gnlsControl
Control Values for gnls Fit
plot.lmList
Plot an lmList Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdConstruct
Construct pdMat Objects
ACF.lme
Autocorrelation Function for lme Residuals
LDEsysMat
Generate system matrix for LDEs
simulate.lme
Simulate results from lme models
Oxboys
Heights of Boys in Oxford
Relaxin
Assay for Relaxin
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
collapse
Collapse According to Groups
corAR1
AR(1) Correlation Structure
summary.gls
Summarize a gls Object
getData.gls
Extract gls Object Data
varComb
Combination of Variance Functions
gnlsStruct
Generalized Nonlinear Least Squares Structure
varFunc
Variance Function Structure
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
plot.compareFits
Plot a compareFits Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
reStruct
Random Effects Structure
recalc.reStruct
Recalculate for an reStruct Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Matrix
Assign Matrix Values
Dim.pdMat
Dimensions of a pdMat Object
Tetracycline2
Pharmacokinetics of tetracycline
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
formula.pdMat
Extract pdMat Formula
groupedData
Construct a groupedData Object
lmeControl
Control Values for lme Fit
pdFactor
Square-Root Factor of a Positive-Definite Matrix
predict.gls
Predictions from a gls Object
residuals.glsStruct
Calculate glsStruct Residuals
residuals.lme
Extract lme Residuals
varWeights.glsStruct
Variance Weights for glsStruct Object
Oats
Split-plot Experiment on Varieties of Oats
corMatrix.corStruct
Matrix of a corStruct Object
getData.lme
Extract lme Object Data
getGroupsFormula
Extract Grouping Formula
lmeObject
Fitted lme Object
model.matrix.reStruct
reStruct Model Matrix
nlsList.selfStart
nlsList Fit from a selfStart Function
plot.nffGroupedData
Plot an nffGroupedData Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
residuals.lmList
Extract lmList Residuals
print.summary.pdMat
Print a summary.pdMat Object
varWeights
Extract Variance Function Weights
summary.modelStruct
Summarize a modelStruct Object
IGF
Radioimmunoassay of IGF-I Protein
Initialize.corStruct
Initialize corStruct Object
compareFits
Compare Fitted Objects
getGroups.corStruct
Extract corStruct Groups
lme.groupedData
LME fit from groupedData Object
nlmeControl
Control Values for nlme Fit
predict.nlme
Predictions from an nlme Object
recalc.modelStruct
Recalculate for a modelStruct Object
intervals.lme
Confidence Intervals on lme Parameters
BIC.logLik
BIC of a logLik Object
Pixel
X-ray pixel intensities over time
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
asTable
Convert groupedData to a matrix
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
summary.lmList
Summarize an lmList Object
plot.augPred
Plot an augPred Object
varPower
Power Variance Function
varFixed
Fixed Variance Function
PBG
Effect of Phenylbiguanide on Blood Pressure
getGroups.lme
Extract lme Object Groups
Covariate.varFunc
Assign varFunc Covariate
logLik.corStruct
Extract corStruct Log-Likelihood
pdDiag
Diagonal Positive-Definite Matrix
pairs.lmList
Pairs Plot of an lmList Object
predict.lme
Predictions from an lme Object
plot.intervals.lmList
Plot lmList Confidence Intervals
pairs.lme
Pairs Plot of an lme Object
logLik.gnls
Log-Likelihood of a gnls Object
recalc.corStruct
Recalculate for corStruct Object
lme.lmList
LME fit from lmList Object