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nlme (version 3.1-93)
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
3.1-93
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
August 16th, 2009
Functions in nlme (3.1-93)
Search all functions
Cefamandole
Pharmacokinetics of Cefamandole
Dim
Extract Dimensions from an Object
BodyWeight
Rat weight over time for different diets
Names.pdMat
Names of a pdMat Object
[.pdMat
Subscript a pdMat Object
BIC
Bayesian Information Criterion
Initialize.lmeStruct
Initialize an lmeStruct Object
Relaxin
Assay for Relaxin
Names.pdBlocked
Names of a pdBlocked Object
Nitrendipene
Assay of nitrendipene
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
MathAchSchool
School demographic data for MathAchieve
corAR1
AR(1) Correlation Structure
asOneFormula
Combine Formulas of a Set of Objects
Ovary
Counts of Ovarian Follicles
anova.gls
Compare Likelihoods of Fitted Objects
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Oxide
Variability in Semiconductor Manufacturing
Covariate.varFunc
Assign varFunc Covariate
Dim.pdMat
Dimensions of a pdMat Object
coef.gnls
Extract gnls Coefficients
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
bdf
Language scores
anova.lme
Compare Likelihoods of Fitted Objects
RatPupWeight
The weight of rat pups
corMatrix.corStruct
Matrix of a corStruct Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
nlmeObject
Fitted nlme Object
intervals
Confidence Intervals on Coefficients
phenoModel
Model function for the Phenobarb data
Soybean
Growth of soybean plants
pdFactor
Square-Root Factor of a Positive-Definite Matrix
collapse
Collapse According to Groups
lmList
List of lm Objects with a Common Model
corGaus
Gaussian Correlation Structure
corFactor
Factor of a Correlation Matrix
corMatrix
Extract Correlation Matrix
getCovariate.varFunc
Extract varFunc Covariate
corSpatial
Spatial Correlation Structure
plot.lmList
Plot an lmList Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
corRatio
Rational Quadratic Correlation Structure
fitted.lmList
Extract lmList Fitted Values
IGF
Radioimmunoassay of IGF-I Protein
fixef.lmList
Extract lmList Fixed Effects
coef.modelStruct
Extract modelStruct Object Coefficients
ergoStool
Ergometrics experiment with stool types
predict.gnls
Predictions from a gnls Object
summary.lme
Summarize an lme Object
getCovariate.corStruct
Extract corStruct Object Covariate
intervals.lmList
Confidence Intervals on lmList Coefficients
plot.ranef.lme
Plot a ranef.lme Object
getGroups.gls
Extract gls Object Groups
plot.ranef.lmList
Plot a ranef.lmList Object
glsControl
Control Values for gls Fit
getResponseFormula
Extract Formula Specifying Response Variable
pairs.compareFits
Pairs Plot of compareFits Object
ACF.gls
Autocorrelation Function for gls Residuals
Dim.corStruct
Dimensions of a corStruct Object
getData.gls
Extract gls Object Data
nlmeControl
Control Values for nlme Fit
Milk
Protein content of cows' milk
quinModel
Model function for the Quinidine data
residuals.gnlsStruct
Calculate gnlsStruct Residuals
lmeStruct
Linear Mixed-Effects Structure
Tetracycline1
Pharmacokinetics of tetracycline
recalc.reStruct
Recalculate for an reStruct Object
pdMat
Positive-Definite Matrix
logLik.lmList
Log-Likelihood of an lmList Object
Meat
Tenderness of meat
logDet.corStruct
Extract corStruct Log-Determinant
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
Oats
Split-plot Experiment on Varieties of Oats
model.matrix.reStruct
reStruct Model Matrix
lmeControl
Control Values for lme Fit
coef.corStruct
Coefficients of a corStruct Object
Orthodont
Growth curve data on an orthdontic measurement
getData.lme
Extract lme Object Data
getGroups
Extract Grouping Factors from an Object
plot.Variogram
Plot a Variogram Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
nlmeStruct
Nonlinear Mixed-Effects Structure
gnlsObject
Fitted gnls Object
Remifentanil
Pharmacokinetics of remifentanil
lme
Linear Mixed-Effects Models
as.matrix.corStruct
Matrix of a corStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
splitFormula
Split a Formula
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
Quinidine
Quinidine Kinetics
simulate.lme
Simulate results from lme models
update.varFunc
Update varFunc Object
corExp
Exponential Correlation Structure
Dim.corSpatial
Dimensions of a corSpatial Object
LDEsysMat
Generate system matrix for LDEs
varConstPower
Constant Plus Power Variance Function
plot.intervals.lmList
Plot lmList Confidence Intervals
corClasses
Correlation Structure Classes
Muscle
Contraction of heart muscle sections
getData
Extract Data from an Object
varClasses
Variance Function Classes
pdIdent
Multiple of the Identity Positive-Definite Matrix
varWeights
Extract Variance Function Weights
asTable
Convert groupedData to a matrix
corSpher
Spherical Correlation Structure
varWeights.glsStruct
Variance Weights for glsStruct Object
lme.lmList
LME fit from lmList Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
varFunc
Variance Function Structure
varIdent
Constant Variance Function
lmeScale
Scale for lme Optimization
Matrix
Assign Matrix Values
logLik.varFunc
Extract varFunc logLik
coef.reStruct
reStruct Object Coefficients
varExp
Exponential Variance Function
recalc
Recalculate Condensed Linear Model Object
lme.groupedData
LME fit from groupedData Object
getCovariate.data.frame
Extract Data Frame Covariate
corSymm
General Correlation Structure
getData.lmList
Extract lmList Object Data
nlsList.selfStart
nlsList Fit from a selfStart Function
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
plot.nmGroupedData
Plot an nmGroupedData Object
pdDiag
Diagonal Positive-Definite Matrix
nlme.nlsList
NLME fit from nlsList Object
pooledSD
Extract Pooled Standard Deviation
Covariate
Assign Covariate Values
isBalanced
Check a Design for Balance
Rail
Evaluation of Stress in Railway Rails
Tetracycline2
Pharmacokinetics of tetracycline
corLin
Linear Correlation Structure
getGroupsFormula
Extract Grouping Formula
logDet.pdMat
Extract Log-Determinant from a pdMat Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
qqnorm.gls
Normal Plot of Residuals from a gls Object
predict.lme
Predictions from an lme Object
plot.gls
Plot a gls Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
reStruct
Random Effects Structure
getGroups.varFunc
Extract varFunc Groups
Matrix.pdMat
Assign Matrix to a pdMat Object
pairs.lmList
Pairs Plot of an lmList Object
Initialize.varFunc
Initialize varFunc Object
Spruce
Growth of Spruce Trees
random.effects
Extract Random Effects
residuals.glsStruct
Calculate glsStruct Residuals
recalc.corStruct
Recalculate for corStruct Object
plot.ACF
Plot an ACF Object
residuals.lme
Extract lme Residuals
PBG
Effect of Phenylbiguanide on Blood Pressure
VarCorr
Extract variance and correlation components
summary.varFunc
Summarize varFunc Object
summary.pdMat
Summarize a pdMat Object
Variogram.default
Calculate Semi-variogram
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Wheat2
Wheat Yield Trials
as.matrix.reStruct
Matrices of an reStruct Object
varComb
Combination of Variance Functions
groupedData
Construct a groupedData Object
corARMA
ARMA(p,q) Correlation Structure
fixed.effects
Extract Fixed Effects
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.lme
Plot an lme or nls object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
corCompSymm
Compound Symmetry Correlation Structure
formula.pdMat
Extract pdMat Formula
lmList.groupedData
lmList Fit from a groupedData Object
glsStruct
Generalized Least Squares Structure
summary.nlsList
Summarize an nlsList Object
update.modelStruct
Update a modelStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
logDet.reStruct
Extract reStruct Log-Determinants
Matrix.reStruct
Assign reStruct Matrices
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
getCovariate
Extract Covariate from an Object
formula.pdBlocked
Extract pdBlocked Formula
gapply
Apply a Function by Groups
getVarCov
Extract variance-covariance matrix
Glucose
Glucose levels over time
glsObject
Fitted gls Object
Gasoline
Refinery yield of gasoline
Initialize.corStruct
Initialize corStruct Object
Glucose2
Glucose Levels Following Alcohol Ingestion
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Phenobarb
Phenobarbitol Kinetics
pdConstruct.pdBlocked
Construct pdBlocked Objects
Dialyzer
High-Flux Hemodialyzer
Names.reStruct
Names of an reStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
allCoef
Extract Coefficients from a Set of Objects
balancedGrouped
Create a groupedData object from a matrix
corFactor.corStruct
Factor of a corStruct Object Matrix
fitted.glsStruct
Calculate glsStruct Fitted Values
ACF.lme
Autocorrelation Function for lme Residuals
Variogram.corExp
Calculate Semi-variogram for a corExp Object
getGroups.data.frame
Extract Groups from a Data Frame
getGroups.lmList
Extract lmList Object Groups
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
fdHess
Finite difference Hessian
corCAR1
Continuous AR(1) Correlation Structure
getGroups.corStruct
Extract corStruct Groups
intervals.gls
Confidence Intervals on gls Parameters
logDet
Extract the Logarithm of the Determinant
gsummary
Summarize by Groups
coef.lmList
Extract lmList Coefficients
logLik.corStruct
Extract corStruct Log-Likelihood
isInitialized
Check if Object is Initialized
nlsList
List of nls Objects with a Common Model
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
predict.lmList
Predictions from an lmList Object
print.summary.pdMat
Print a summary.pdMat Object
summary.modelStruct
Summarize a modelStruct Object
ranef.lmList
Extract lmList Random Effects
pdBlocked
Positive-Definite Block Diagonal Matrix
solve.reStruct
Apply Solve to an reStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
residuals.lmList
Extract lmList Residuals
plot.compareFits
Plot a compareFits Object
residuals.lmeStruct
Calculate lmeStruct Residuals
varWeights.lmeStruct
Variance Weights for lmeStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
varFixed
Fixed Variance Function
varPower
Power Variance Function
Assay
Bioassay on Cell Culture Plate
Wheat
Yields by growing conditions
needUpdate
Check if Update is Needed
pairs.lme
Pairs Plot of an lme Object
predict.gls
Predictions from a gls Object
ACF
Autocorrelation Function
BIC.logLik
BIC of a logLik Object
Initialize.glsStruct
Initialize a glsStruct Object
Gun
Methods for firing naval guns
Pixel
X-ray pixel intensities over time
Earthquake
Earthquake Intensity
MathAchieve
Mathematics achievement scores
Coef
Assign Values to Coefficients
lmeObject
Fitted lme Object
coef.lme
Extract lme Coefficients
predict.nlme
Predictions from an nlme Object
compareFits
Compare Fitted Objects
collapse.groupedData
Collapse a groupedData Object
corNatural
General correlation in natural parameterization
as.matrix.pdMat
Matrix of a pdMat Object
logLik.lme
Log-Likelihood of an lme Object
plot.augPred
Plot an augPred Object
print.varFunc
Print a varFunc Object
summary.gls
Summarize a gls Object
Names.formula
Extract Names from a formula
Machines
Productivity Scores for Machines and Workers
Variogram
Calculate Semi-variogram
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Wafer
Modeling of Analog MOS Circuits
coef.varFunc
varFunc Object Coefficients
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
pdClasses
Positive-Definite Matrix Classes
nlme
Nonlinear Mixed-Effects Models
pdConstruct
Construct pdMat Objects
pdSymm
General Positive-Definite Matrix
recalc.modelStruct
Recalculate for a modelStruct Object
summary.corStruct
Summarize a corStruct Object
summary.lmList
Summarize an lmList Object
Fatigue
Cracks caused by metal fatigue
Initialize.reStruct
Initialize reStruct Object
Initialize
Initialize Object
Names
Names Associated with an Object
augPred
Augmented Predictions
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
coef.pdMat
pdMat Object Coefficients
getResponse
Extract Response Variable from an Object
fitted.lme
Extract lme Fitted Values
gls
Fit Linear Model Using Generalized Least Squares
gnlsControl
Control Values for gnls Fit
pdLogChol
General Positive-Definite Matrix
ranef.lme
Extract lme Random Effects
residuals.gls
Extract gls Residuals
recalc.varFunc
Recalculate for varFunc Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
comparePred
Compare Predictions
intervals.lme
Confidence Intervals on lme Parameters
Oxboys
Heights of Boys in Oxford
getCovariateFormula
Extract Covariates Formula
getGroups.lme
Extract lme Object Groups
formula.reStruct
Extract reStruct Object Formula