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nlme (version 3.1-92)
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
100,391
Version
3.1-92
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
May 24th, 2009
Functions in nlme (3.1-92)
Search all functions
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Tetracycline2
Pharmacokinetics of tetracycline
ACF
Autocorrelation Function
Gasoline
Refinery yield of gasoline
BodyWeight
Rat weight over time for different diets
BIC
Bayesian Information Criterion
Glucose
Glucose levels over time
Cefamandole
Pharmacokinetics of Cefamandole
ACF.lme
Autocorrelation Function for lme Residuals
Initialize.lmeStruct
Initialize an lmeStruct Object
ACF.gls
Autocorrelation Function for gls Residuals
Oats
Split-plot Experiment on Varieties of Oats
as.matrix.pdMat
Matrix of a pdMat Object
Names.formula
Extract Names from a formula
Relaxin
Assay for Relaxin
Ovary
Counts of Ovarian Follicles
Oxboys
Heights of Boys in Oxford
Wafer
Modeling of Analog MOS Circuits
VarCorr
Extract variance and correlation components
coef.corStruct
Coefficients of a corStruct Object
Muscle
Contraction of heart muscle sections
coef.gnls
Extract gnls Coefficients
Spruce
Growth of Spruce Trees
RatPupWeight
The weight of rat pups
Matrix
Assign Matrix Values
nlsList
List of nls Objects with a Common Model
logLik.varFunc
Extract varFunc logLik
coef.varFunc
varFunc Object Coefficients
Tetracycline1
Pharmacokinetics of tetracycline
fitted.lmeStruct
Calculate lmeStruct Fitted Values
Initialize.glsStruct
Initialize a glsStruct Object
corGaus
Gaussian Correlation Structure
Initialize
Initialize Object
Fatigue
Cracks caused by metal fatigue
fitted.lme
Extract lme Fitted Values
collapse
Collapse According to Groups
IGF
Radioimmunoassay of IGF-I Protein
Initialize.reStruct
Initialize reStruct Object
Meat
Tenderness of meat
MathAchSchool
School demographic data for MathAchieve
Names
Names Associated with an Object
Names.pdMat
Names of a pdMat Object
glsControl
Control Values for gls Fit
getData
Extract Data from an Object
getGroupsFormula
Extract Grouping Formula
corFactor
Factor of a Correlation Matrix
asOneFormula
Combine Formulas of a Set of Objects
Rail
Evaluation of Stress in Railway Rails
summary.nlsList
Summarize an nlsList Object
getGroups.lmList
Extract lmList Object Groups
BIC.logLik
BIC of a logLik Object
Wheat
Yields by growing conditions
corFactor.corStruct
Factor of a corStruct Object Matrix
MathAchieve
Mathematics achievement scores
Covariate
Assign Covariate Values
Phenobarb
Phenobarbitol Kinetics
asTable
Convert groupedData to a matrix
formula.pdBlocked
Extract pdBlocked Formula
logDet.pdMat
Extract Log-Determinant from a pdMat Object
Remifentanil
Pharmacokinetics of remifentanil
Initialize.corStruct
Initialize corStruct Object
Names.reStruct
Names of an reStruct Object
recalc
Recalculate Condensed Linear Model Object
Variogram.default
Calculate Semi-variogram
Coef
Assign Values to Coefficients
Initialize.varFunc
Initialize varFunc Object
comparePred
Compare Predictions
Wheat2
Wheat Yield Trials
coef.modelStruct
Extract modelStruct Object Coefficients
balancedGrouped
Create a groupedData object from a matrix
varIdent
Constant Variance Function
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
random.effects
Extract Random Effects
pdMat
Positive-Definite Matrix
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Dim.corSpatial
Dimensions of a corSpatial Object
corExp
Exponential Correlation Structure
varWeights.glsStruct
Variance Weights for glsStruct Object
summary.pdMat
Summarize a pdMat Object
Covariate.varFunc
Assign varFunc Covariate
varClasses
Variance Function Classes
formula.pdMat
Extract pdMat Formula
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
pooledSD
Extract Pooled Standard Deviation
print.varFunc
Print a varFunc Object
coef.reStruct
reStruct Object Coefficients
pdLogChol
General Positive-Definite Matrix
getCovariate.data.frame
Extract Data Frame Covariate
predict.lme
Predictions from an lme Object
gapply
Apply a Function by Groups
splitFormula
Split a Formula
logLik.lmList
Log-Likelihood of an lmList Object
plot.intervals.lmList
Plot lmList Confidence Intervals
corARMA
ARMA(p,q) Correlation Structure
corSpher
Spherical Correlation Structure
corSpatial
Spatial Correlation Structure
augPred
Augmented Predictions
[.pdMat
Subscript a pdMat Object
Dim.corStruct
Dimensions of a corStruct Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Quinidine
Quinidine Kinetics
varConstPower
Constant Plus Power Variance Function
model.matrix.reStruct
reStruct Model Matrix
recalc.modelStruct
Recalculate for a modelStruct Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
Dialyzer
High-Flux Hemodialyzer
recalc.corStruct
Recalculate for corStruct Object
pdConstruct
Construct pdMat Objects
plot.lmList
Plot an lmList Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
coef.lmList
Extract lmList Coefficients
Pixel
X-ray pixel intensities over time
pdDiag
Diagonal Positive-Definite Matrix
corRatio
Rational Quadratic Correlation Structure
pairs.lmList
Pairs Plot of an lmList Object
plot.ranef.lmList
Plot a ranef.lmList Object
lme.groupedData
LME fit from groupedData Object
coef.lme
Extract lme Coefficients
plot.nfnGroupedData
Plot an nfnGroupedData Object
as.matrix.reStruct
Matrices of an reStruct Object
predict.gnls
Predictions from a gnls Object
getCovariate.corStruct
Extract corStruct Object Covariate
varWeights
Extract Variance Function Weights
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
corLin
Linear Correlation Structure
predict.nlme
Predictions from an nlme Object
recalc.reStruct
Recalculate for an reStruct Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
print.summary.pdMat
Print a summary.pdMat Object
summary.lmList
Summarize an lmList Object
getCovariate.varFunc
Extract varFunc Covariate
fitted.lmList
Extract lmList Fitted Values
predict.lmList
Predictions from an lmList Object
nlsList.selfStart
nlsList Fit from a selfStart Function
getResponse
Extract Response Variable from an Object
summary.modelStruct
Summarize a modelStruct Object
summary.gls
Summarize a gls Object
PBG
Effect of Phenylbiguanide on Blood Pressure
residuals.gnlsStruct
Calculate gnlsStruct Residuals
getGroups.gls
Extract gls Object Groups
getGroups.corStruct
Extract corStruct Groups
getData.lme
Extract lme Object Data
getCovariateFormula
Extract Covariates Formula
update.modelStruct
Update a modelStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
getData.gls
Extract gls Object Data
summary.lme
Summarize an lme Object
logLik.corStruct
Extract corStruct Log-Likelihood
intervals.lmList
Confidence Intervals on lmList Coefficients
gnlsStruct
Generalized Nonlinear Least Squares Structure
fixed.effects
Extract Fixed Effects
varFunc
Variance Function Structure
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Dim
Extract Dimensions from an Object
gls
Fit Linear Model Using Generalized Least Squares
Gun
Methods for firing naval guns
Milk
Protein content of cows' milk
Nitrendipene
Assay of nitrendipene
gnls
Fit Nonlinear Model Using Generalized Least Squares
Orthodont
Growth curve data on an orthdontic measurement
formula.reStruct
Extract reStruct Object Formula
Dim.pdMat
Dimensions of a pdMat Object
Soybean
Growth of soybean plants
LDEsysMat
Generate system matrix for LDEs
Oxide
Variability in Semiconductor Manufacturing
compareFits
Compare Fitted Objects
Variogram.corLin
Calculate Semi-variogram for a corLin Object
residuals.gls
Extract gls Residuals
bdf
Language scores
varExp
Exponential Variance Function
Matrix.reStruct
Assign reStruct Matrices
Matrix.pdMat
Assign Matrix to a pdMat Object
logLik.lme
Log-Likelihood of an lme Object
residuals.glsStruct
Calculate glsStruct Residuals
varWeights.lmeStruct
Variance Weights for lmeStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
isBalanced
Check a Design for Balance
Machines
Productivity Scores for Machines and Workers
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
ranef.lmList
Extract lmList Random Effects
update.varFunc
Update varFunc Object
anova.lme
Compare Likelihoods of Fitted Objects
plot.compareFits
Plot a compareFits Object
plot.ranef.lme
Plot a ranef.lme Object
allCoef
Extract Coefficients from a Set of Objects
collapse.groupedData
Collapse a groupedData Object
Assay
Bioassay on Cell Culture Plate
nlme.nlsList
NLME fit from nlsList Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corAR1
AR(1) Correlation Structure
anova.gls
Compare Likelihoods of Fitted Objects
pdIdent
Multiple of the Identity Positive-Definite Matrix
fixef.lmList
Extract lmList Fixed Effects
corCompSymm
Compound Symmetry Correlation Structure
summary.corStruct
Summarize a corStruct Object
Variogram
Calculate Semi-variogram
reStruct
Random Effects Structure
predict.gls
Predictions from a gls Object
lmeControl
Control Values for lme Fit
glsObject
Fitted gls Object
plot.lme
Plot an lme or nls object
coef.pdMat
pdMat Object Coefficients
corSymm
General Correlation Structure
corClasses
Correlation Structure Classes
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
residuals.lme
Extract lme Residuals
varPower
Power Variance Function
corNatural
General correlation in natural parameterization
Variogram.corExp
Calculate Semi-variogram for a corExp Object
lmeObject
Fitted lme Object
lmeScale
Scale for lme Optimization
corMatrix.corStruct
Matrix of a corStruct Object
plot.nmGroupedData
Plot an nmGroupedData Object
residuals.lmList
Extract lmList Residuals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
isInitialized
Check if Object is Initialized
getGroups.varFunc
Extract varFunc Groups
glsStruct
Generalized Least Squares Structure
getGroups
Extract Grouping Factors from an Object
getVarCov
Extract variance-covariance matrix
plot.augPred
Plot an augPred Object
Glucose2
Glucose Levels Following Alcohol Ingestion
logDet.reStruct
Extract reStruct Log-Determinants
logLik.gnls
Log-Likelihood of a gnls Object
fitted.glsStruct
Calculate glsStruct Fitted Values
getData.lmList
Extract lmList Object Data
logDet
Extract the Logarithm of the Determinant
gsummary
Summarize by Groups
groupedData
Construct a groupedData Object
intervals
Confidence Intervals on Coefficients
getCovariate
Extract Covariate from an Object
plot.gls
Plot a gls Object
lmeStruct
Linear Mixed-Effects Structure
getGroups.data.frame
Extract Groups from a Data Frame
getResponseFormula
Extract Formula Specifying Response Variable
lmList.groupedData
lmList Fit from a groupedData Object
ranef.lme
Extract lme Random Effects
gnlsControl
Control Values for gnls Fit
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
quinModel
Model function for the Quinidine data
corMatrix
Extract Correlation Matrix
lme.lmList
LME fit from lmList Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
ergoStool
Ergometrics experiment with stool types
pairs.lme
Pairs Plot of an lme Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
simulate.lme
Simulate results from lme models
lme
Linear Mixed-Effects Models
corCAR1
Continuous AR(1) Correlation Structure
pdNatural
General Positive-Definite Matrix in Natural Parametrization
Names.pdBlocked
Names of a pdBlocked Object
fdHess
Finite difference Hessian
pdBlocked
Positive-Definite Block Diagonal Matrix
recalc.varFunc
Recalculate for varFunc Object
logDet.corStruct
Extract corStruct Log-Determinant
pdClasses
Positive-Definite Matrix Classes
nlmeObject
Fitted nlme Object
lmList
List of lm Objects with a Common Model
gnlsObject
Fitted gnls Object
pdSymm
General Positive-Definite Matrix
phenoModel
Model function for the Phenobarb data
plot.nffGroupedData
Plot an nffGroupedData Object
varFixed
Fixed Variance Function
intervals.gls
Confidence Intervals on gls Parameters
solve.reStruct
Apply Solve to an reStruct Object
intervals.lme
Confidence Intervals on lme Parameters
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
summary.varFunc
Summarize varFunc Object
residuals.lmeStruct
Calculate lmeStruct Residuals
plot.Variogram
Plot a Variogram Object
getGroups.lme
Extract lme Object Groups
nlme
Nonlinear Mixed-Effects Models
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
nlmeStruct
Nonlinear Mixed-Effects Structure
Earthquake
Earthquake Intensity
plot.ACF
Plot an ACF Object
pairs.compareFits
Pairs Plot of compareFits Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
needUpdate
Check if Update is Needed
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
nlmeControl
Control Values for nlme Fit
varComb
Combination of Variance Functions