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nlme (version 3.1-104)
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
3.1-104
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
May 23rd, 2012
Functions in nlme (3.1-104)
Search all functions
ACF.lme
Autocorrelation Function for lme Residuals
Dim.corStruct
Dimensions of a corStruct Object
Assay
Bioassay on Cell Culture Plate
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
ACF.gls
Autocorrelation Function for gls Residuals
BodyWeight
Rat weight over time for different diets
Coef
Assign Values to Coefficients
Covariate.varFunc
Assign varFunc Covariate
Covariate
Assign Covariate Values
Dialyzer
High-Flux Hemodialyzer
Dim.corSpatial
Dimensions of a corSpatial Object
Dim
Extract Dimensions from an Object
[.pdMat
Subscript a pdMat Object
Earthquake
Earthquake Intensity
Dim.pdMat
Dimensions of a pdMat Object
Glucose
Glucose levels over time
Gun
Methods for firing naval guns
Gasoline
Refinery yield of gasoline
Glucose2
Glucose Levels Following Alcohol Ingestion
ACF
Autocorrelation Function
Cefamandole
Pharmacokinetics of Cefamandole
Initialize.glsStruct
Initialize a glsStruct Object
Initialize.corStruct
Initialize corStruct Object
Initialize.varFunc
Initialize varFunc Object
Initialize
Initialize Object
Initialize.reStruct
Initialize reStruct Object
Muscle
Contraction of heart muscle sections
Matrix
Assign Matrix Values
Machines
Productivity Scores for Machines and Workers
MathAchSchool
School demographic data for MathAchieve
Nitrendipene
Assay of nitrendipene
Matrix.pdMat
Assign Matrix to a pdMat Object
Meat
Tenderness of meat
Initialize.lmeStruct
Initialize an lmeStruct Object
MathAchieve
Mathematics achievement scores
Milk
Protein content of cows' milk
IGF
Radioimmunoassay of IGF-I Protein
Matrix.reStruct
Assign reStruct Matrices
Pixel
X-ray pixel intensities over time
PBG
Effect of Phenylbiguanide on Blood Pressure
Names.formula
Extract Names from a formula
Rail
Evaluation of Stress in Railway Rails
Orthodont
Growth curve data on an orthdontic measurement
Remifentanil
Pharmacokinetics of remifentanil
Phenobarb
Phenobarbitol Kinetics
Oxide
Variability in Semiconductor Manufacturing
Names
Names Associated with an Object
Relaxin
Assay for Relaxin
Quinidine
Quinidine Kinetics
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Spruce
Growth of Spruce Trees
Tetracycline2
Pharmacokinetics of tetracycline
Tetracycline1
Pharmacokinetics of tetracycline
Oats
Split-plot Experiment on Varieties of Oats
Ovary
Counts of Ovarian Follicles
VarCorr
Extract variance and correlation components
Names.pdMat
Names of a pdMat Object
RatPupWeight
The weight of rat pups
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Soybean
Growth of soybean plants
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Names.pdBlocked
Names of a pdBlocked Object
Names.reStruct
Names of an reStruct Object
LDEsysMat
Generate system matrix for LDEs
Variogram
Calculate Semi-variogram
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
as.matrix.pdMat
Matrix of a pdMat Object
Wheat2
Wheat Yield Trials
anova.gls
Compare Likelihoods of Fitted Objects
as.matrix.corStruct
Matrix of a corStruct Object
Wheat
Yields by growing conditions
augPred
Augmented Predictions
Wafer
Modeling of Analog MOS Circuits
balancedGrouped
Create a groupedData object from a matrix
allCoef
Extract Coefficients from a Set of Objects
bdf
Language scores
coef.gnls
Extract gnls Coefficients
coef.reStruct
reStruct Object Coefficients
asOneFormula
Combine Formulas of a Set of Objects
coef.lmList
Extract lmList Coefficients
coef.varFunc
varFunc Object Coefficients
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
collapse
Collapse According to Groups
comparePred
Compare Predictions
asTable
Convert groupedData to a matrix
anova.lme
Compare Likelihoods of Fitted Objects
coef.lme
Extract lme Coefficients
coef.corStruct
Coefficients of a corStruct Object
coef.modelStruct
Extract modelStruct Object Coefficients
corCAR1
Continuous AR(1) Correlation Structure
collapse.groupedData
Collapse a groupedData Object
corClasses
Correlation Structure Classes
corAR1
AR(1) Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
corARMA
ARMA(p,q) Correlation Structure
corCompSymm
Compound Symmetry Correlation Structure
corFactor
Factor of a Correlation Matrix
compareFits
Compare Fitted Objects
corMatrix.corStruct
Matrix of a corStruct Object
coef.pdMat
pdMat Object Coefficients
corMatrix
Extract Correlation Matrix
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corLin
Linear Correlation Structure
corGaus
Gaussian Correlation Structure
Variogram.default
Calculate Semi-variogram
corExp
Exponential Correlation Structure
corNatural
General correlation in natural parameterization
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corSpatial
Spatial Correlation Structure
corSymm
General Correlation Structure
fdHess
Finite difference Hessian
ergoStool
Ergometrics experiment with stool types
fitted.lme
Extract lme Fitted Values
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
fitted.glsStruct
Calculate glsStruct Fitted Values
fixed.effects
Extract Fixed Effects
formula.pdMat
Extract pdMat Formula
formula.pdBlocked
Extract pdBlocked Formula
gapply
Apply a Function by Groups
corRatio
Rational Quadratic Correlation Structure
getGroups.corStruct
Extract corStruct Groups
getCovariateFormula
Extract Covariates Formula
fixef.lmList
Extract lmList Fixed Effects
getCovariate
Extract Covariate from an Object
corSpher
Spherical Correlation Structure
getGroups.lmList
Extract lmList Object Groups
getGroups.data.frame
Extract Groups from a Data Frame
formula.reStruct
Extract reStruct Object Formula
fitted.lmList
Extract lmList Fitted Values
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getCovariate.corStruct
Extract corStruct Object Covariate
getGroups.varFunc
Extract varFunc Groups
getResponseFormula
Extract Formula Specifying Response Variable
getCovariate.varFunc
Extract varFunc Covariate
getData.lmList
Extract lmList Object Data
getResponse
Extract Response Variable from an Object
getData.lme
Extract lme Object Data
getCovariate.data.frame
Extract Data Frame Covariate
getGroups.gls
Extract gls Object Groups
getVarCov
Extract variance-covariance matrix
getGroups.lme
Extract lme Object Groups
getGroups
Extract Grouping Factors from an Object
getData.gls
Extract gls Object Data
gls
Fit Linear Model Using Generalized Least Squares
glsObject
Fitted gls Object
getData
Extract Data from an Object
glsControl
Control Values for gls Fit
getGroupsFormula
Extract Grouping Formula
gnlsObject
Fitted gnls Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
intervals.lmList
Confidence Intervals on lmList Coefficients
lmList.groupedData
lmList Fit from a groupedData Object
gsummary
Summarize by Groups
lme.lmList
LME fit from lmList Object
intervals.gls
Confidence Intervals on gls Parameters
intervals.lme
Confidence Intervals on lme Parameters
isBalanced
Check a Design for Balance
groupedData
Construct a groupedData Object
glsStruct
Generalized Least Squares Structure
lme
Linear Mixed-Effects Models
lmeObject
Fitted lme Object
lmList
List of lm Objects with a Common Model
gnlsStruct
Generalized Nonlinear Least Squares Structure
gnlsControl
Control Values for gnls Fit
lme.groupedData
LME fit from groupedData Object
isInitialized
Check if Object is Initialized
logDet.reStruct
Extract reStruct Log-Determinants
logLik.lme
Log-Likelihood of an lme Object
logLik.corStruct
Extract corStruct Log-Likelihood
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logDet.corStruct
Extract corStruct Log-Determinant
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
model.matrix.reStruct
reStruct Model Matrix
nlme.nlsList
NLME fit from nlsList Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
needUpdate
Check if Update is Needed
lmeControl
Control Values for lme Fit
logDet
Extract the Logarithm of the Determinant
lmeStruct
Linear Mixed-Effects Structure
logLik.varFunc
Extract varFunc logLik
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
nlme
Nonlinear Mixed-Effects Models
logLik.gnls
Log-Likelihood of a gnls Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
logLik.lmList
Log-Likelihood of an lmList Object
nlmeControl
Control Values for nlme Fit
lmeScale
Scale for lme Optimization
nlmeStruct
Nonlinear Mixed-Effects Structure
nlmeObject
Fitted nlme Object
pdDiag
Diagonal Positive-Definite Matrix
pairs.lme
Pairs Plot of an lme Object
pdLogChol
General Positive-Definite Matrix
pairs.compareFits
Pairs Plot of compareFits Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdClasses
Positive-Definite Matrix Classes
pdNatural
General Positive-Definite Matrix in Natural Parametrization
plot.ACF
Plot an ACF Object
pairs.lmList
Pairs Plot of an lmList Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdConstruct
Construct pdMat Objects
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
plot.Variogram
Plot a Variogram Object
phenoModel
Model function for the Phenobarb data
pdSymm
General Positive-Definite Matrix
plot.nffGroupedData
Plot an nffGroupedData Object
plot.augPred
Plot an augPred Object
plot.ranef.lmList
Plot a ranef.lmList Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
plot.gls
Plot a gls Object
pdMat
Positive-Definite Matrix
predict.nlme
Predictions from an nlme Object
recalc.varFunc
Recalculate for varFunc Object
quinModel
Model function for the Quinidine data
plot.lmList
Plot an lmList Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.compareFits
Plot a compareFits Object
recalc.corStruct
Recalculate for corStruct Object
predict.lmList
Predictions from an lmList Object
reStruct
Random Effects Structure
predict.gnls
Predictions from a gnls Object
ranef.lme
Extract lme Random Effects
plot.ranef.lme
Plot a ranef.lme Object
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.nfnGroupedData
Plot an nfnGroupedData Object
predict.gls
Predictions from a gls Object
random.effects
Extract Random Effects
pooledSD
Extract Pooled Standard Deviation
print.summary.pdMat
Print a summary.pdMat Object
recalc
Recalculate Condensed Linear Model Object
recalc.reStruct
Recalculate for an reStruct Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
plot.nmGroupedData
Plot an nmGroupedData Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
plot.lme
Plot an lme or nls object
Fatigue
Cracks caused by metal fatigue
Oxboys
Heights of Boys in Oxford
as.matrix.reStruct
Matrices of an reStruct Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
intervals
Confidence Intervals on Coefficients
nlsList
List of nls Objects with a Common Model
residuals.lmList
Extract lmList Residuals
print.varFunc
Print a varFunc Object
varClasses
Variance Function Classes
residuals.lmeStruct
Calculate lmeStruct Residuals
residuals.gls
Extract gls Residuals
residuals.glsStruct
Calculate glsStruct Residuals
varFixed
Fixed Variance Function
residuals.lme
Extract lme Residuals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
varFunc
Variance Function Structure
simulate.lme
Simulate Results from
lme
Models
summary.pdMat
Summarize a pdMat Object
summary.lme
Summarize an lme Object
varExp
Exponential Variance Function
summary.corStruct
Summarize a corStruct Object
update.modelStruct
Update a modelStruct Object
summary.modelStruct
Summarize a modelStruct Object
varComb
Combination of Variance Functions
splitFormula
Split a Formula
varConstPower
Constant Plus Power Variance Function
nlsList.selfStart
nlsList Fit from a selfStart Function
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
recalc.modelStruct
Recalculate for a modelStruct Object
ranef.lmList
Extract lmList Random Effects
summary.gls
Summarize a gls Object
summary.nlsList
Summarize an nlsList Object
summary.varFunc
Summarize varFunc Object
predict.lme
Predictions from an lme Object
pdBlocked
Positive-Definite Block Diagonal Matrix
summary.lmList
Summarize an lmList Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
update.varFunc
Update varFunc Object
varPower
Power Variance Function
varIdent
Constant Variance Function
varWeights.glsStruct
Variance Weights for glsStruct Object
solve.reStruct
Apply Solve to an reStruct Object
varWeights
Extract Variance Function Weights
varWeights.lmeStruct
Variance Weights for lmeStruct Object