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nlme (version 3.1-131)
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
3.1-131
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
February 6th, 2017
Functions in nlme (3.1-131)
Search all functions
anova.gls
Compare Likelihoods of Fitted Objects
anova.lme
Compare Likelihoods of Fitted Objects
as.matrix.corStruct
Matrix of a corStruct Object
allCoef
Extract Coefficients from a Set of Objects
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
ACF.lme
Autocorrelation Function for lme Residuals
as.matrix.reStruct
Matrices of an reStruct Object
as.matrix.pdMat
Matrix of a pdMat Object
ACF
Autocorrelation Function
ACF.gls
Autocorrelation Function for gls Residuals
asTable
Convert groupedData to a matrix
augPred
Augmented Predictions
coef.corStruct
Coefficients of a corStruct Object
coef.gnls
Extract gnls Coefficients
BodyWeight
Rat weight over time for different diets
bdf
Language scores
Cefamandole
Pharmacokinetics of Cefamandole
balancedGrouped
Create a groupedData object from a matrix
asOneFormula
Combine Formulas of a Set of Objects
Assay
Bioassay on Cell Culture Plate
coef.pdMat
pdMat Object Coefficients
coef.reStruct
reStruct Object Coefficients
coef.varFunc
varFunc Object Coefficients
collapse.groupedData
Collapse a groupedData Object
Coef
Assign Values to Coefficients
coef.lme
Extract lme Coefficients
collapse
Collapse According to Groups
compareFits
Compare Fitted Objects
coef.lmList
Extract lmList Coefficients
coef.modelStruct
Extract modelStruct Object Coefficients
corClasses
Correlation Structure Classes
corCompSymm
Compound Symmetry Correlation Structure
corExp
Exponential Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
ergoStool
Ergometrics experiment with stool types
corSpatial
Spatial Correlation Structure
[.pdMat
Subscript a pdMat Object
corRatio
Rational Quadratic Correlation Structure
Dim.pdMat
Dimensions of a pdMat Object
Earthquake
Earthquake Intensity
corARMA
ARMA(p,q) Correlation Structure
corCAR1
Continuous AR(1) Correlation Structure
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corNatural
General correlation in natural parameterization
Dim.corStruct
Dimensions of a corStruct Object
Dim
Extract Dimensions from an Object
corSpher
Spherical Correlation Structure
corSymm
General Correlation Structure
Covariate
Assign Covariate Values
Covariate.varFunc
Assign varFunc Covariate
fitted.lme
Extract lme Fitted Values
fitted.lmeStruct
Calculate lmeStruct Fitted Values
comparePred
Compare Predictions
corAR1
AR(1) Correlation Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
corLin
Linear Correlation Structure
corMatrix.corStruct
Matrix of a corStruct Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getCovariate.data.frame
Extract Data Frame Covariate
getCovariate
Extract Covariate from an Object
formula.reStruct
Extract reStruct Object Formula
gapply
Apply a Function by Groups
getData.lme
Extract lme Object Data
getData.lmList
Extract lmList Object Data
fixed.effects
Extract Fixed Effects
getGroups
Extract Grouping Factors from an Object
fixef.lmList
Extract lmList Fixed Effects
Gasoline
Refinery yield of gasoline
getVarCov
Extract variance-covariance matrix
gls-internal
Auxiliary functions used by gls
getGroups.lme
Extract lme Object Groups
getGroups.lmList
Extract lmList Object Groups
getCovariate.corStruct
Extract corStruct Object Covariate
getGroups.gls
Extract gls Object Groups
getGroups.varFunc
Extract varFunc Groups
corFactor
Factor of a Correlation Matrix
lme.lmList
LME fit from lmList Object
corGaus
Gaussian Correlation Structure
lme
Linear Mixed-Effects Models
intervals.lme
Confidence Intervals on lme Parameters
intervals.lmList
Confidence Intervals on lmList Coefficients
IGF
Radioimmunoassay of IGF-I Protein
Gun
Methods for firing naval guns
getGroupsFormula
Extract Grouping Formula
corMatrix
Extract Correlation Matrix
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
Dim.corSpatial
Dimensions of a corSpatial Object
Dialyzer
High-Flux Hemodialyzer
formula.pdMat
Extract pdMat Formula
formula.pdBlocked
Extract pdBlocked Formula
Initialize.reStruct
Initialize reStruct Object
Initialize.varFunc
Initialize varFunc Object
Fatigue
Cracks caused by metal fatigue
fdHess
Finite difference Hessian
lmList.groupedData
lmList Fit from a groupedData Object
lmeStruct
Linear Mixed-Effects Structure
logLik.corStruct
Extract corStruct Log-Likelihood
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
logDet.reStruct
Extract reStruct Log-Determinants
Nitrendipene
Assay of nitrendipene
gnlsObject
Fitted gnls Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
Names.reStruct
Names of an reStruct Object
needUpdate
Check if Update is Needed
Initialize.corStruct
Initialize corStruct Object
Initialize.glsStruct
Initialize a glsStruct Object
isBalanced
Check a Design for Balance
isInitialized
Check if Object is Initialized
logLik.reStruct
Calculate reStruct Log-Likelihood
glsControl
Control Values for gls Fit
gls
Fit Linear Model Using Generalized Least Squares
Muscle
Contraction of heart muscle sections
model.matrix.reStruct
reStruct Model Matrix
logLik.varFunc
Extract varFunc logLik
Glucose
Glucose levels over time
Glucose2
Glucose Levels Following Alcohol Ingestion
Initialize
Initialize Object
lme.groupedData
LME fit from groupedData Object
Initialize.lmeStruct
Initialize an lmeStruct Object
logDet
Extract the Logarithm of the Determinant
logDet.pdMat
Extract Log-Determinant from a pdMat Object
LDEsysMat
Generate system matrix for LDEs
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdLogChol
General Positive-Definite Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an
pdNatural
General Positive-Definite Matrix in Natural Parametrization
plot.ranef.lmList
Plot a ranef.lmList Object
plot.ranef.lme
Plot a ranef.lme Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
update.varFunc
Update varFunc Object
varClasses
Variance Function Classes
residuals.glsStruct
Calculate glsStruct Residuals
Quinidine
Quinidine Kinetics
varFixed
Fixed Variance Function
varFunc
Variance Function Structure
fitted.lmList
Extract lmList Fitted Values
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getData.gls
Extract gls Object Data
getData
Extract Data from an Object
glsObject
Fitted gls Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
gnlsControl
Control Values for gnls Fit
glsStruct
Generalized Least Squares Structure
Orthodont
Growth curve data on an orthdontic measurement
lmeControl
Specifying Control Values for lme Fit
lmeObject
Fitted lme Object
Ovary
Counts of Ovarian Follicles
pdMat
Positive-Definite Matrix
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
plot.ACF
Plot an ACF Object
plot.augPred
Plot an augPred Object
plot.lmList
Plot an lmList Object
plot.nffGroupedData
Plot an nffGroupedData Object
predict.nlme
Predictions from an nlme Object
getResponse
Extract Response Variable from an Object
getResponseFormula
Extract Formula Specifying Response Variable
gsummary
Summarize by Groups
getGroups.corStruct
Extract corStruct Groups
groupedData
Construct a groupedData Object
getGroups.data.frame
Extract Groups from a Data Frame
getCovariate.varFunc
Extract varFunc Covariate
getCovariateFormula
Extract Covariates Formula
print.summary.pdMat
Print a summary.pdMat Object
intervals
Confidence Intervals on Coefficients
intervals.gls
Confidence Intervals on gls Parameters
Meat
Tenderness of meat
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
Milk
Protein content of cows' milk
nlmeControl
Control Values for nlme Fit
logLik.lme
Log-Likelihood of an lme Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Matrix.reStruct
Assign reStruct Matrices
nlmeObject
Fitted nlme Object
pairs.lmList
Pairs Plot of an lmList Object
Machines
Productivity Scores for Machines and Workers
Oxboys
Heights of Boys in Oxford
MathAchieve
Mathematics achievement scores
nlmeStruct
Nonlinear Mixed-Effects Structure
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdConstruct
Construct pdMat Objects
plot.compareFits
Plot a compareFits Object
Oxide
Variability in Semiconductor Manufacturing
nlsList
List of nls Objects with a Common Model
plot.gls
Plot a gls Object
plot.intervals.lmList
Plot lmList Confidence Intervals
recalc
Recalculate Condensed Linear Model Object
recalc.varFunc
Recalculate for varFunc Object
Relaxin
Assay for Relaxin
Spruce
Growth of Spruce Trees
plot.lme
Plot an lme or nls object
print.varFunc
Print a varFunc Object
recalc.corStruct
Recalculate for corStruct Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
lmList
List of lm Objects with a Common Model
nlme
Nonlinear Mixed-Effects Models
nlme.nlsList
NLME fit from nlsList Object
Names
Names Associated with an Object
Names.formula
Extract Names from a formula
logDet.corStruct
Extract corStruct Log-Determinant
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
pdClasses
Positive-Definite Matrix Classes
pdBlocked
Positive-Definite Block Diagonal Matrix
PBG
Effect of Phenylbiguanide on Blood Pressure
plot.Variogram
Plot a Variogram Object
pdDiag
Diagonal Positive-Definite Matrix
pdConstruct.pdBlocked
Construct pdBlocked Objects
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
residuals.lmeStruct
Calculate lmeStruct Residuals
pooledSD
Extract Pooled Standard Deviation
random.effects
Extract Random Effects
ranef.lme
Extract lme Random Effects
residuals.lme
Extract lme Residuals
solve.reStruct
Apply Solve to an reStruct Object
varComb
Combination of Variance Functions
varConstPower
Constant Plus Power Variance Function
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdSymm
General Positive-Definite Matrix
pdFactor
Square-Root Factor of a Positive-Definite Matrix
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Phenobarb
Phenobarbitol Kinetics
predict.gls
Predictions from a gls Object
predict.gnls
Predictions from a gnls Object
quinModel
Model function for the Quinidine data
summary.lmList
Summarize an lmList Object
summary.modelStruct
Summarize a modelStruct Object
summary.corStruct
Summarize a corStruct Object
Remifentanil
Pharmacokinetics of remifentanil
residuals.gls
Extract gls Residuals
Rail
Evaluation of Stress in Railway Rails
Variogram.corExp
Calculate Semi-variogram for a corExp Object
varIdent
Constant Variance Function
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Variogram
Calculate Semi-variogram
Wheat
Yields by growing conditions
Wheat2
Wheat Yield Trials
Names.pdBlocked
Names of a pdBlocked Object
Names.pdMat
Names of a pdMat Object
Matrix
Assign Matrix Values
MathAchSchool
School demographic data for MathAchieve
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
nlsList.selfStart
nlsList Fit from a selfStart Function
pairs.compareFits
Pairs Plot of compareFits Object
Oats
Split-plot Experiment on Varieties of Oats
phenoModel
Model function for the Phenobarb data
Pixel
X-ray pixel intensities over time
pairs.lme
Pairs Plot of an lme Object
plot.nmGroupedData
Plot an nmGroupedData Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
predict.lme
Predictions from an lme Object
predict.lmList
Predictions from an lmList Object
recalc.modelStruct
Recalculate for a modelStruct Object
residuals.lmList
Extract lmList Residuals
summary.lme
Summarize an lme Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
summary.gls
Summarize a Generalized Least Squares
recalc.reStruct
Recalculate for an reStruct Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
varPower
Power Variance Function
summary.pdMat
Summarize a pdMat Object
summary.nlsList
Summarize an nlsList Object
reStruct
Random Effects Structure
simulate.lme
Simulate Results from
summary.varFunc
Summarize varFunc Object
Tetracycline1
Pharmacokinetics of tetracycline
Wafer
Modeling of Analog MOS Circuits
varExp
Exponential Variance Function
VarCorr
Extract variance and correlation components
varWeights.glsStruct
Variance Weights for glsStruct Object
varWeights
Extract Variance Function Weights
varWeights.lmeStruct
Variance Weights for lmeStruct Object
ranef.lmList
Extract lmList Random Effects
RatPupWeight
The weight of rat pups
Soybean
Growth of soybean plants
splitFormula
Split a Formula
Variogram.default
Calculate Semi-variogram
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Tetracycline2
Pharmacokinetics of tetracycline
update.modelStruct
Update a modelStruct Object