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nlme (version 3.1-107)
Linear and Nonlinear Mixed Effects Models
Description
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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Install
install.packages('nlme')
Monthly Downloads
98,563
Version
3.1-107
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
January 12th, 2013
Functions in nlme (3.1-107)
Search functions
ACF
Autocorrelation Function
Matrix.reStruct
Assign reStruct Matrices
[.pdMat
Subscript a pdMat Object
Oxboys
Heights of Boys in Oxford
Covariate
Assign Covariate Values
Spruce
Growth of Spruce Trees
Cefamandole
Pharmacokinetics of Cefamandole
Initialize
Initialize Object
Initialize.glsStruct
Initialize a glsStruct Object
Gun
Methods for firing naval guns
formula.pdBlocked
Extract pdBlocked Formula
Names.reStruct
Names of an reStruct Object
formula.pdMat
Extract pdMat Formula
Gasoline
Refinery yield of gasoline
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Names.pdBlocked
Names of a pdBlocked Object
coef.varFunc
varFunc Object Coefficients
Matrix
Assign Matrix Values
Earthquake
Earthquake Intensity
Coef
Assign Values to Coefficients
Names.pdMat
Names of a pdMat Object
Milk
Protein content of cows' milk
Names.formula
Extract Names from a formula
getData.lme
Extract lme Object Data
Dim.pdMat
Dimensions of a pdMat Object
IGF
Radioimmunoassay of IGF-I Protein
Matrix.pdMat
Assign Matrix to a pdMat Object
Phenobarb
Phenobarbitol Kinetics
Dim.corStruct
Dimensions of a corStruct Object
Quinidine
Quinidine Kinetics
model.matrix.reStruct
reStruct Model Matrix
getCovariate.corStruct
Extract corStruct Object Covariate
Rail
Evaluation of Stress in Railway Rails
compareFits
Compare Fitted Objects
Variogram
Calculate Semi-variogram
Initialize.corStruct
Initialize corStruct Object
Soybean
Growth of soybean plants
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
gsummary
Summarize by Groups
Assay
Bioassay on Cell Culture Plate
coef.lme
Extract lme Coefficients
Variogram.corExp
Calculate Semi-variogram for a corExp Object
lmeObject
Fitted lme Object
needUpdate
Check if Update is Needed
Tetracycline2
Pharmacokinetics of tetracycline
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
nlsList.selfStart
nlsList Fit from a selfStart Function
coef.reStruct
reStruct Object Coefficients
balancedGrouped
Create a groupedData object from a matrix
nlmeStruct
Nonlinear Mixed-Effects Structure
corLin
Linear Correlation Structure
Relaxin
Assay for Relaxin
recalc.varFunc
Recalculate for varFunc Object
Oxide
Variability in Semiconductor Manufacturing
asOneFormula
Combine Formulas of a Set of Objects
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
coef.modelStruct
Extract modelStruct Object Coefficients
Initialize.lmeStruct
Initialize an lmeStruct Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
lmList
List of lm Objects with a Common Model
as.matrix.reStruct
Matrices of an reStruct Object
Wafer
Modeling of Analog MOS Circuits
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
asTable
Convert groupedData to a matrix
logLik.lme
Log-Likelihood of an lme Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
varClasses
Variance Function Classes
coef.pdMat
pdMat Object Coefficients
Variogram.corLin
Calculate Semi-variogram for a corLin Object
corExp
Exponential Correlation Structure
getResponseFormula
Extract Formula Specifying Response Variable
Dim
Extract Dimensions from an Object
getResponse
Extract Response Variable from an Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
VarCorr
Extract variance and correlation components
corFactor.corStruct
Factor of a corStruct Object Matrix
collapse
Collapse According to Groups
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
fdHess
Finite difference Hessian
getGroups.gls
Extract gls Object Groups
corFactor
Factor of a Correlation Matrix
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getCovariate.data.frame
Extract Data Frame Covariate
splitFormula
Split a Formula
MathAchieve
Mathematics achievement scores
gnlsObject
Fitted gnls Object
print.summary.pdMat
Print a summary.pdMat Object
corSpatial
Spatial Correlation Structure
corAR1
AR(1) Correlation Structure
glsControl
Control Values for gls Fit
MathAchSchool
School demographic data for MathAchieve
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.lme
Extract lme Residuals
getCovariate
Extract Covariate from an Object
pdConstruct
Construct pdMat Objects
corGaus
Gaussian Correlation Structure
logDet.pdMat
Extract Log-Determinant from a pdMat Object
fixed.effects
Extract Fixed Effects
Oats
Split-plot Experiment on Varieties of Oats
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
residuals.lmList
Extract lmList Residuals
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
pdLogChol
General Positive-Definite Matrix
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
Nitrendipene
Assay of nitrendipene
groupedData
Construct a groupedData Object
getCovariateFormula
Extract Covariates Formula
getGroups
Extract Grouping Factors from an Object
predict.lme
Predictions from an lme Object
logDet.corStruct
Extract corStruct Log-Determinant
pdDiag
Diagonal Positive-Definite Matrix
summary.lmList
Summarize an lmList Object
Ovary
Counts of Ovarian Follicles
predict.gls
Predictions from a gls Object
logDet
Extract the Logarithm of the Determinant
residuals.glsStruct
Calculate glsStruct Residuals
as.matrix.pdMat
Matrix of a pdMat Object
nlmeObject
Fitted nlme Object
solve.reStruct
Apply Solve to an reStruct Object
intervals.lmList
Confidence Intervals on lmList Coefficients
getGroups.varFunc
Extract varFunc Groups
plot.lmList
Plot an lmList Object
getGroups.lme
Extract lme Object Groups
logLik.lmList
Log-Likelihood of an lmList Object
plot.intervals.lmList
Plot lmList Confidence Intervals
lmeScale
Scale for lme Optimization
gnls
Fit Nonlinear Model Using Generalized Least Squares
qqnorm.gls
Normal Plot of Residuals from a gls Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
update.varFunc
Update varFunc Object
isInitialized
Check if Object is Initialized
fixef.lmList
Extract lmList Fixed Effects
nlmeControl
Control Values for nlme Fit
plot.ranef.lme
Plot a ranef.lme Object
varComb
Combination of Variance Functions
getCovariate.varFunc
Extract varFunc Covariate
intervals.lme
Confidence Intervals on lme Parameters
summary.gls
Summarize a gls Object
Variogram.default
Calculate Semi-variogram
update.modelStruct
Update a modelStruct Object
summary.nlsList
Summarize an nlsList Object
varExp
Exponential Variance Function
plot.gls
Plot a gls Object
pairs.compareFits
Pairs Plot of compareFits Object
recalc.reStruct
Recalculate for an reStruct Object
anova.gls
Compare Likelihoods of Fitted Objects
Wheat2
Wheat Yield Trials
corARMA
ARMA(p,q) Correlation Structure
lme.lmList
LME fit from lmList Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
plot.compareFits
Plot a compareFits Object
predict.nlme
Predictions from an nlme Object
nlme.nlsList
NLME fit from nlsList Object
pdMat
Positive-Definite Matrix
plot.ranef.lmList
Plot a ranef.lmList Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
glsObject
Fitted gls Object
getVarCov
Extract variance-covariance matrix
lmeControl
Control Values for lme Fit
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
varFixed
Fixed Variance Function
ranef.lme
Extract lme Random Effects
residuals.gls
Extract gls Residuals
plot.Variogram
Plot a Variogram Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
corCompSymm
Compound Symmetry Correlation Structure
predict.gnls
Predictions from a gnls Object
varConstPower
Constant Plus Power Variance Function
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
summary.varFunc
Summarize varFunc Object
corSpher
Spherical Correlation Structure
intervals
Confidence Intervals on Coefficients
pdSymm
General Positive-Definite Matrix
summary.pdMat
Summarize a pdMat Object
pairs.lmList
Pairs Plot of an lmList Object
comparePred
Compare Predictions
lmList.groupedData
lmList Fit from a groupedData Object
recalc
Recalculate Condensed Linear Model Object
residuals.lmeStruct
Calculate lmeStruct Residuals
varIdent
Constant Variance Function
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
recalc.modelStruct
Recalculate for a modelStruct Object
predict.lmList
Predictions from an lmList Object
ranef.lmList
Extract lmList Random Effects
nlme
Nonlinear Mixed-Effects Models
pdClasses
Positive-Definite Matrix Classes
phenoModel
Model function for the Phenobarb data
varWeights.glsStruct
Variance Weights for glsStruct Object
Glucose2
Glucose Levels Following Alcohol Ingestion
lme.groupedData
LME fit from groupedData Object
summary.modelStruct
Summarize a modelStruct Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
summary.lme
Summarize an lme Object
reStruct
Random Effects Structure
Glucose
Glucose levels over time
simulate.lme
Simulate Results from
lme
Models
anova.lme
Compare Likelihoods of Fitted Objects
varWeights.lmeStruct
Variance Weights for lmeStruct Object
corClasses
Correlation Structure Classes
corRatio
Rational Quadratic Correlation Structure
getData.lmList
Extract lmList Object Data
LDEsysMat
Generate system matrix for LDEs
BodyWeight
Rat weight over time for different diets
PBG
Effect of Phenylbiguanide on Blood Pressure
Remifentanil
Pharmacokinetics of remifentanil
Pixel
X-ray pixel intensities over time
Dialyzer
High-Flux Hemodialyzer
ACF.gls
Autocorrelation Function for gls Residuals
Covariate.varFunc
Assign varFunc Covariate
Machines
Productivity Scores for Machines and Workers
corSymm
General Correlation Structure
Initialize.varFunc
Initialize varFunc Object
fitted.lmList
Extract lmList Fitted Values
getGroupsFormula
Extract Grouping Formula
Dim.corSpatial
Dimensions of a corSpatial Object
as.matrix.corStruct
Matrix of a corStruct Object
bdf
Language scores
intervals.gls
Confidence Intervals on gls Parameters
pairs.lme
Pairs Plot of an lme Object
fitted.lme
Extract lme Fitted Values
RatPupWeight
The weight of rat pups
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
corNatural
General correlation in natural parameterization
lme
Linear Mixed-Effects Models
Muscle
Contraction of heart muscle sections
ergoStool
Ergometrics experiment with stool types
Tetracycline1
Pharmacokinetics of tetracycline
gls
Fit Linear Model Using Generalized Least Squares
plot.nmGroupedData
Plot an nmGroupedData Object
fitted.glsStruct
Calculate glsStruct Fitted Values
Fatigue
Cracks caused by metal fatigue
formula.reStruct
Extract reStruct Object Formula
corCAR1
Continuous AR(1) Correlation Structure
plot.lme
Plot an lme or nls object
quinModel
Model function for the Quinidine data
Wheat
Yields by growing conditions
getData
Extract Data from an Object
nlsList
List of nls Objects with a Common Model
getData.gls
Extract gls Object Data
Meat
Tenderness of meat
pdFactor
Square-Root Factor of a Positive-Definite Matrix
varFunc
Variance Function Structure
varWeights
Extract Variance Function Weights
summary.corStruct
Summarize a corStruct Object
varPower
Power Variance Function
pdConstruct.pdBlocked
Construct pdBlocked Objects
plot.augPred
Plot an augPred Object
glsStruct
Generalized Least Squares Structure
Orthodont
Growth curve data on an orthdontic measurement
recalc.corStruct
Recalculate for corStruct Object
isBalanced
Check a Design for Balance
lmeStruct
Linear Mixed-Effects Structure
coef.lmList
Extract lmList Coefficients
logLik.corStruct
Extract corStruct Log-Likelihood
coef.gnls
Extract gnls Coefficients
plot.ACF
Plot an ACF Object
corMatrix
Extract Correlation Matrix
pdBlocked
Positive-Definite Block Diagonal Matrix
pooledSD
Extract Pooled Standard Deviation
print.varFunc
Print a varFunc Object
allCoef
Extract Coefficients from a Set of Objects
gapply
Apply a Function by Groups
corMatrix.corStruct
Matrix of a corStruct Object
getGroups.corStruct
Extract corStruct Groups
getGroups.lmList
Extract lmList Object Groups
logDet.reStruct
Extract reStruct Log-Determinants
plot.nffGroupedData
Plot an nffGroupedData Object
gnlsControl
Control Values for gnls Fit
ACF.lme
Autocorrelation Function for lme Residuals
logLik.varFunc
Extract varFunc logLik
coef.corStruct
Coefficients of a corStruct Object
Names
Names Associated with an Object
augPred
Augmented Predictions
logLik.reStruct
Calculate reStruct Log-Likelihood
random.effects
Extract Random Effects
Initialize.reStruct
Initialize reStruct Object
collapse.groupedData
Collapse a groupedData Object
logLik.gnls
Log-Likelihood of a gnls Object