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nlme (version 3.1-103)
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
3.1-103
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
January 16th, 2012
Functions in nlme (3.1-103)
Search functions
Assay
Bioassay on Cell Culture Plate
ACF.lme
Autocorrelation Function for lme Residuals
Dialyzer
High-Flux Hemodialyzer
BodyWeight
Rat weight over time for different diets
LDEsysMat
Generate system matrix for LDEs
Covariate.varFunc
Assign varFunc Covariate
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Relaxin
Assay for Relaxin
ACF.gls
Autocorrelation Function for gls Residuals
Dim.corSpatial
Dimensions of a corSpatial Object
Earthquake
Earthquake Intensity
Nitrendipene
Assay of nitrendipene
Initialize.varFunc
Initialize varFunc Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Fatigue
Cracks caused by metal fatigue
Spruce
Growth of Spruce Trees
ergoStool
Ergometrics experiment with stool types
corSpatial
Spatial Correlation Structure
Initialize
Initialize Object
Names.pdMat
Names of a pdMat Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Variogram
Calculate Semi-variogram
gnls
Fit Nonlinear Model Using Generalized Least Squares
Phenobarb
Phenobarbitol Kinetics
MathAchSchool
School demographic data for MathAchieve
corExp
Exponential Correlation Structure
lmeStruct
Linear Mixed-Effects Structure
coef.lme
Extract lme Coefficients
Initialize.lmeStruct
Initialize an lmeStruct Object
Matrix
Assign Matrix Values
Gasoline
Refinery yield of gasoline
formula.reStruct
Extract reStruct Object Formula
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Meat
Tenderness of meat
Soybean
Growth of soybean plants
Pixel
X-ray pixel intensities over time
Orthodont
Growth curve data on an orthdontic measurement
PBG
Effect of Phenylbiguanide on Blood Pressure
corSpher
Spherical Correlation Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
anova.lme
Compare Likelihoods of Fitted Objects
Names.formula
Extract Names from a formula
Coef
Assign Values to Coefficients
nlsList
List of nls Objects with a Common Model
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
getGroups.varFunc
Extract varFunc Groups
Wheat
Yields by growing conditions
nlsList.selfStart
nlsList Fit from a selfStart Function
anova.gls
Compare Likelihoods of Fitted Objects
corMatrix
Extract Correlation Matrix
Initialize.reStruct
Initialize reStruct Object
Rail
Evaluation of Stress in Railway Rails
Milk
Protein content of cows' milk
Ovary
Counts of Ovarian Follicles
predict.lmList
Predictions from an lmList Object
corCompSymm
Compound Symmetry Correlation Structure
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Wheat2
Wheat Yield Trials
Oxboys
Heights of Boys in Oxford
MathAchieve
Mathematics achievement scores
Machines
Productivity Scores for Machines and Workers
update.modelStruct
Update a modelStruct Object
fixed.effects
Extract Fixed Effects
gnlsControl
Control Values for gnls Fit
Covariate
Assign Covariate Values
Dim
Extract Dimensions from an Object
Initialize.corStruct
Initialize corStruct Object
getGroups.lme
Extract lme Object Groups
getGroups.gls
Extract gls Object Groups
isBalanced
Check a Design for Balance
glsControl
Control Values for gls Fit
nlme.nlsList
NLME fit from nlsList Object
Gun
Methods for firing naval guns
Tetracycline2
Pharmacokinetics of tetracycline
getGroups.corStruct
Extract corStruct Groups
Initialize.glsStruct
Initialize a glsStruct Object
Matrix.pdMat
Assign Matrix to a pdMat Object
Variogram.default
Calculate Semi-variogram
Glucose
Glucose levels over time
asOneFormula
Combine Formulas of a Set of Objects
gapply
Apply a Function by Groups
splitFormula
Split a Formula
coef.modelStruct
Extract modelStruct Object Coefficients
groupedData
Construct a groupedData Object
formula.pdMat
Extract pdMat Formula
collapse.groupedData
Collapse a groupedData Object
getCovariate.corStruct
Extract corStruct Object Covariate
Oats
Split-plot Experiment on Varieties of Oats
intervals.gls
Confidence Intervals on gls Parameters
getData.lme
Extract lme Object Data
[.pdMat
Subscript a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
pdBlocked
Positive-Definite Block Diagonal Matrix
getResponseFormula
Extract Formula Specifying Response Variable
VarCorr
Extract variance and correlation components
RatPupWeight
The weight of rat pups
Wafer
Modeling of Analog MOS Circuits
getGroups.data.frame
Extract Groups from a Data Frame
ACF
Autocorrelation Function
Cefamandole
Pharmacokinetics of Cefamandole
corClasses
Correlation Structure Classes
corFactor
Factor of a Correlation Matrix
lmeObject
Fitted lme Object
Muscle
Contraction of heart muscle sections
pairs.lme
Pairs Plot of an lme Object
model.matrix.reStruct
reStruct Model Matrix
nlmeObject
Fitted nlme Object
compareFits
Compare Fitted Objects
varExp
Exponential Variance Function
getCovariate
Extract Covariate from an Object
pdDiag
Diagonal Positive-Definite Matrix
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Tetracycline1
Pharmacokinetics of tetracycline
Variogram.corExp
Calculate Semi-variogram for a corExp Object
pdConstruct
Construct pdMat Objects
nlmeStruct
Nonlinear Mixed-Effects Structure
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
lmeScale
Scale for lme Optimization
coef.pdMat
pdMat Object Coefficients
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
asTable
Convert groupedData to a matrix
lmList.groupedData
lmList Fit from a groupedData Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
coef.varFunc
varFunc Object Coefficients
plot.gls
Plot a gls Object
fitted.lme
Extract lme Fitted Values
as.matrix.reStruct
Matrices of an reStruct Object
getData
Extract Data from an Object
pairs.lmList
Pairs Plot of an lmList Object
plot.compareFits
Plot a compareFits Object
fdHess
Finite difference Hessian
pdNatural
General Positive-Definite Matrix in Natural Parametrization
formula.pdBlocked
Extract pdBlocked Formula
residuals.lmeStruct
Calculate lmeStruct Residuals
fitted.lmList
Extract lmList Fitted Values
pdSymm
General Positive-Definite Matrix
plot.nfnGroupedData
Plot an nfnGroupedData Object
logLik.lme
Log-Likelihood of an lme Object
residuals.lme
Extract lme Residuals
intervals.lme
Confidence Intervals on lme Parameters
corLin
Linear Correlation Structure
reStruct
Random Effects Structure
logLik.lmList
Log-Likelihood of an lmList Object
getCovariateFormula
Extract Covariates Formula
needUpdate
Check if Update is Needed
recalc.corStruct
Recalculate for corStruct Object
residuals.lmList
Extract lmList Residuals
residuals.glsStruct
Calculate glsStruct Residuals
fixef.lmList
Extract lmList Fixed Effects
quinModel
Model function for the Quinidine data
nlme
Nonlinear Mixed-Effects Models
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getData.gls
Extract gls Object Data
getCovariate.varFunc
Extract varFunc Covariate
IGF
Radioimmunoassay of IGF-I Protein
varComb
Combination of Variance Functions
logLik.gnls
Log-Likelihood of a gnls Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
coef.corStruct
Coefficients of a corStruct Object
logDet.reStruct
Extract reStruct Log-Determinants
coef.lmList
Extract lmList Coefficients
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
coef.reStruct
reStruct Object Coefficients
plot.Variogram
Plot a Variogram Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
phenoModel
Model function for the Phenobarb data
lme
Linear Mixed-Effects Models
isInitialized
Check if Object is Initialized
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
recalc.modelStruct
Recalculate for a modelStruct Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
lme.lmList
LME fit from lmList Object
lme.groupedData
LME fit from groupedData Object
plot.augPred
Plot an augPred Object
plot.nffGroupedData
Plot an nffGroupedData Object
logLik.varFunc
Extract varFunc logLik
residuals.gls
Extract gls Residuals
plot.nmGroupedData
Plot an nmGroupedData Object
solve.reStruct
Apply Solve to an reStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
intervals.lmList
Confidence Intervals on lmList Coefficients
gls
Fit Linear Model Using Generalized Least Squares
varWeights
Extract Variance Function Weights
logDet
Extract the Logarithm of the Determinant
nlmeControl
Control Values for nlme Fit
getGroupsFormula
Extract Grouping Formula
plot.lme
Plot an lme or nls object
lmeControl
Control Values for lme Fit
predict.lme
Predictions from an lme Object
corRatio
Rational Quadratic Correlation Structure
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
plot.intervals.lmList
Plot lmList Confidence Intervals
recalc.reStruct
Recalculate for an reStruct Object
gnlsObject
Fitted gnls Object
summary.varFunc
Summarize varFunc Object
plot.ranef.lme
Plot a ranef.lme Object
recalc.varFunc
Recalculate for varFunc Object
predict.gls
Predictions from a gls Object
summary.corStruct
Summarize a corStruct Object
predict.nlme
Predictions from an nlme Object
update.varFunc
Update varFunc Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
getGroups
Extract Grouping Factors from an Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
corCAR1
Continuous AR(1) Correlation Structure
summary.nlsList
Summarize an nlsList Object
pdClasses
Positive-Definite Matrix Classes
pdIdent
Multiple of the Identity Positive-Definite Matrix
print.varFunc
Print a varFunc Object
summary.lmList
Summarize an lmList Object
augPred
Augmented Predictions
Dim.pdMat
Dimensions of a pdMat Object
corGaus
Gaussian Correlation Structure
varPower
Power Variance Function
varClasses
Variance Function Classes
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
Dim.corStruct
Dimensions of a corStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
lmList
List of lm Objects with a Common Model
plot.ACF
Plot an ACF Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
random.effects
Extract Random Effects
comparePred
Compare Predictions
as.matrix.pdMat
Matrix of a pdMat Object
summary.lme
Summarize an lme Object
Oxide
Variability in Semiconductor Manufacturing
logLik.glsStruct
Log-Likelihood of a glsStruct Object
pdLogChol
General Positive-Definite Matrix
recalc
Recalculate Condensed Linear Model Object
pooledSD
Extract Pooled Standard Deviation
corMatrix.corStruct
Matrix of a corStruct Object
simulate.lme
Simulate Results from
lme
Models
plot.lmList
Plot an lmList Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
corFactor.corStruct
Factor of a corStruct Object Matrix
summary.pdMat
Summarize a pdMat Object
varIdent
Constant Variance Function
ranef.lme
Extract lme Random Effects
coef.gnls
Extract gnls Coefficients
varWeights.glsStruct
Variance Weights for glsStruct Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
corNatural
General correlation in natural parameterization
pdConstruct.pdBlocked
Construct pdBlocked Objects
ranef.lmList
Extract lmList Random Effects
corAR1
AR(1) Correlation Structure
Quinidine
Quinidine Kinetics
plot.ranef.lmList
Plot a ranef.lmList Object
getResponse
Extract Response Variable from an Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
intervals
Confidence Intervals on Coefficients
Matrix.reStruct
Assign reStruct Matrices
gsummary
Summarize by Groups
getVarCov
Extract variance-covariance matrix
logDet.corStruct
Extract corStruct Log-Determinant
balancedGrouped
Create a groupedData object from a matrix
glsObject
Fitted gls Object
allCoef
Extract Coefficients from a Set of Objects
predict.gnls
Predictions from a gnls Object
varFixed
Fixed Variance Function
varConstPower
Constant Plus Power Variance Function
summary.gls
Summarize a gls Object
bdf
Language scores
corARMA
ARMA(p,q) Correlation Structure
as.matrix.corStruct
Matrix of a corStruct Object
pdMat
Positive-Definite Matrix
varFunc
Variance Function Structure
summary.modelStruct
Summarize a modelStruct Object
collapse
Collapse According to Groups
getGroups.lmList
Extract lmList Object Groups
Glucose2
Glucose Levels Following Alcohol Ingestion
Remifentanil
Pharmacokinetics of remifentanil
getCovariate.data.frame
Extract Data Frame Covariate
getData.lmList
Extract lmList Object Data
Names
Names Associated with an Object
logLik.corStruct
Extract corStruct Log-Likelihood
print.summary.pdMat
Print a summary.pdMat Object
pairs.compareFits
Pairs Plot of compareFits Object
corSymm
General Correlation Structure
glsStruct
Generalized Least Squares Structure
Names.reStruct
Names of an reStruct Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa