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nlme (version 3.1-94)
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
117,966
Version
3.1-94
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
September 4th, 2009
Functions in nlme (3.1-94)
Search functions
BIC
Bayesian Information Criterion
getData.lmList
Extract lmList Object Data
Dialyzer
High-Flux Hemodialyzer
pdBlocked
Positive-Definite Block Diagonal Matrix
ACF.gls
Autocorrelation Function for gls Residuals
residuals.lmeStruct
Calculate lmeStruct Residuals
Muscle
Contraction of heart muscle sections
Initialize
Initialize Object
BodyWeight
Rat weight over time for different diets
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
[.pdMat
Subscript a pdMat Object
corCompSymm
Compound Symmetry Correlation Structure
Quinidine
Quinidine Kinetics
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
corFactor
Factor of a Correlation Matrix
bdf
Language scores
corMatrix.corStruct
Matrix of a corStruct Object
corARMA
ARMA(p,q) Correlation Structure
summary.gls
Summarize a gls Object
fixed.effects
Extract Fixed Effects
corSymm
General Correlation Structure
formula.pdMat
Extract pdMat Formula
varWeights.glsStruct
Variance Weights for glsStruct Object
getGroups.gls
Extract gls Object Groups
fdHess
Finite difference Hessian
formula.pdBlocked
Extract pdBlocked Formula
getCovariate.corStruct
Extract corStruct Object Covariate
lmeStruct
Linear Mixed-Effects Structure
getResponse
Extract Response Variable from an Object
intervals
Confidence Intervals on Coefficients
lme.lmList
LME fit from lmList Object
Names
Names Associated with an Object
nlsList.selfStart
nlsList Fit from a selfStart Function
Names.formula
Extract Names from a formula
intervals.lmList
Confidence Intervals on lmList Coefficients
Initialize.lmeStruct
Initialize an lmeStruct Object
Ovary
Counts of Ovarian Follicles
gnlsStruct
Generalized Nonlinear Least Squares Structure
Cefamandole
Pharmacokinetics of Cefamandole
Oxboys
Heights of Boys in Oxford
lmeControl
Control Values for lme Fit
BIC.logLik
BIC of a logLik Object
Dim.corSpatial
Dimensions of a corSpatial Object
logLik.reStruct
Calculate reStruct Log-Likelihood
groupedData
Construct a groupedData Object
ACF
Autocorrelation Function
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
LDEsysMat
Generate system matrix for LDEs
augPred
Augmented Predictions
Orthodont
Growth curve data on an orthdontic measurement
corRatio
Rational Quadratic Correlation Structure
Initialize.glsStruct
Initialize a glsStruct Object
asOneFormula
Combine Formulas of a Set of Objects
nlmeStruct
Nonlinear Mixed-Effects Structure
getCovariateFormula
Extract Covariates Formula
Matrix.reStruct
Assign reStruct Matrices
nlmeObject
Fitted nlme Object
coef.modelStruct
Extract modelStruct Object Coefficients
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
ranef.lmList
Extract lmList Random Effects
getGroups.lme
Extract lme Object Groups
anova.lme
Compare Likelihoods of Fitted Objects
pdLogChol
General Positive-Definite Matrix
Earthquake
Earthquake Intensity
model.matrix.reStruct
reStruct Model Matrix
corCAR1
Continuous AR(1) Correlation Structure
corMatrix
Extract Correlation Matrix
VarCorr
Extract variance and correlation components
recalc.modelStruct
Recalculate for a modelStruct Object
corFactor.corStruct
Factor of a corStruct Object Matrix
getGroups.lmList
Extract lmList Object Groups
pdMat
Positive-Definite Matrix
phenoModel
Model function for the Phenobarb data
lmList
List of lm Objects with a Common Model
recalc
Recalculate Condensed Linear Model Object
simulate.lme
Simulate results from lme models
plot.intervals.lmList
Plot lmList Confidence Intervals
residuals.glsStruct
Calculate glsStruct Residuals
Oxide
Variability in Semiconductor Manufacturing
varComb
Combination of Variance Functions
Remifentanil
Pharmacokinetics of remifentanil
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
ACF.lme
Autocorrelation Function for lme Residuals
splitFormula
Split a Formula
Nitrendipene
Assay of nitrendipene
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
formula.reStruct
Extract reStruct Object Formula
Glucose
Glucose levels over time
summary.corStruct
Summarize a corStruct Object
as.matrix.pdMat
Matrix of a pdMat Object
getVarCov
Extract variance-covariance matrix
summary.varFunc
Summarize varFunc Object
Fatigue
Cracks caused by metal fatigue
coef.gnls
Extract gnls Coefficients
Relaxin
Assay for Relaxin
update.modelStruct
Update a modelStruct Object
getGroups.corStruct
Extract corStruct Groups
varClasses
Variance Function Classes
logDet.reStruct
Extract reStruct Log-Determinants
plot.ranef.lmList
Plot a ranef.lmList Object
collapse.groupedData
Collapse a groupedData Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
residuals.gls
Extract gls Residuals
plot.lme
Plot an lme or nls object
pdIdent
Multiple of the Identity Positive-Definite Matrix
Names.pdMat
Names of a pdMat Object
summary.lmList
Summarize an lmList Object
summary.nlsList
Summarize an nlsList Object
corClasses
Correlation Structure Classes
corGaus
Gaussian Correlation Structure
corAR1
AR(1) Correlation Structure
fitted.lmList
Extract lmList Fitted Values
glsObject
Fitted gls Object
getGroups
Extract Grouping Factors from an Object
getData.gls
Extract gls Object Data
plot.gls
Plot a gls Object
gnlsObject
Fitted gnls Object
varExp
Exponential Variance Function
nlmeControl
Control Values for nlme Fit
Dim.pdMat
Dimensions of a pdMat Object
predict.nlme
Predictions from an nlme Object
corSpher
Spherical Correlation Structure
predict.gnls
Predictions from a gnls Object
intervals.gls
Confidence Intervals on gls Parameters
intervals.lme
Confidence Intervals on lme Parameters
lmeObject
Fitted lme Object
Dim.corStruct
Dimensions of a corStruct Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
gnlsControl
Control Values for gnls Fit
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
gsummary
Summarize by Groups
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logDet.corStruct
Extract corStruct Log-Determinant
anova.gls
Compare Likelihoods of Fitted Objects
pairs.lme
Pairs Plot of an lme Object
corNatural
General correlation in natural parameterization
plot.ACF
Plot an ACF Object
getGroupsFormula
Extract Grouping Formula
pdSymm
General Positive-Definite Matrix
pdConstruct
Construct pdMat Objects
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
varFixed
Fixed Variance Function
lme
Linear Mixed-Effects Models
corSpatial
Spatial Correlation Structure
ranef.lme
Extract lme Random Effects
pairs.lmList
Pairs Plot of an lmList Object
lme.groupedData
LME fit from groupedData Object
random.effects
Extract Random Effects
logLik.lme
Log-Likelihood of an lme Object
pooledSD
Extract Pooled Standard Deviation
logLik.lmList
Log-Likelihood of an lmList Object
print.varFunc
Print a varFunc Object
summary.pdMat
Summarize a pdMat Object
getResponseFormula
Extract Formula Specifying Response Variable
getCovariate.varFunc
Extract varFunc Covariate
isBalanced
Check a Design for Balance
nlme.nlsList
NLME fit from nlsList Object
pairs.compareFits
Pairs Plot of compareFits Object
nlme
Nonlinear Mixed-Effects Models
plot.augPred
Plot an augPred Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.ranef.lme
Plot a ranef.lme Object
residuals.lme
Extract lme Residuals
qqnorm.gls
Normal Plot of Residuals from a gls Object
update.varFunc
Update varFunc Object
reStruct
Random Effects Structure
predict.lmList
Predictions from an lmList Object
Initialize.reStruct
Initialize reStruct Object
Assay
Bioassay on Cell Culture Plate
Meat
Tenderness of meat
Machines
Productivity Scores for Machines and Workers
Matrix
Assign Matrix Values
Rail
Evaluation of Stress in Railway Rails
Wheat
Yields by growing conditions
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram
Calculate Semi-variogram
Pixel
X-ray pixel intensities over time
collapse
Collapse According to Groups
Matrix.pdMat
Assign Matrix to a pdMat Object
Variogram.default
Calculate Semi-variogram
corExp
Exponential Correlation Structure
Wheat2
Wheat Yield Trials
asTable
Convert groupedData to a matrix
Coef
Assign Values to Coefficients
Milk
Protein content of cows' milk
coef.lme
Extract lme Coefficients
coef.reStruct
reStruct Object Coefficients
Dim
Extract Dimensions from an Object
pdClasses
Positive-Definite Matrix Classes
Soybean
Growth of soybean plants
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
residuals.lmList
Extract lmList Residuals
ergoStool
Ergometrics experiment with stool types
recalc.corStruct
Recalculate for corStruct Object
fitted.glsStruct
Calculate glsStruct Fitted Values
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getGroups.varFunc
Extract varFunc Groups
logDet
Extract the Logarithm of the Determinant
recalc.reStruct
Recalculate for an reStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
gapply
Apply a Function by Groups
balancedGrouped
Create a groupedData object from a matrix
needUpdate
Check if Update is Needed
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fixef.lmList
Extract lmList Fixed Effects
glsControl
Control Values for gls Fit
getData
Extract Data from an Object
plot.lmList
Plot an lmList Object
gls
Fit Linear Model Using Generalized Least Squares
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varPower
Power Variance Function
plot.compareFits
Plot a compareFits Object
varWeights
Extract Variance Function Weights
varIdent
Constant Variance Function
residuals.nlmeStruct
Calculate nlmeStruct Residuals
Phenobarb
Phenobarbitol Kinetics
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
coef.corStruct
Coefficients of a corStruct Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
as.matrix.reStruct
Matrices of an reStruct Object
compareFits
Compare Fitted Objects
fitted.lme
Extract lme Fitted Values
fitted.lmeStruct
Calculate lmeStruct Fitted Values
logLik.corStruct
Extract corStruct Log-Likelihood
logLik.varFunc
Extract varFunc logLik
logLik.glsStruct
Log-Likelihood of a glsStruct Object
plot.nmGroupedData
Plot an nmGroupedData Object
summary.lme
Summarize an lme Object
summary.modelStruct
Summarize a modelStruct Object
Gun
Methods for firing naval guns
IGF
Radioimmunoassay of IGF-I Protein
Initialize.varFunc
Initialize varFunc Object
RatPupWeight
The weight of rat pups
coef.lmList
Extract lmList Coefficients
lmeScale
Scale for lme Optimization
pdNatural
General Positive-Definite Matrix in Natural Parametrization
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Covariate.varFunc
Assign varFunc Covariate
Tetracycline1
Pharmacokinetics of tetracycline
Gasoline
Refinery yield of gasoline
PBG
Effect of Phenylbiguanide on Blood Pressure
coef.varFunc
varFunc Object Coefficients
comparePred
Compare Predictions
glsStruct
Generalized Least Squares Structure
lmList.groupedData
lmList Fit from a groupedData Object
logLik.gnls
Log-Likelihood of a gnls Object
pdDiag
Diagonal Positive-Definite Matrix
quinModel
Model function for the Quinidine data
solve.reStruct
Apply Solve to an reStruct Object
predict.gls
Predictions from a gls Object
Covariate
Assign Covariate Values
corLin
Linear Correlation Structure
getCovariate.data.frame
Extract Data Frame Covariate
gnls
Fit Nonlinear Model Using Generalized Least Squares
isInitialized
Check if Object is Initialized
getData.lme
Extract lme Object Data
nlsList
List of nls Objects with a Common Model
pdConstruct.pdBlocked
Construct pdBlocked Objects
predict.lme
Predictions from an lme Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
varFunc
Variance Function Structure
Names.reStruct
Names of an reStruct Object
Wafer
Modeling of Analog MOS Circuits
getCovariate
Extract Covariate from an Object
getGroups.data.frame
Extract Groups from a Data Frame
plot.Variogram
Plot a Variogram Object
varConstPower
Constant Plus Power Variance Function
print.summary.pdMat
Print a summary.pdMat Object
Oats
Split-plot Experiment on Varieties of Oats
Tetracycline2
Pharmacokinetics of tetracycline
coef.pdMat
pdMat Object Coefficients
Initialize.corStruct
Initialize corStruct Object
Spruce
Growth of Spruce Trees
allCoef
Extract Coefficients from a Set of Objects
plot.nffGroupedData
Plot an nffGroupedData Object
MathAchieve
Mathematics achievement scores
Glucose2
Glucose Levels Following Alcohol Ingestion
MathAchSchool
School demographic data for MathAchieve
as.matrix.corStruct
Matrix of a corStruct Object
recalc.varFunc
Recalculate for varFunc Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object