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nlme (version 3.1-109)
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
62,596
Version
3.1-109
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
April 3rd, 2013
Functions in nlme (3.1-109)
Search all functions
Initialize.reStruct
Initialize reStruct Object
Meat
Tenderness of meat
Coef
Assign Values to Coefficients
Initialize.varFunc
Initialize varFunc Object
Gasoline
Refinery yield of gasoline
coef.corStruct
Coefficients of a corStruct Object
fixed.effects
Extract Fixed Effects
Oxboys
Heights of Boys in Oxford
Covariate.varFunc
Assign varFunc Covariate
ACF
Autocorrelation Function
Matrix
Assign Matrix Values
Assay
Bioassay on Cell Culture Plate
Matrix.pdMat
Assign Matrix to a pdMat Object
corNatural
General correlation in natural parameterization
Variogram.default
Calculate Semi-variogram
Muscle
Contraction of heart muscle sections
Names.pdBlocked
Names of a pdBlocked Object
intervals.lmList
Confidence Intervals on lmList Coefficients
compareFits
Compare Fitted Objects
Covariate
Assign Covariate Values
Names
Names Associated with an Object
Cefamandole
Pharmacokinetics of Cefamandole
BodyWeight
Rat weight over time for different diets
corFactor
Factor of a Correlation Matrix
Initialize
Initialize Object
Dim.corSpatial
Dimensions of a corSpatial Object
asOneFormula
Combine Formulas of a Set of Objects
Phenobarb
Phenobarbitol Kinetics
Orthodont
Growth curve data on an orthdontic measurement
Earthquake
Earthquake Intensity
[.pdMat
Subscript a pdMat Object
Nitrendipene
Assay of nitrendipene
Oxide
Variability in Semiconductor Manufacturing
Rail
Evaluation of Stress in Railway Rails
Variogram
Calculate Semi-variogram
Tetracycline1
Pharmacokinetics of tetracycline
Spruce
Growth of Spruce Trees
corSymm
General Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
fitted.lme
Extract lme Fitted Values
lmList
List of lm Objects with a Common Model
formula.pdBlocked
Extract pdBlocked Formula
Quinidine
Quinidine Kinetics
Machines
Productivity Scores for Machines and Workers
LDEsysMat
Generate system matrix for LDEs
Ovary
Counts of Ovarian Follicles
Gun
Methods for firing naval guns
augPred
Augmented Predictions
logLik.reStruct
Calculate reStruct Log-Likelihood
VarCorr
Extract variance and correlation components
Names.formula
Extract Names from a formula
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
intervals.lme
Confidence Intervals on lme Parameters
logLik.lmList
Log-Likelihood of an lmList Object
lme.lmList
LME fit from lmList Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
getGroups.lmList
Extract lmList Object Groups
RatPupWeight
The weight of rat pups
coef.lme
Extract lme Coefficients
logLik.corStruct
Extract corStruct Log-Likelihood
IGF
Radioimmunoassay of IGF-I Protein
gnls
Fit Nonlinear Model Using Generalized Least Squares
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
nlmeControl
Control Values for nlme Fit
plot.lmList
Plot an lmList Object
as.matrix.pdMat
Matrix of a pdMat Object
lme.groupedData
LME fit from groupedData Object
Tetracycline2
Pharmacokinetics of tetracycline
pdFactor
Square-Root Factor of a Positive-Definite Matrix
getData.gls
Extract gls Object Data
ACF.gls
Autocorrelation Function for gls Residuals
splitFormula
Split a Formula
isBalanced
Check a Design for Balance
recalc.varFunc
Recalculate for varFunc Object
Remifentanil
Pharmacokinetics of remifentanil
nlmeStruct
Nonlinear Mixed-Effects Structure
gnlsControl
Control Values for gnls Fit
pdBlocked
Positive-Definite Block Diagonal Matrix
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
update.varFunc
Update varFunc Object
anova.lme
Compare Likelihoods of Fitted Objects
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corSpher
Spherical Correlation Structure
nlme.nlsList
NLME fit from nlsList Object
plot.gls
Plot a gls Object
random.effects
Extract Random Effects
formula.pdMat
Extract pdMat Formula
pdDiag
Diagonal Positive-Definite Matrix
varWeights
Extract Variance Function Weights
getGroupsFormula
Extract Grouping Formula
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Initialize.corStruct
Initialize corStruct Object
Dim
Extract Dimensions from an Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
groupedData
Construct a groupedData Object
residuals.lmeStruct
Calculate lmeStruct Residuals
getCovariate.corStruct
Extract corStruct Object Covariate
gnlsObject
Fitted gnls Object
lmeObject
Fitted lme Object
lmList.groupedData
lmList Fit from a groupedData Object
comparePred
Compare Predictions
varComb
Combination of Variance Functions
intervals.gls
Confidence Intervals on gls Parameters
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
coef.lmList
Extract lmList Coefficients
MathAchSchool
School demographic data for MathAchieve
residuals.gls
Extract gls Residuals
ranef.lmList
Extract lmList Random Effects
logDet.pdMat
Extract Log-Determinant from a pdMat Object
corExp
Exponential Correlation Structure
corGaus
Gaussian Correlation Structure
varClasses
Variance Function Classes
Wafer
Modeling of Analog MOS Circuits
corSpatial
Spatial Correlation Structure
summary.lmList
Summarize an lmList Object
ACF.lme
Autocorrelation Function for lme Residuals
residuals.lmList
Extract lmList Residuals
needUpdate
Check if Update is Needed
intervals
Confidence Intervals on Coefficients
Relaxin
Assay for Relaxin
coef.pdMat
pdMat Object Coefficients
pdClasses
Positive-Definite Matrix Classes
logDet.reStruct
Extract reStruct Log-Determinants
getCovariate.varFunc
Extract varFunc Covariate
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
coef.reStruct
reStruct Object Coefficients
recalc
Recalculate Condensed Linear Model Object
residuals.glsStruct
Calculate glsStruct Residuals
fdHess
Finite difference Hessian
phenoModel
Model function for the Phenobarb data
getCovariate
Extract Covariate from an Object
getGroups
Extract Grouping Factors from an Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
gls
Fit Linear Model Using Generalized Least Squares
plot.augPred
Plot an augPred Object
varFixed
Fixed Variance Function
getGroups.varFunc
Extract varFunc Groups
pdSymm
General Positive-Definite Matrix
lmeScale
Scale for lme Optimization
varConstPower
Constant Plus Power Variance Function
nlme
Nonlinear Mixed-Effects Models
summary.pdMat
Summarize a pdMat Object
simulate.lme
Simulate Results from
lme
Models
pdNatural
General Positive-Definite Matrix in Natural Parametrization
corCAR1
Continuous AR(1) Correlation Structure
summary.corStruct
Summarize a corStruct Object
summary.gls
Summarize a gls Object
getGroups.gls
Extract gls Object Groups
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getVarCov
Extract variance-covariance matrix
logLik.varFunc
Extract varFunc logLik
corCompSymm
Compound Symmetry Correlation Structure
recalc.reStruct
Recalculate for an reStruct Object
pooledSD
Extract Pooled Standard Deviation
predict.gnls
Predictions from a gnls Object
getResponse
Extract Response Variable from an Object
predict.lme
Predictions from an lme Object
residuals.lme
Extract lme Residuals
quinModel
Model function for the Quinidine data
varExp
Exponential Variance Function
logDet.corStruct
Extract corStruct Log-Determinant
nlsList
List of nls Objects with a Common Model
residuals.gnlsStruct
Calculate gnlsStruct Residuals
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Glucose
Glucose levels over time
getGroups.data.frame
Extract Groups from a Data Frame
glsObject
Fitted gls Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
update.modelStruct
Update a modelStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
pdConstruct
Construct pdMat Objects
getGroups.corStruct
Extract corStruct Groups
summary.lme
Summarize an lme Object
Wheat
Yields by growing conditions
lmeControl
Control Values for lme Fit
as.matrix.reStruct
Matrices of an reStruct Object
predict.lmList
Predictions from an lmList Object
summary.varFunc
Summarize varFunc Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
model.matrix.reStruct
reStruct Model Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.intervals.lmList
Plot lmList Confidence Intervals
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
Milk
Protein content of cows' milk
Names.pdMat
Names of a pdMat Object
getCovariate.data.frame
Extract Data Frame Covariate
getGroups.lme
Extract lme Object Groups
getCovariateFormula
Extract Covariates Formula
allCoef
Extract Coefficients from a Set of Objects
asTable
Convert groupedData to a matrix
plot.lme
Plot an lme or nls object
varFunc
Variance Function Structure
print.summary.pdMat
Print a summary.pdMat Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
pdMat
Positive-Definite Matrix
coef.modelStruct
Extract modelStruct Object Coefficients
pairs.lmList
Pairs Plot of an lmList Object
collapse.groupedData
Collapse a groupedData Object
corAR1
AR(1) Correlation Structure
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
plot.ranef.lme
Plot a ranef.lme Object
varPower
Power Variance Function
ranef.lme
Extract lme Random Effects
fitted.lmList
Extract lmList Fitted Values
formula.reStruct
Extract reStruct Object Formula
nlsList.selfStart
nlsList Fit from a selfStart Function
isInitialized
Check if Object is Initialized
pairs.compareFits
Pairs Plot of compareFits Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
plot.Variogram
Plot a Variogram Object
summary.modelStruct
Summarize a modelStruct Object
summary.nlsList
Summarize an nlsList Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
Wheat2
Wheat Yield Trials
bdf
Language scores
coef.varFunc
varFunc Object Coefficients
collapse
Collapse According to Groups
corFactor.corStruct
Factor of a corStruct Object Matrix
corARMA
ARMA(p,q) Correlation Structure
corClasses
Correlation Structure Classes
corMatrix.corStruct
Matrix of a corStruct Object
ergoStool
Ergometrics experiment with stool types
gapply
Apply a Function by Groups
getData
Extract Data from an Object
getResponseFormula
Extract Formula Specifying Response Variable
Dialyzer
High-Flux Hemodialyzer
lme
Linear Mixed-Effects Models
Names.reStruct
Names of an reStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
getData.lme
Extract lme Object Data
Glucose2
Glucose Levels Following Alcohol Ingestion
Initialize.glsStruct
Initialize a glsStruct Object
Pixel
X-ray pixel intensities over time
Matrix.reStruct
Assign reStruct Matrices
corMatrix
Extract Correlation Matrix
corRatio
Rational Quadratic Correlation Structure
getData.lmList
Extract lmList Object Data
PBG
Effect of Phenylbiguanide on Blood Pressure
Soybean
Growth of soybean plants
gnlsStruct
Generalized Nonlinear Least Squares Structure
lmeStruct
Linear Mixed-Effects Structure
plot.ACF
Plot an ACF Object
balancedGrouped
Create a groupedData object from a matrix
glsControl
Control Values for gls Fit
predict.gls
Predictions from a gls Object
pdLogChol
General Positive-Definite Matrix
varIdent
Constant Variance Function
pairs.lme
Pairs Plot of an lme Object
solve.reStruct
Apply Solve to an reStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
reStruct
Random Effects Structure
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.nmGroupedData
Plot an nmGroupedData Object
anova.gls
Compare Likelihoods of Fitted Objects
as.matrix.corStruct
Matrix of a corStruct Object
logDet
Extract the Logarithm of the Determinant
logLik.lme
Log-Likelihood of an lme Object
nlmeObject
Fitted nlme Object
plot.ranef.lmList
Plot a ranef.lmList Object
predict.nlme
Predictions from an nlme Object
recalc.corStruct
Recalculate for corStruct Object
Fatigue
Cracks caused by metal fatigue
Initialize.lmeStruct
Initialize an lmeStruct Object
MathAchieve
Mathematics achievement scores
Variogram.corExp
Calculate Semi-variogram for a corExp Object
corLin
Linear Correlation Structure
Dim.pdMat
Dimensions of a pdMat Object
coef.gnls
Extract gnls Coefficients
Oats
Split-plot Experiment on Varieties of Oats
glsStruct
Generalized Least Squares Structure
gsummary
Summarize by Groups
plot.compareFits
Plot a compareFits Object
recalc.modelStruct
Recalculate for a modelStruct Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
Dim.corStruct
Dimensions of a corStruct Object
print.varFunc
Print a varFunc Object
logLik.gnls
Log-Likelihood of a gnls Object
fixef.lmList
Extract lmList Fixed Effects