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nlme (version 3.1-121)
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
3.1-121
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
June 29th, 2015
Functions in nlme (3.1-121)
Search all functions
varPower
Power Variance Function
varWeights
Extract Variance Function Weights
BodyWeight
Rat weight over time for different diets
Dim.pdMat
Dimensions of a pdMat Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Dim
Extract Dimensions from an Object
Glucose
Glucose levels over time
Initialize.reStruct
Initialize reStruct Object
Gasoline
Refinery yield of gasoline
Fatigue
Cracks caused by metal fatigue
Initialize.corStruct
Initialize corStruct Object
MathAchieve
Mathematics achievement scores
Names.pdBlocked
Names of a pdBlocked Object
Oxboys
Heights of Boys in Oxford
Rail
Evaluation of Stress in Railway Rails
PBG
Effect of Phenylbiguanide on Blood Pressure
Phenobarb
Phenobarbitol Kinetics
Soybean
Growth of soybean plants
Initialize.lmeStruct
Initialize an lmeStruct Object
Relaxin
Assay for Relaxin
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Spruce
Growth of Spruce Trees
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Wheat
Yields by growing conditions
anova.gls
Compare Likelihoods of Fitted Objects
Wheat2
Wheat Yield Trials
coef.varFunc
varFunc Object Coefficients
coef.pdMat
pdMat Object Coefficients
coef.gnls
Extract gnls Coefficients
corCompSymm
Compound Symmetry Correlation Structure
corRatio
Rational Quadratic Correlation Structure
corGaus
Gaussian Correlation Structure
compareFits
Compare Fitted Objects
corExp
Exponential Correlation Structure
corSpatial
Spatial Correlation Structure
corMatrix.corStruct
Matrix of a corStruct Object
corARMA
ARMA(p,q) Correlation Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
corSpher
Spherical Correlation Structure
getCovariate.data.frame
Extract Data Frame Covariate
getData.gls
Extract gls Object Data
formula.reStruct
Extract reStruct Object Formula
getGroups.corStruct
Extract corStruct Groups
getGroups.data.frame
Extract Groups from a Data Frame
getGroups.varFunc
Extract varFunc Groups
getGroups.lmList
Extract lmList Object Groups
glsControl
Control Values for gls Fit
getGroups.lme
Extract lme Object Groups
getResponse
Extract Response Variable from an Object
gls
Fit Linear Model Using Generalized Least Squares
getData.lmList
Extract lmList Object Data
glsStruct
Generalized Least Squares Structure
isInitialized
Check if Object is Initialized
gnlsControl
Control Values for gnls Fit
isBalanced
Check a Design for Balance
gls-internal
Auxiliary functions used by gls
lmeObject
Fitted lme Object
logDet
Extract the Logarithm of the Determinant
logDet.corStruct
Extract corStruct Log-Determinant
lme.lmList
LME fit from lmList Object
logLik.corStruct
Extract corStruct Log-Likelihood
getGroups.gls
Extract gls Object Groups
logLik.lme
Log-Likelihood of an lme Object
logLik.varFunc
Extract varFunc logLik
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
needUpdate
Check if Update is Needed
model.matrix.reStruct
reStruct Model Matrix
pdBlocked
Positive-Definite Block Diagonal Matrix
pdDiag
Diagonal Positive-Definite Matrix
plot.ACF
Plot an ACF Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pdSymm
General Positive-Definite Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.Variogram
Plot a Variogram Object
plot.augPred
Plot an augPred Object
plot.lmList
Plot an lmList Object
plot.nmGroupedData
Plot an nmGroupedData Object
plot.compareFits
Plot a compareFits Object
plot.ranef.lmList
Plot a ranef.lmList Object
pooledSD
Extract Pooled Standard Deviation
plot.ranef.lme
Plot a ranef.lme Object
predict.gls
Predictions from a gls Object
plot.nffGroupedData
Plot an nffGroupedData Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
ranef.lme
Extract lme Random Effects
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.lmList
Extract lmList Residuals
summary.corStruct
Summarize a corStruct Object
simulate.lme
Simulate Results from
lme
Models
residuals.nlmeStruct
Calculate nlmeStruct Residuals
residuals.lmeStruct
Calculate lmeStruct Residuals
splitFormula
Split a Formula
summary.nlsList
Summarize an nlsList Object
summary.pdMat
Summarize a pdMat Object
varFixed
Fixed Variance Function
varExp
Exponential Variance Function
varComb
Combination of Variance Functions
[.pdMat
Subscript a pdMat Object
Ovary
Counts of Ovarian Follicles
Nitrendipene
Assay of nitrendipene
Tetracycline1
Pharmacokinetics of tetracycline
Cefamandole
Pharmacokinetics of Cefamandole
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Dim.corStruct
Dimensions of a corStruct Object
Dim.corSpatial
Dimensions of a corSpatial Object
corSymm
General Correlation Structure
LDEsysMat
Generate system matrix for LDEs
lmList
List of lm Objects with a Common Model
Assay
Bioassay on Cell Culture Plate
Dialyzer
High-Flux Hemodialyzer
coef.corStruct
Coefficients of a corStruct Object
Matrix
Assign Matrix Values
getResponseFormula
Extract Formula Specifying Response Variable
Machines
Productivity Scores for Machines and Workers
collapse.groupedData
Collapse a groupedData Object
Orthodont
Growth curve data on an orthdontic measurement
VarCorr
Extract variance and correlation components
Oxide
Variability in Semiconductor Manufacturing
Initialize
Initialize Object
MathAchSchool
School demographic data for MathAchieve
Wafer
Modeling of Analog MOS Circuits
pdMat
Positive-Definite Matrix
fitted.lme
Extract lme Fitted Values
ACF.gls
Autocorrelation Function for gls Residuals
RatPupWeight
The weight of rat pups
Gun
Methods for firing naval guns
Initialize.varFunc
Initialize varFunc Object
Quinidine
Quinidine Kinetics
Matrix.pdMat
Assign Matrix to a pdMat Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Names
Names Associated with an Object
Oats
Split-plot Experiment on Varieties of Oats
gsummary
Summarize by Groups
Pixel
X-ray pixel intensities over time
Initialize.glsStruct
Initialize a glsStruct Object
getData
Extract Data from an Object
Remifentanil
Pharmacokinetics of remifentanil
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
logLik.gnls
Log-Likelihood of a gnls Object
intervals.lme
Confidence Intervals on lme Parameters
update.varFunc
Update varFunc Object
corFactor
Factor of a Correlation Matrix
getGroupsFormula
Extract Grouping Formula
phenoModel
Model function for the Phenobarb data
glsObject
Fitted gls Object
gnlsObject
Fitted gnls Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Variogram.default
Calculate Semi-variogram
Milk
Protein content of cows' milk
getCovariate.corStruct
Extract corStruct Object Covariate
getData.lme
Extract lme Object Data
Names.formula
Extract Names from a formula
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
allCoef
Extract Coefficients from a Set of Objects
as.matrix.corStruct
Matrix of a corStruct Object
Earthquake
Earthquake Intensity
anova.lme
Compare Likelihoods of Fitted Objects
Covariate
Assign Covariate Values
bdf
Language scores
Coef
Assign Values to Coefficients
Names.reStruct
Names of an reStruct Object
corAR1
AR(1) Correlation Structure
augPred
Augmented Predictions
Tetracycline2
Pharmacokinetics of tetracycline
pairs.lme
Pairs Plot of an lme Object
IGF
Radioimmunoassay of IGF-I Protein
comparePred
Compare Predictions
balancedGrouped
Create a groupedData object from a matrix
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdIdent
Multiple of the Identity Positive-Definite Matrix
logLik.reStruct
Calculate reStruct Log-Likelihood
Variogram
Calculate Semi-variogram
intervals.gls
Confidence Intervals on gls Parameters
summary.gls
Summarize a gls Object
recalc.modelStruct
Recalculate for a modelStruct Object
logDet.reStruct
Extract reStruct Log-Determinants
asTable
Convert groupedData to a matrix
asOneFormula
Combine Formulas of a Set of Objects
plot.gls
Plot a gls Object
lmList.groupedData
lmList Fit from a groupedData Object
ergoStool
Ergometrics experiment with stool types
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
pairs.compareFits
Pairs Plot of compareFits Object
Meat
Tenderness of meat
pdConstruct.pdBlocked
Construct pdBlocked Objects
update.modelStruct
Update a modelStruct Object
print.varFunc
Print a varFunc Object
corMatrix
Extract Correlation Matrix
fdHess
Finite difference Hessian
gnlsStruct
Generalized Nonlinear Least Squares Structure
pdFactor
Square-Root Factor of a Positive-Definite Matrix
corClasses
Correlation Structure Classes
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
Names.pdMat
Names of a pdMat Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
nlmeControl
Control Values for nlme Fit
getCovariateFormula
Extract Covariates Formula
corCAR1
Continuous AR(1) Correlation Structure
intervals
Confidence Intervals on Coefficients
fixef.lmList
Extract lmList Fixed Effects
gapply
Apply a Function by Groups
predict.nlme
Predictions from an nlme Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
pairs.lmList
Pairs Plot of an lmList Object
summary.lmList
Summarize an lmList Object
recalc
Recalculate Condensed Linear Model Object
coef.reStruct
reStruct Object Coefficients
lmeStruct
Linear Mixed-Effects Structure
as.matrix.reStruct
Matrices of an reStruct Object
getCovariate
Extract Covariate from an Object
fitted.lmList
Extract lmList Fitted Values
ACF.lme
Autocorrelation Function for lme Residuals
summary.varFunc
Summarize varFunc Object
formula.pdMat
Extract pdMat Formula
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
fixed.effects
Extract Fixed Effects
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
nlmeObject
Fitted nlme Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
getGroups
Extract Grouping Factors from an Object
logLik.lmList
Log-Likelihood of an lmList Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
ACF
Autocorrelation Function
pdConstruct
Construct pdMat Objects
nlme
Nonlinear Mixed-Effects Models
varWeights.glsStruct
Variance Weights for glsStruct Object
recalc.varFunc
Recalculate for varFunc Object
nlsList.selfStart
nlsList Fit from a selfStart Function
varFunc
Variance Function Structure
varConstPower
Constant Plus Power Variance Function
Covariate.varFunc
Assign varFunc Covariate
nlmeStruct
Nonlinear Mixed-Effects Structure
varIdent
Constant Variance Function
coef.lmList
Extract lmList Coefficients
logDet.pdMat
Extract Log-Determinant from a pdMat Object
print.summary.pdMat
Print a summary.pdMat Object
getCovariate.varFunc
Extract varFunc Covariate
plot.nfnGroupedData
Plot an nfnGroupedData Object
residuals.lme
Extract lme Residuals
summary.modelStruct
Summarize a modelStruct Object
Matrix.reStruct
Assign reStruct Matrices
fitted.lmeStruct
Calculate lmeStruct Fitted Values
qqnorm.gls
Normal Plot of Residuals from a gls Object
solve.reStruct
Apply Solve to an reStruct Object
corLin
Linear Correlation Structure
Muscle
Contraction of heart muscle sections
random.effects
Extract Random Effects
quinModel
Model function for the Quinidine data
recalc.corStruct
Recalculate for corStruct Object
ranef.lmList
Extract lmList Random Effects
formula.pdBlocked
Extract pdBlocked Formula
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
summary.lme
Summarize an lme Object
lme.groupedData
LME fit from groupedData Object
as.matrix.pdMat
Matrix of a pdMat Object
corFactor.corStruct
Factor of a corStruct Object Matrix
pdClasses
Positive-Definite Matrix Classes
corNatural
General correlation in natural parameterization
intervals.lmList
Confidence Intervals on lmList Coefficients
coef.modelStruct
Extract modelStruct Object Coefficients
predict.gnls
Predictions from a gnls Object
predict.lmList
Predictions from an lmList Object
recalc.reStruct
Recalculate for an reStruct Object
getVarCov
Extract variance-covariance matrix
collapse
Collapse According to Groups
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
groupedData
Construct a groupedData Object
nlme.nlsList
NLME fit from nlsList Object
plot.intervals.lmList
Plot lmList Confidence Intervals
pdLogChol
General Positive-Definite Matrix
lme
Linear Mixed-Effects Models
reStruct
Random Effects Structure
residuals.glsStruct
Calculate glsStruct Residuals
predict.lme
Predictions from an lme Object
plot.lme
Plot an lme or nls object
varClasses
Variance Function Classes
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
coef.lme
Extract lme Coefficients
lmeControl
Control Values for lme Fit
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
nlsList
List of nls Objects with a Common Model
residuals.gls
Extract gls Residuals