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nlme (version 3.1-112)
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
3.1-112
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
October 3rd, 2013
Functions in nlme (3.1-112)
Search all functions
Matrix
Assign Matrix Values
Meat
Tenderness of meat
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Matrix.reStruct
Assign reStruct Matrices
Gun
Methods for firing naval guns
Dim.corSpatial
Dimensions of a corSpatial Object
Dim
Extract Dimensions from an Object
LDEsysMat
Generate system matrix for LDEs
Glucose
Glucose levels over time
Cefamandole
Pharmacokinetics of Cefamandole
Phenobarb
Phenobarbitol Kinetics
Earthquake
Earthquake Intensity
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
RatPupWeight
The weight of rat pups
Quinidine
Quinidine Kinetics
Glucose2
Glucose Levels Following Alcohol Ingestion
Remifentanil
Pharmacokinetics of remifentanil
corMatrix.corStruct
Matrix of a corStruct Object
Rail
Evaluation of Stress in Railway Rails
corSymm
General Correlation Structure
Variogram.corLin
Calculate Semi-variogram for a corLin Object
nlme
Nonlinear Mixed-Effects Models
Fatigue
Cracks caused by metal fatigue
compareFits
Compare Fitted Objects
VarCorr
Extract variance and correlation components
intervals
Confidence Intervals on Coefficients
coef.varFunc
varFunc Object Coefficients
pdIdent
Multiple of the Identity Positive-Definite Matrix
ACF.gls
Autocorrelation Function for gls Residuals
corExp
Exponential Correlation Structure
getGroupsFormula
Extract Grouping Formula
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
MathAchieve
Mathematics achievement scores
pdConstruct
Construct pdMat Objects
update.modelStruct
Update a modelStruct Object
Initialize.varFunc
Initialize varFunc Object
Tetracycline1
Pharmacokinetics of tetracycline
Initialize.lmeStruct
Initialize an lmeStruct Object
Dim.corStruct
Dimensions of a corStruct Object
anova.gls
Compare Likelihoods of Fitted Objects
glsControl
Control Values for gls Fit
print.summary.pdMat
Print a summary.pdMat Object
lmeScale
Scale for lme Optimization
plot.gls
Plot a gls Object
Muscle
Contraction of heart muscle sections
glsStruct
Generalized Least Squares Structure
Names.pdBlocked
Names of a pdBlocked Object
Pixel
X-ray pixel intensities over time
Variogram.corExp
Calculate Semi-variogram for a corExp Object
corAR1
AR(1) Correlation Structure
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Wheat
Yields by growing conditions
lmeControl
Control Values for lme Fit
Tetracycline2
Pharmacokinetics of tetracycline
getVarCov
Extract variance-covariance matrix
Covariate.varFunc
Assign varFunc Covariate
PBG
Effect of Phenylbiguanide on Blood Pressure
lmeStruct
Linear Mixed-Effects Structure
corRatio
Rational Quadratic Correlation Structure
bdf
Language scores
coef.lmList
Extract lmList Coefficients
as.matrix.reStruct
Matrices of an reStruct Object
gls
Fit Linear Model Using Generalized Least Squares
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
coef.lme
Extract lme Coefficients
coef.pdMat
pdMat Object Coefficients
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Variogram
Calculate Semi-variogram
ergoStool
Ergometrics experiment with stool types
plot.ranef.lme
Plot a ranef.lme Object
Oxide
Variability in Semiconductor Manufacturing
logLik.varFunc
Extract varFunc logLik
fitted.lme
Extract lme Fitted Values
lme.groupedData
LME fit from groupedData Object
Relaxin
Assay for Relaxin
varFixed
Fixed Variance Function
as.matrix.corStruct
Matrix of a corStruct Object
pdMat
Positive-Definite Matrix
Soybean
Growth of soybean plants
getData
Extract Data from an Object
predict.gnls
Predictions from a gnls Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
summary.modelStruct
Summarize a modelStruct Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
corMatrix
Extract Correlation Matrix
corFactor.corStruct
Factor of a corStruct Object Matrix
formula.pdMat
Extract pdMat Formula
coef.reStruct
reStruct Object Coefficients
getGroups.gls
Extract gls Object Groups
Coef
Assign Values to Coefficients
nlme.nlsList
NLME fit from nlsList Object
getCovariate.varFunc
Extract varFunc Covariate
print.varFunc
Print a varFunc Object
as.matrix.pdMat
Matrix of a pdMat Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
plot.lmList
Plot an lmList Object
corSpatial
Spatial Correlation Structure
gls-internal
Auxiliary functions used by gls
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getCovariateFormula
Extract Covariates Formula
getData.gls
Extract gls Object Data
getGroups.lme
Extract lme Object Groups
summary.gls
Summarize a gls Object
fitted.glsStruct
Calculate glsStruct Fitted Values
anova.lme
Compare Likelihoods of Fitted Objects
nlsList
List of nls Objects with a Common Model
balancedGrouped
Create a groupedData object from a matrix
logLik.corStruct
Extract corStruct Log-Likelihood
pdLogChol
General Positive-Definite Matrix
pdSymm
General Positive-Definite Matrix
residuals.gnlsStruct
Calculate gnlsStruct Residuals
needUpdate
Check if Update is Needed
logLik.lme
Log-Likelihood of an lme Object
corARMA
ARMA(p,q) Correlation Structure
plot.lme
Plot an lme or nls object
gnlsObject
Fitted gnls Object
getGroups.data.frame
Extract Groups from a Data Frame
getResponseFormula
Extract Formula Specifying Response Variable
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
plot.nffGroupedData
Plot an nffGroupedData Object
getData.lmList
Extract lmList Object Data
fitted.lmList
Extract lmList Fitted Values
varExp
Exponential Variance Function
intervals.lmList
Confidence Intervals on lmList Coefficients
logDet.pdMat
Extract Log-Determinant from a pdMat Object
getResponse
Extract Response Variable from an Object
recalc.varFunc
Recalculate for varFunc Object
summary.lmList
Summarize an lmList Object
corNatural
General correlation in natural parameterization
varPower
Power Variance Function
getCovariate
Extract Covariate from an Object
plot.ranef.lmList
Plot a ranef.lmList Object
getGroups.corStruct
Extract corStruct Groups
residuals.gls
Extract gls Residuals
pdBlocked
Positive-Definite Block Diagonal Matrix
intervals.lme
Confidence Intervals on lme Parameters
recalc.corStruct
Recalculate for corStruct Object
summary.corStruct
Summarize a corStruct Object
logDet
Extract the Logarithm of the Determinant
recalc
Recalculate Condensed Linear Model Object
isInitialized
Check if Object is Initialized
gnlsStruct
Generalized Nonlinear Least Squares Structure
residuals.lmeStruct
Calculate lmeStruct Residuals
nlsList.selfStart
nlsList Fit from a selfStart Function
pdNatural
General Positive-Definite Matrix in Natural Parametrization
plot.compareFits
Plot a compareFits Object
groupedData
Construct a groupedData Object
lmList.groupedData
lmList Fit from a groupedData Object
ranef.lme
Extract lme Random Effects
pairs.lmList
Pairs Plot of an lmList Object
lme.lmList
LME fit from lmList Object
plot.Variogram
Plot a Variogram Object
pdDiag
Diagonal Positive-Definite Matrix
pdFactor
Square-Root Factor of a Positive-Definite Matrix
plot.augPred
Plot an augPred Object
predict.lme
Predictions from an lme Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
residuals.lme
Extract lme Residuals
ACF.lme
Autocorrelation Function for lme Residuals
Initialize.reStruct
Initialize reStruct Object
fixef.lmList
Extract lmList Fixed Effects
getGroups
Extract Grouping Factors from an Object
logLik.reStruct
Calculate reStruct Log-Likelihood
gnlsControl
Control Values for gnls Fit
nlmeStruct
Nonlinear Mixed-Effects Structure
[.pdMat
Subscript a pdMat Object
Machines
Productivity Scores for Machines and Workers
reStruct
Random Effects Structure
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
ACF
Autocorrelation Function
summary.varFunc
Summarize varFunc Object
varComb
Combination of Variance Functions
getCovariate.data.frame
Extract Data Frame Covariate
Milk
Protein content of cows' milk
Gasoline
Refinery yield of gasoline
fitted.lmeStruct
Calculate lmeStruct Fitted Values
Covariate
Assign Covariate Values
Variogram.default
Calculate Semi-variogram
intervals.gls
Confidence Intervals on gls Parameters
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Ovary
Counts of Ovarian Follicles
Oats
Split-plot Experiment on Varieties of Oats
Wheat2
Wheat Yield Trials
corGaus
Gaussian Correlation Structure
lmeObject
Fitted lme Object
coef.modelStruct
Extract modelStruct Object Coefficients
pdConstruct.pdBlocked
Construct pdBlocked Objects
formula.pdBlocked
Extract pdBlocked Formula
logLik.glsStruct
Log-Likelihood of a glsStruct Object
augPred
Augmented Predictions
Initialize
Initialize Object
corClasses
Correlation Structure Classes
varWeights
Extract Variance Function Weights
Names.formula
Extract Names from a formula
nlmeObject
Fitted nlme Object
quinModel
Model function for the Quinidine data
pdClasses
Positive-Definite Matrix Classes
recalc.modelStruct
Recalculate for a modelStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
summary.lme
Summarize an lme Object
asTable
Convert groupedData to a matrix
model.matrix.reStruct
reStruct Model Matrix
gapply
Apply a Function by Groups
coef.gnls
Extract gnls Coefficients
Initialize.corStruct
Initialize corStruct Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
plot.nmGroupedData
Plot an nmGroupedData Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
residuals.lmList
Extract lmList Residuals
getGroups.lmList
Extract lmList Object Groups
Assay
Bioassay on Cell Culture Plate
corSpher
Spherical Correlation Structure
collapse
Collapse According to Groups
logDet.corStruct
Extract corStruct Log-Determinant
isBalanced
Check a Design for Balance
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
phenoModel
Model function for the Phenobarb data
corLin
Linear Correlation Structure
corFactor
Factor of a Correlation Matrix
Nitrendipene
Assay of nitrendipene
BodyWeight
Rat weight over time for different diets
nlmeControl
Control Values for nlme Fit
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
Orthodont
Growth curve data on an orthdontic measurement
random.effects
Extract Random Effects
coef.corStruct
Coefficients of a corStruct Object
IGF
Radioimmunoassay of IGF-I Protein
pairs.lme
Pairs Plot of an lme Object
splitFormula
Split a Formula
corCAR1
Continuous AR(1) Correlation Structure
varIdent
Constant Variance Function
lmList
List of lm Objects with a Common Model
getData.lme
Extract lme Object Data
allCoef
Extract Coefficients from a Set of Objects
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
varWeights.glsStruct
Variance Weights for glsStruct Object
update.varFunc
Update varFunc Object
pooledSD
Extract Pooled Standard Deviation
predict.gls
Predictions from a gls Object
Names
Names Associated with an Object
ranef.lmList
Extract lmList Random Effects
plot.intervals.lmList
Plot lmList Confidence Intervals
varClasses
Variance Function Classes
predict.nlme
Predictions from an nlme Object
simulate.lme
Simulate Results from
lme
Models
Names.reStruct
Names of an reStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
plot.ACF
Plot an ACF Object
predict.lmList
Predictions from an lmList Object
Dim.pdMat
Dimensions of a pdMat Object
Names.pdMat
Names of a pdMat Object
gsummary
Summarize by Groups
lme
Linear Mixed-Effects Models
varWeights.lmeStruct
Variance Weights for lmeStruct Object
MathAchSchool
School demographic data for MathAchieve
Spruce
Growth of Spruce Trees
Wafer
Modeling of Analog MOS Circuits
asOneFormula
Combine Formulas of a Set of Objects
glsObject
Fitted gls Object
getGroups.varFunc
Extract varFunc Groups
comparePred
Compare Predictions
pairs.compareFits
Pairs Plot of compareFits Object
solve.reStruct
Apply Solve to an reStruct Object
summary.nlsList
Summarize an nlsList Object
varConstPower
Constant Plus Power Variance Function
Matrix.pdMat
Assign Matrix to a pdMat Object
summary.pdMat
Summarize a pdMat Object
fixed.effects
Extract Fixed Effects
collapse.groupedData
Collapse a groupedData Object
recalc.reStruct
Recalculate for an reStruct Object
Oxboys
Heights of Boys in Oxford
getCovariate.corStruct
Extract corStruct Object Covariate
gnls
Fit Nonlinear Model Using Generalized Least Squares
fdHess
Finite difference Hessian
varFunc
Variance Function Structure
Dialyzer
High-Flux Hemodialyzer
formula.reStruct
Extract reStruct Object Formula
corCompSymm
Compound Symmetry Correlation Structure
logDet.reStruct
Extract reStruct Log-Determinants
Initialize.glsStruct
Initialize a glsStruct Object
logLik.lmList
Log-Likelihood of an lmList Object