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nlme (version 3.1-115)
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
3.1-115
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
March 9th, 2014
Functions in nlme (3.1-115)
Search all functions
augPred
Augmented Predictions
ACF.gls
Autocorrelation Function for gls Residuals
intervals
Confidence Intervals on Coefficients
nlmeStruct
Nonlinear Mixed-Effects Structure
plot.compareFits
Plot a compareFits Object
MathAchieve
Mathematics achievement scores
plot.ACF
Plot an ACF Object
ranef.lme
Extract lme Random Effects
corLin
Linear Correlation Structure
lmeObject
Fitted lme Object
logDet
Extract the Logarithm of the Determinant
lme.lmList
LME fit from lmList Object
recalc.reStruct
Recalculate for an reStruct Object
Variogram.default
Calculate Semi-variogram
predict.gnls
Predictions from a gnls Object
summary.gls
Summarize a gls Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
IGF
Radioimmunoassay of IGF-I Protein
Names.pdBlocked
Names of a pdBlocked Object
gls
Fit Linear Model Using Generalized Least Squares
glsStruct
Generalized Least Squares Structure
asTable
Convert groupedData to a matrix
logDet.pdMat
Extract Log-Determinant from a pdMat Object
corClasses
Correlation Structure Classes
corSpatial
Spatial Correlation Structure
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
getGroups.lme
Extract lme Object Groups
logLik.lme
Log-Likelihood of an lme Object
Cefamandole
Pharmacokinetics of Cefamandole
BodyWeight
Rat weight over time for different diets
Names.pdMat
Names of a pdMat Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
corExp
Exponential Correlation Structure
Initialize.varFunc
Initialize varFunc Object
Tetracycline1
Pharmacokinetics of tetracycline
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
plot.lmList
Plot an lmList Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
Glucose
Glucose levels over time
coef.gnls
Extract gnls Coefficients
gnlsObject
Fitted gnls Object
corFactor
Factor of a Correlation Matrix
Milk
Protein content of cows' milk
fdHess
Finite difference Hessian
nlme.nlsList
NLME fit from nlsList Object
varClasses
Variance Function Classes
Wheat2
Wheat Yield Trials
Muscle
Contraction of heart muscle sections
coef.lme
Extract lme Coefficients
plot.intervals.lmList
Plot lmList Confidence Intervals
Meat
Tenderness of meat
getData.gls
Extract gls Object Data
pairs.lme
Pairs Plot of an lme Object
corNatural
General correlation in natural parameterization
gnls
Fit Nonlinear Model Using Generalized Least Squares
needUpdate
Check if Update is Needed
gnlsStruct
Generalized Nonlinear Least Squares Structure
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
RatPupWeight
The weight of rat pups
Spruce
Growth of Spruce Trees
corMatrix
Extract Correlation Matrix
pdLogChol
General Positive-Definite Matrix
lmList.groupedData
lmList Fit from a groupedData Object
as.matrix.reStruct
Matrices of an reStruct Object
coef.varFunc
varFunc Object Coefficients
Oats
Split-plot Experiment on Varieties of Oats
Earthquake
Earthquake Intensity
getGroups.lmList
Extract lmList Object Groups
Assay
Bioassay on Cell Culture Plate
Initialize.lmeStruct
Initialize an lmeStruct Object
gsummary
Summarize by Groups
VarCorr
Extract variance and correlation components
nlsList
List of nls Objects with a Common Model
pdConstruct
Construct pdMat Objects
Dim.corStruct
Dimensions of a corStruct Object
getData
Extract Data from an Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
Covariate.varFunc
Assign varFunc Covariate
[.pdMat
Subscript a pdMat Object
Names.formula
Extract Names from a formula
pdBlocked
Positive-Definite Block Diagonal Matrix
predict.gls
Predictions from a gls Object
varConstPower
Constant Plus Power Variance Function
getCovariate
Extract Covariate from an Object
summary.varFunc
Summarize varFunc Object
corRatio
Rational Quadratic Correlation Structure
getVarCov
Extract variance-covariance matrix
logDet.corStruct
Extract corStruct Log-Determinant
Initialize.corStruct
Initialize corStruct Object
Ovary
Counts of Ovarian Follicles
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
MathAchSchool
School demographic data for MathAchieve
corSpher
Spherical Correlation Structure
logLik.reStruct
Calculate reStruct Log-Likelihood
fixef.lmList
Extract lmList Fixed Effects
quinModel
Model function for the Quinidine data
fixed.effects
Extract Fixed Effects
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
PBG
Effect of Phenylbiguanide on Blood Pressure
as.matrix.pdMat
Matrix of a pdMat Object
summary.lme
Summarize an lme Object
logLik.corStruct
Extract corStruct Log-Likelihood
pdClasses
Positive-Definite Matrix Classes
predict.nlme
Predictions from an nlme Object
print.summary.pdMat
Print a summary.pdMat Object
getGroupsFormula
Extract Grouping Formula
coef.lmList
Extract lmList Coefficients
pdDiag
Diagonal Positive-Definite Matrix
residuals.lme
Extract lme Residuals
summary.pdMat
Summarize a pdMat Object
formula.reStruct
Extract reStruct Object Formula
isBalanced
Check a Design for Balance
Dim.pdMat
Dimensions of a pdMat Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
summary.nlsList
Summarize an nlsList Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
Coef
Assign Values to Coefficients
recalc
Recalculate Condensed Linear Model Object
lme.groupedData
LME fit from groupedData Object
nlmeControl
Control Values for nlme Fit
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Dim
Extract Dimensions from an Object
random.effects
Extract Random Effects
pdSymm
General Positive-Definite Matrix
Dim.corSpatial
Dimensions of a corSpatial Object
ACF
Autocorrelation Function
Glucose2
Glucose Levels Following Alcohol Ingestion
LDEsysMat
Generate system matrix for LDEs
corSymm
General Correlation Structure
pooledSD
Extract Pooled Standard Deviation
residuals.nlmeStruct
Calculate nlmeStruct Residuals
update.varFunc
Update varFunc Object
collapse.groupedData
Collapse a groupedData Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
getCovariate.corStruct
Extract corStruct Object Covariate
getCovariateFormula
Extract Covariates Formula
ergoStool
Ergometrics experiment with stool types
formula.pdMat
Extract pdMat Formula
pairs.lmList
Pairs Plot of an lmList Object
corCompSymm
Compound Symmetry Correlation Structure
summary.modelStruct
Summarize a modelStruct Object
Initialize.reStruct
Initialize reStruct Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
corARMA
ARMA(p,q) Correlation Structure
gapply
Apply a Function by Groups
anova.gls
Compare Likelihoods of Fitted Objects
allCoef
Extract Coefficients from a Set of Objects
getData.lmList
Extract lmList Object Data
Tetracycline2
Pharmacokinetics of tetracycline
intervals.lme
Confidence Intervals on lme Parameters
predict.lmList
Predictions from an lmList Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
comparePred
Compare Predictions
fitted.lme
Extract lme Fitted Values
formula.pdBlocked
Extract pdBlocked Formula
Remifentanil
Pharmacokinetics of remifentanil
coef.modelStruct
Extract modelStruct Object Coefficients
intervals.lmList
Confidence Intervals on lmList Coefficients
logLik.glsStruct
Log-Likelihood of a glsStruct Object
lmList
List of lm Objects with a Common Model
varWeights.glsStruct
Variance Weights for glsStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
varFunc
Variance Function Structure
plot.lme
Plot an lme or nls object
lmeStruct
Linear Mixed-Effects Structure
Initialize.glsStruct
Initialize a glsStruct Object
isInitialized
Check if Object is Initialized
nlmeObject
Fitted nlme Object
nlsList.selfStart
nlsList Fit from a selfStart Function
logLik.lmList
Log-Likelihood of an lmList Object
Wheat
Yields by growing conditions
pdIdent
Multiple of the Identity Positive-Definite Matrix
plot.augPred
Plot an augPred Object
as.matrix.corStruct
Matrix of a corStruct Object
plot.ranef.lmList
Plot a ranef.lmList Object
Soybean
Growth of soybean plants
corAR1
AR(1) Correlation Structure
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
reStruct
Random Effects Structure
getGroups.corStruct
Extract corStruct Groups
plot.nmGroupedData
Plot an nmGroupedData Object
glsObject
Fitted gls Object
bdf
Language scores
Machines
Productivity Scores for Machines and Workers
lmeControl
Control Values for lme Fit
balancedGrouped
Create a groupedData object from a matrix
varWeights
Extract Variance Function Weights
phenoModel
Model function for the Phenobarb data
plot.nfnGroupedData
Plot an nfnGroupedData Object
varExp
Exponential Variance Function
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
logDet.reStruct
Extract reStruct Log-Determinants
varComb
Combination of Variance Functions
qqnorm.gls
Normal Plot of Residuals from a gls Object
residuals.lmList
Extract lmList Residuals
Fatigue
Cracks caused by metal fatigue
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Covariate
Assign Covariate Values
asOneFormula
Combine Formulas of a Set of Objects
corGaus
Gaussian Correlation Structure
getGroups
Extract Grouping Factors from an Object
Matrix
Assign Matrix Values
Wafer
Modeling of Analog MOS Circuits
getGroups.gls
Extract gls Object Groups
coef.reStruct
reStruct Object Coefficients
anova.lme
Compare Likelihoods of Fitted Objects
plot.nffGroupedData
Plot an nffGroupedData Object
logLik.varFunc
Extract varFunc logLik
residuals.gls
Extract gls Residuals
Initialize
Initialize Object
Gun
Methods for firing naval guns
recalc.modelStruct
Recalculate for a modelStruct Object
splitFormula
Split a Formula
varPower
Power Variance Function
Oxide
Variability in Semiconductor Manufacturing
coef.corStruct
Coefficients of a corStruct Object
gnlsControl
Control Values for gnls Fit
Oxboys
Heights of Boys in Oxford
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
nlme
Nonlinear Mixed-Effects Models
compareFits
Compare Fitted Objects
corMatrix.corStruct
Matrix of a corStruct Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
model.matrix.reStruct
reStruct Model Matrix
Pixel
X-ray pixel intensities over time
gls-internal
Auxiliary functions used by gls
pdMat
Positive-Definite Matrix
getGroups.varFunc
Extract varFunc Groups
Names
Names Associated with an Object
Names.reStruct
Names of an reStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
Relaxin
Assay for Relaxin
corCAR1
Continuous AR(1) Correlation Structure
print.varFunc
Print a varFunc Object
glsControl
Control Values for gls Fit
recalc.corStruct
Recalculate for corStruct Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
summary.corStruct
Summarize a corStruct Object
summary.lmList
Summarize an lmList Object
pairs.compareFits
Pairs Plot of compareFits Object
predict.lme
Predictions from an lme Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Nitrendipene
Assay of nitrendipene
Dialyzer
High-Flux Hemodialyzer
plot.ranef.lme
Plot a ranef.lme Object
update.modelStruct
Update a modelStruct Object
Gasoline
Refinery yield of gasoline
collapse
Collapse According to Groups
coef.pdMat
pdMat Object Coefficients
plot.Variogram
Plot a Variogram Object
getGroups.data.frame
Extract Groups from a Data Frame
varIdent
Constant Variance Function
varFixed
Fixed Variance Function
Matrix.reStruct
Assign reStruct Matrices
Matrix.pdMat
Assign Matrix to a pdMat Object
Rail
Evaluation of Stress in Railway Rails
getData.lme
Extract lme Object Data
Phenobarb
Phenobarbitol Kinetics
Variogram
Calculate Semi-variogram
fitted.lmList
Extract lmList Fitted Values
Orthodont
Growth curve data on an orthdontic measurement
Quinidine
Quinidine Kinetics
groupedData
Construct a groupedData Object
simulate.lme
Simulate Results from
lme
Models
lme
Linear Mixed-Effects Models
intervals.gls
Confidence Intervals on gls Parameters
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
solve.reStruct
Apply Solve to an reStruct Object
residuals.lmeStruct
Calculate lmeStruct Residuals
getCovariate.varFunc
Extract varFunc Covariate
getCovariate.data.frame
Extract Data Frame Covariate
recalc.varFunc
Recalculate for varFunc Object
ACF.lme
Autocorrelation Function for lme Residuals
getResponseFormula
Extract Formula Specifying Response Variable
plot.gls
Plot a gls Object
getResponse
Extract Response Variable from an Object
corFactor.corStruct
Factor of a corStruct Object Matrix
varWeights.lmeStruct
Variance Weights for lmeStruct Object
ranef.lmList
Extract lmList Random Effects