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nlme (version 3.1-106)
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
90,554
Version
3.1-106
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
December 6th, 2012
Functions in nlme (3.1-106)
Search all functions
Glucose2
Glucose Levels Following Alcohol Ingestion
ACF.gls
Autocorrelation Function for gls Residuals
Oxide
Variability in Semiconductor Manufacturing
BodyWeight
Rat weight over time for different diets
asTable
Convert groupedData to a matrix
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Orthodont
Growth curve data on an orthdontic measurement
corCompSymm
Compound Symmetry Correlation Structure
Initialize.corStruct
Initialize corStruct Object
Phenobarb
Phenobarbitol Kinetics
Dim
Extract Dimensions from an Object
collapse.groupedData
Collapse a groupedData Object
Rail
Evaluation of Stress in Railway Rails
Tetracycline2
Pharmacokinetics of tetracycline
corLin
Linear Correlation Structure
Earthquake
Earthquake Intensity
allCoef
Extract Coefficients from a Set of Objects
Covariate
Assign Covariate Values
Oats
Split-plot Experiment on Varieties of Oats
Covariate.varFunc
Assign varFunc Covariate
Relaxin
Assay for Relaxin
fixed.effects
Extract Fixed Effects
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Quinidine
Quinidine Kinetics
Fatigue
Cracks caused by metal fatigue
as.matrix.pdMat
Matrix of a pdMat Object
Initialize.reStruct
Initialize reStruct Object
Names.formula
Extract Names from a formula
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Dim.corSpatial
Dimensions of a corSpatial Object
MathAchieve
Mathematics achievement scores
coef.corStruct
Coefficients of a corStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
corClasses
Correlation Structure Classes
getGroups
Extract Grouping Factors from an Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
coef.lme
Extract lme Coefficients
fitted.lmeStruct
Calculate lmeStruct Fitted Values
Dim.pdMat
Dimensions of a pdMat Object
Oxboys
Heights of Boys in Oxford
Variogram.default
Calculate Semi-variogram
Gun
Methods for firing naval guns
corCAR1
Continuous AR(1) Correlation Structure
Soybean
Growth of soybean plants
coef.reStruct
reStruct Object Coefficients
Wafer
Modeling of Analog MOS Circuits
Initialize
Initialize Object
formula.pdMat
Extract pdMat Formula
[.pdMat
Subscript a pdMat Object
RatPupWeight
The weight of rat pups
Remifentanil
Pharmacokinetics of remifentanil
corFactor.corStruct
Factor of a corStruct Object Matrix
getGroups.varFunc
Extract varFunc Groups
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Pixel
X-ray pixel intensities over time
Glucose
Glucose levels over time
Dialyzer
High-Flux Hemodialyzer
balancedGrouped
Create a groupedData object from a matrix
coef.lmList
Extract lmList Coefficients
Initialize.varFunc
Initialize varFunc Object
coef.pdMat
pdMat Object Coefficients
PBG
Effect of Phenylbiguanide on Blood Pressure
corFactor
Factor of a Correlation Matrix
compareFits
Compare Fitted Objects
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
getCovariateFormula
Extract Covariates Formula
asOneFormula
Combine Formulas of a Set of Objects
anova.gls
Compare Likelihoods of Fitted Objects
Matrix
Assign Matrix Values
comparePred
Compare Predictions
fixef.lmList
Extract lmList Fixed Effects
coef.modelStruct
Extract modelStruct Object Coefficients
Machines
Productivity Scores for Machines and Workers
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Matrix.reStruct
Assign reStruct Matrices
Tetracycline1
Pharmacokinetics of tetracycline
corRatio
Rational Quadratic Correlation Structure
logDet.reStruct
Extract reStruct Log-Determinants
gsummary
Summarize by Groups
gnlsControl
Control Values for gnls Fit
corExp
Exponential Correlation Structure
getData
Extract Data from an Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
Muscle
Contraction of heart muscle sections
corSymm
General Correlation Structure
glsControl
Control Values for gls Fit
corMatrix.corStruct
Matrix of a corStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
corGaus
Gaussian Correlation Structure
intervals.lme
Confidence Intervals on lme Parameters
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
MathAchSchool
School demographic data for MathAchieve
Spruce
Growth of Spruce Trees
corSpher
Spherical Correlation Structure
logLik.lmList
Log-Likelihood of an lmList Object
getGroups.lme
Extract lme Object Groups
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
getCovariate.data.frame
Extract Data Frame Covariate
fitted.lme
Extract lme Fitted Values
fdHess
Finite difference Hessian
plot.nfnGroupedData
Plot an nfnGroupedData Object
fitted.lmList
Extract lmList Fitted Values
VarCorr
Extract variance and correlation components
recalc.reStruct
Recalculate for an reStruct Object
collapse
Collapse According to Groups
getCovariate.corStruct
Extract corStruct Object Covariate
plot.ranef.lme
Plot a ranef.lme Object
corAR1
AR(1) Correlation Structure
gnlsStruct
Generalized Nonlinear Least Squares Structure
getData.gls
Extract gls Object Data
getCovariate
Extract Covariate from an Object
intervals
Confidence Intervals on Coefficients
gapply
Apply a Function by Groups
groupedData
Construct a groupedData Object
corARMA
ARMA(p,q) Correlation Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
getResponseFormula
Extract Formula Specifying Response Variable
summary.modelStruct
Summarize a modelStruct Object
gnlsObject
Fitted gnls Object
nlme
Nonlinear Mixed-Effects Models
solve.reStruct
Apply Solve to an reStruct Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
plot.ACF
Plot an ACF Object
lmList
List of lm Objects with a Common Model
corNatural
General correlation in natural parameterization
getGroups.data.frame
Extract Groups from a Data Frame
lme.lmList
LME fit from lmList Object
nlsList.selfStart
nlsList Fit from a selfStart Function
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
pdSymm
General Positive-Definite Matrix
pairs.lmList
Pairs Plot of an lmList Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pairs.compareFits
Pairs Plot of compareFits Object
corMatrix
Extract Correlation Matrix
predict.nlme
Predictions from an nlme Object
getCovariate.varFunc
Extract varFunc Covariate
pdDiag
Diagonal Positive-Definite Matrix
recalc.varFunc
Recalculate for varFunc Object
summary.lmList
Summarize an lmList Object
quinModel
Model function for the Quinidine data
getGroupsFormula
Extract Grouping Formula
predict.lmList
Predictions from an lmList Object
isInitialized
Check if Object is Initialized
lmeScale
Scale for lme Optimization
isBalanced
Check a Design for Balance
glsObject
Fitted gls Object
splitFormula
Split a Formula
varClasses
Variance Function Classes
getData.lmList
Extract lmList Object Data
logDet.corStruct
Extract corStruct Log-Determinant
varWeights
Extract Variance Function Weights
glsStruct
Generalized Least Squares Structure
getData.lme
Extract lme Object Data
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
simulate.lme
Simulate Results from
lme
Models
plot.compareFits
Plot a compareFits Object
lme
Linear Mixed-Effects Models
residuals.lmList
Extract lmList Residuals
plot.Variogram
Plot a Variogram Object
ranef.lme
Extract lme Random Effects
lmList.groupedData
lmList Fit from a groupedData Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
logLik.gnls
Log-Likelihood of a gnls Object
residuals.glsStruct
Calculate glsStruct Residuals
lme.groupedData
LME fit from groupedData Object
needUpdate
Check if Update is Needed
varExp
Exponential Variance Function
logLik.lme
Log-Likelihood of an lme Object
pdConstruct
Construct pdMat Objects
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pairs.lme
Pairs Plot of an lme Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
varConstPower
Constant Plus Power Variance Function
lmeObject
Fitted lme Object
intervals.lmList
Confidence Intervals on lmList Coefficients
plot.lme
Plot an lme or nls object
plot.lmList
Plot an lmList Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
plot.nmGroupedData
Plot an nmGroupedData Object
recalc.modelStruct
Recalculate for a modelStruct Object
nlmeObject
Fitted nlme Object
pdClasses
Positive-Definite Matrix Classes
summary.nlsList
Summarize an nlsList Object
ranef.lmList
Extract lmList Random Effects
logDet
Extract the Logarithm of the Determinant
varIdent
Constant Variance Function
reStruct
Random Effects Structure
pdFactor
Square-Root Factor of a Positive-Definite Matrix
update.modelStruct
Update a modelStruct Object
varComb
Combination of Variance Functions
recalc.corStruct
Recalculate for corStruct Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
predict.gnls
Predictions from a gnls Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
summary.pdMat
Summarize a pdMat Object
varWeights.glsStruct
Variance Weights for glsStruct Object
intervals.gls
Confidence Intervals on gls Parameters
summary.lme
Summarize an lme Object
varPower
Power Variance Function
residuals.lmeStruct
Calculate lmeStruct Residuals
pooledSD
Extract Pooled Standard Deviation
residuals.nlmeStruct
Calculate nlmeStruct Residuals
plot.augPred
Plot an augPred Object
ACF
Autocorrelation Function
residuals.gnlsStruct
Calculate gnlsStruct Residuals
Variogram
Calculate Semi-variogram
varFunc
Variance Function Structure
summary.varFunc
Summarize varFunc Object
ACF.lme
Autocorrelation Function for lme Residuals
Initialize.glsStruct
Initialize a glsStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Names.pdBlocked
Names of a pdBlocked Object
ergoStool
Ergometrics experiment with stool types
Ovary
Counts of Ovarian Follicles
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
Milk
Protein content of cows' milk
formula.reStruct
Extract reStruct Object Formula
getVarCov
Extract variance-covariance matrix
model.matrix.reStruct
reStruct Model Matrix
getGroups.gls
Extract gls Object Groups
nlme.nlsList
NLME fit from nlsList Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.gls
Plot a gls Object
print.varFunc
Print a varFunc Object
predict.lme
Predictions from an lme Object
random.effects
Extract Random Effects
summary.corStruct
Summarize a corStruct Object
residuals.gls
Extract gls Residuals
recalc
Recalculate Condensed Linear Model Object
update.varFunc
Update varFunc Object
Meat
Tenderness of meat
Names
Names Associated with an Object
Names.reStruct
Names of an reStruct Object
Gasoline
Refinery yield of gasoline
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Wheat2
Wheat Yield Trials
bdf
Language scores
as.matrix.reStruct
Matrices of an reStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
corSpatial
Spatial Correlation Structure
Dim.corStruct
Dimensions of a corStruct Object
nlsList
List of nls Objects with a Common Model
nlmeControl
Control Values for nlme Fit
Initialize.lmeStruct
Initialize an lmeStruct Object
Names.pdMat
Names of a pdMat Object
coef.varFunc
varFunc Object Coefficients
plot.nffGroupedData
Plot an nffGroupedData Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
residuals.lme
Extract lme Residuals
print.summary.pdMat
Print a summary.pdMat Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
summary.gls
Summarize a gls Object
Assay
Bioassay on Cell Culture Plate
Coef
Assign Values to Coefficients
LDEsysMat
Generate system matrix for LDEs
Matrix.pdMat
Assign Matrix to a pdMat Object
augPred
Augmented Predictions
gls
Fit Linear Model Using Generalized Least Squares
lmeControl
Control Values for lme Fit
Nitrendipene
Assay of nitrendipene
formula.pdBlocked
Extract pdBlocked Formula
lmeStruct
Linear Mixed-Effects Structure
getGroups.corStruct
Extract corStruct Groups
logLik.varFunc
Extract varFunc logLik
getResponse
Extract Response Variable from an Object
IGF
Radioimmunoassay of IGF-I Protein
Wheat
Yields by growing conditions
Variogram.corExp
Calculate Semi-variogram for a corExp Object
pdMat
Positive-Definite Matrix
Cefamandole
Pharmacokinetics of Cefamandole
coef.gnls
Extract gnls Coefficients
pdBlocked
Positive-Definite Block Diagonal Matrix
phenoModel
Model function for the Phenobarb data
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.ranef.lmList
Plot a ranef.lmList Object
pdLogChol
General Positive-Definite Matrix
varFixed
Fixed Variance Function
predict.gls
Predictions from a gls Object
nlmeStruct
Nonlinear Mixed-Effects Structure
logLik.corStruct
Extract corStruct Log-Likelihood
getGroups.lmList
Extract lmList Object Groups