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nlme (version 3.1-108)
Linear and Nonlinear Mixed Effects Models
Description
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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Install
install.packages('nlme')
Monthly Downloads
98,563
Version
3.1-108
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
January 27th, 2013
Functions in nlme (3.1-108)
Search functions
Covariate
Assign Covariate Values
BodyWeight
Rat weight over time for different diets
Coef
Assign Values to Coefficients
Machines
Productivity Scores for Machines and Workers
Variogram.default
Calculate Semi-variogram
Gasoline
Refinery yield of gasoline
LDEsysMat
Generate system matrix for LDEs
ACF
Autocorrelation Function
MathAchieve
Mathematics achievement scores
VarCorr
Extract variance and correlation components
Initialize.corStruct
Initialize corStruct Object
allCoef
Extract Coefficients from a Set of Objects
Covariate.varFunc
Assign varFunc Covariate
coef.modelStruct
Extract modelStruct Object Coefficients
Matrix.reStruct
Assign reStruct Matrices
Fatigue
Cracks caused by metal fatigue
PBG
Effect of Phenylbiguanide on Blood Pressure
corAR1
AR(1) Correlation Structure
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Initialize.glsStruct
Initialize a glsStruct Object
collapse
Collapse According to Groups
anova.lme
Compare Likelihoods of Fitted Objects
Meat
Tenderness of meat
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
lmList.groupedData
lmList Fit from a groupedData Object
fitted.glsStruct
Calculate glsStruct Fitted Values
coef.gnls
Extract gnls Coefficients
Ovary
Counts of Ovarian Follicles
Wheat2
Wheat Yield Trials
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
Glucose2
Glucose Levels Following Alcohol Ingestion
[.pdMat
Subscript a pdMat Object
Wafer
Modeling of Analog MOS Circuits
Initialize
Initialize Object
Initialize.varFunc
Initialize varFunc Object
getData
Extract Data from an Object
getGroups.lme
Extract lme Object Groups
Oats
Split-plot Experiment on Varieties of Oats
Names
Names Associated with an Object
corExp
Exponential Correlation Structure
Dim.pdMat
Dimensions of a pdMat Object
Orthodont
Growth curve data on an orthdontic measurement
Glucose
Glucose levels over time
getGroups.corStruct
Extract corStruct Groups
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Spruce
Growth of Spruce Trees
coef.pdMat
pdMat Object Coefficients
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
corSpatial
Spatial Correlation Structure
corSpher
Spherical Correlation Structure
getGroups.gls
Extract gls Object Groups
as.matrix.reStruct
Matrices of an reStruct Object
Nitrendipene
Assay of nitrendipene
logLik.glsStruct
Log-Likelihood of a glsStruct Object
predict.gnls
Predictions from a gnls Object
logLik.lmList
Log-Likelihood of an lmList Object
formula.pdBlocked
Extract pdBlocked Formula
formula.reStruct
Extract reStruct Object Formula
nlme.nlsList
NLME fit from nlsList Object
lme.lmList
LME fit from lmList Object
getCovariate.varFunc
Extract varFunc Covariate
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
fixed.effects
Extract Fixed Effects
nlmeStruct
Nonlinear Mixed-Effects Structure
getGroups.varFunc
Extract varFunc Groups
phenoModel
Model function for the Phenobarb data
collapse.groupedData
Collapse a groupedData Object
pdSymm
General Positive-Definite Matrix
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
pdConstruct
Construct pdMat Objects
getResponse
Extract Response Variable from an Object
gsummary
Summarize by Groups
Cefamandole
Pharmacokinetics of Cefamandole
Wheat
Yields by growing conditions
logLik.lme
Log-Likelihood of an lme Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
quinModel
Model function for the Quinidine data
ACF.gls
Autocorrelation Function for gls Residuals
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
augPred
Augmented Predictions
ergoStool
Ergometrics experiment with stool types
print.summary.pdMat
Print a summary.pdMat Object
isBalanced
Check a Design for Balance
lme
Linear Mixed-Effects Models
logDet
Extract the Logarithm of the Determinant
Matrix.pdMat
Assign Matrix to a pdMat Object
glsStruct
Generalized Least Squares Structure
nlmeObject
Fitted nlme Object
plot.lme
Plot an lme or nls object
groupedData
Construct a groupedData Object
update.modelStruct
Update a modelStruct Object
varIdent
Constant Variance Function
Muscle
Contraction of heart muscle sections
corLin
Linear Correlation Structure
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
summary.lmList
Summarize an lmList Object
Matrix
Assign Matrix Values
corMatrix
Extract Correlation Matrix
coef.varFunc
varFunc Object Coefficients
corMatrix.corStruct
Matrix of a corStruct Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
solve.reStruct
Apply Solve to an reStruct Object
pairs.lme
Pairs Plot of an lme Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
coef.reStruct
reStruct Object Coefficients
plot.intervals.lmList
Plot lmList Confidence Intervals
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
pdConstruct.pdBlocked
Construct pdBlocked Objects
coef.corStruct
Coefficients of a corStruct Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
varFunc
Variance Function Structure
coef.lme
Extract lme Coefficients
ACF.lme
Autocorrelation Function for lme Residuals
qqnorm.gls
Normal Plot of Residuals from a gls Object
logLik.reStruct
Calculate reStruct Log-Likelihood
Assay
Bioassay on Cell Culture Plate
Dim.corStruct
Dimensions of a corStruct Object
Dim.corSpatial
Dimensions of a corSpatial Object
varComb
Combination of Variance Functions
Tetracycline1
Pharmacokinetics of tetracycline
Remifentanil
Pharmacokinetics of remifentanil
plot.nfnGroupedData
Plot an nfnGroupedData Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
varWeights
Extract Variance Function Weights
getGroupsFormula
Extract Grouping Formula
predict.gls
Predictions from a gls Object
Variogram
Calculate Semi-variogram
logDet.reStruct
Extract reStruct Log-Determinants
plot.gls
Plot a gls Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
recalc.modelStruct
Recalculate for a modelStruct Object
pdClasses
Positive-Definite Matrix Classes
as.matrix.pdMat
Matrix of a pdMat Object
pdDiag
Diagonal Positive-Definite Matrix
predict.lmList
Predictions from an lmList Object
fdHess
Finite difference Hessian
getCovariateFormula
Extract Covariates Formula
reStruct
Random Effects Structure
pdNatural
General Positive-Definite Matrix in Natural Parametrization
lme.groupedData
LME fit from groupedData Object
plot.augPred
Plot an augPred Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
lmeObject
Fitted lme Object
recalc.reStruct
Recalculate for an reStruct Object
asOneFormula
Combine Formulas of a Set of Objects
plot.compareFits
Plot a compareFits Object
Dialyzer
High-Flux Hemodialyzer
lmeStruct
Linear Mixed-Effects Structure
print.varFunc
Print a varFunc Object
residuals.glsStruct
Calculate glsStruct Residuals
recalc.varFunc
Recalculate for varFunc Object
corFactor
Factor of a Correlation Matrix
gapply
Apply a Function by Groups
fitted.lme
Extract lme Fitted Values
intervals.lme
Confidence Intervals on lme Parameters
simulate.lme
Simulate Results from
lme
Models
IGF
Radioimmunoassay of IGF-I Protein
lmeScale
Scale for lme Optimization
bdf
Language scores
model.matrix.reStruct
reStruct Model Matrix
Oxide
Variability in Semiconductor Manufacturing
summary.varFunc
Summarize varFunc Object
varClasses
Variance Function Classes
varConstPower
Constant Plus Power Variance Function
splitFormula
Split a Formula
varWeights.glsStruct
Variance Weights for glsStruct Object
Phenobarb
Phenobarbitol Kinetics
Tetracycline2
Pharmacokinetics of tetracycline
fitted.lmList
Extract lmList Fitted Values
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
getData.lme
Extract lme Object Data
logLik.varFunc
Extract varFunc logLik
corClasses
Correlation Structure Classes
intervals.gls
Confidence Intervals on gls Parameters
plot.Variogram
Plot a Variogram Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
corRatio
Rational Quadratic Correlation Structure
getGroups
Extract Grouping Factors from an Object
recalc
Recalculate Condensed Linear Model Object
Pixel
X-ray pixel intensities over time
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
getResponseFormula
Extract Formula Specifying Response Variable
update.varFunc
Update varFunc Object
corARMA
ARMA(p,q) Correlation Structure
ranef.lme
Extract lme Random Effects
getCovariate.data.frame
Extract Data Frame Covariate
recalc.corStruct
Recalculate for corStruct Object
nlsList.selfStart
nlsList Fit from a selfStart Function
getCovariate
Extract Covariate from an Object
isInitialized
Check if Object is Initialized
intervals.lmList
Confidence Intervals on lmList Coefficients
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
nlme
Nonlinear Mixed-Effects Models
plot.ACF
Plot an ACF Object
pairs.lmList
Pairs Plot of an lmList Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
Dim
Extract Dimensions from an Object
Initialize.reStruct
Initialize reStruct Object
anova.gls
Compare Likelihoods of Fitted Objects
coef.lmList
Extract lmList Coefficients
getCovariate.corStruct
Extract corStruct Object Covariate
corSymm
General Correlation Structure
gnlsControl
Control Values for gnls Fit
logDet.corStruct
Extract corStruct Log-Determinant
lmList
List of lm Objects with a Common Model
pairs.compareFits
Pairs Plot of compareFits Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
plot.lmList
Plot an lmList Object
varFixed
Fixed Variance Function
summary.modelStruct
Summarize a modelStruct Object
RatPupWeight
The weight of rat pups
Names.formula
Extract Names from a formula
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
getVarCov
Extract variance-covariance matrix
Oxboys
Heights of Boys in Oxford
Gun
Methods for firing naval guns
Initialize.lmeStruct
Initialize an lmeStruct Object
glsControl
Control Values for gls Fit
pdMat
Positive-Definite Matrix
Names.pdMat
Names of a pdMat Object
Soybean
Growth of soybean plants
intervals
Confidence Intervals on Coefficients
summary.pdMat
Summarize a pdMat Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
predict.lme
Predictions from an lme Object
formula.pdMat
Extract pdMat Formula
getGroups.data.frame
Extract Groups from a Data Frame
summary.nlsList
Summarize an nlsList Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
nlsList
List of nls Objects with a Common Model
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
residuals.lmeStruct
Calculate lmeStruct Residuals
Names.pdBlocked
Names of a pdBlocked Object
nlmeControl
Control Values for nlme Fit
corGaus
Gaussian Correlation Structure
Earthquake
Earthquake Intensity
Relaxin
Assay for Relaxin
plot.nmGroupedData
Plot an nmGroupedData Object
Milk
Protein content of cows' milk
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
as.matrix.corStruct
Matrix of a corStruct Object
getGroups.lmList
Extract lmList Object Groups
corNatural
General correlation in natural parameterization
gls
Fit Linear Model Using Generalized Least Squares
random.effects
Extract Random Effects
plot.nffGroupedData
Plot an nffGroupedData Object
gnlsObject
Fitted gnls Object
needUpdate
Check if Update is Needed
MathAchSchool
School demographic data for MathAchieve
residuals.gls
Extract gls Residuals
varPower
Power Variance Function
varExp
Exponential Variance Function
Names.reStruct
Names of an reStruct Object
predict.nlme
Predictions from an nlme Object
asTable
Convert groupedData to a matrix
corCompSymm
Compound Symmetry Correlation Structure
lmeControl
Control Values for lme Fit
plot.ranef.lme
Plot a ranef.lme Object
pooledSD
Extract Pooled Standard Deviation
balancedGrouped
Create a groupedData object from a matrix
Quinidine
Quinidine Kinetics
residuals.lme
Extract lme Residuals
plot.ranef.lmList
Plot a ranef.lmList Object
pdBlocked
Positive-Definite Block Diagonal Matrix
summary.lme
Summarize an lme Object
comparePred
Compare Predictions
summary.gls
Summarize a gls Object
residuals.lmList
Extract lmList Residuals
fixef.lmList
Extract lmList Fixed Effects
summary.corStruct
Summarize a corStruct Object
compareFits
Compare Fitted Objects
glsObject
Fitted gls Object
pdLogChol
General Positive-Definite Matrix
Rail
Evaluation of Stress in Railway Rails
getData.lmList
Extract lmList Object Data
corCAR1
Continuous AR(1) Correlation Structure
logLik.corStruct
Extract corStruct Log-Likelihood
ranef.lmList
Extract lmList Random Effects
getData.gls
Extract gls Object Data