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nlme (version 3.1-111)
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
3.1-111
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
September 8th, 2013
Functions in nlme (3.1-111)
Search functions
Dim.pdMat
Dimensions of a pdMat Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Names.formula
Extract Names from a formula
LDEsysMat
Generate system matrix for LDEs
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Assay
Bioassay on Cell Culture Plate
Nitrendipene
Assay of nitrendipene
Names.pdBlocked
Names of a pdBlocked Object
fitted.glsStruct
Calculate glsStruct Fitted Values
Gun
Methods for firing naval guns
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Initialize.varFunc
Initialize varFunc Object
Wheat2
Wheat Yield Trials
Soybean
Growth of soybean plants
ACF.lme
Autocorrelation Function for lme Residuals
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
MathAchSchool
School demographic data for MathAchieve
BodyWeight
Rat weight over time for different diets
Muscle
Contraction of heart muscle sections
Dialyzer
High-Flux Hemodialyzer
as.matrix.reStruct
Matrices of an reStruct Object
corAR1
AR(1) Correlation Structure
anova.gls
Compare Likelihoods of Fitted Objects
ergoStool
Ergometrics experiment with stool types
Covariate.varFunc
Assign varFunc Covariate
Matrix
Assign Matrix Values
fdHess
Finite difference Hessian
Gasoline
Refinery yield of gasoline
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Earthquake
Earthquake Intensity
Meat
Tenderness of meat
Oats
Split-plot Experiment on Varieties of Oats
Oxboys
Heights of Boys in Oxford
coef.lmList
Extract lmList Coefficients
Variogram.default
Calculate Semi-variogram
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
Ovary
Counts of Ovarian Follicles
Dim
Extract Dimensions from an Object
Relaxin
Assay for Relaxin
Initialize.glsStruct
Initialize a glsStruct Object
RatPupWeight
The weight of rat pups
ACF.gls
Autocorrelation Function for gls Residuals
coef.lme
Extract lme Coefficients
Variogram.corExp
Calculate Semi-variogram for a corExp Object
gls
Fit Linear Model Using Generalized Least Squares
coef.corStruct
Coefficients of a corStruct Object
Quinidine
Quinidine Kinetics
Wheat
Yields by growing conditions
Initialize.corStruct
Initialize corStruct Object
asOneFormula
Combine Formulas of a Set of Objects
coef.pdMat
pdMat Object Coefficients
Remifentanil
Pharmacokinetics of remifentanil
corRatio
Rational Quadratic Correlation Structure
Variogram
Calculate Semi-variogram
corMatrix
Extract Correlation Matrix
getCovariate.corStruct
Extract corStruct Object Covariate
Oxide
Variability in Semiconductor Manufacturing
corNatural
General correlation in natural parameterization
formula.reStruct
Extract reStruct Object Formula
Tetracycline1
Pharmacokinetics of tetracycline
nlme.nlsList
NLME fit from nlsList Object
collapse.groupedData
Collapse a groupedData Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
corClasses
Correlation Structure Classes
corSpatial
Spatial Correlation Structure
allCoef
Extract Coefficients from a Set of Objects
getData.lme
Extract lme Object Data
gnlsControl
Control Values for gnls Fit
Tetracycline2
Pharmacokinetics of tetracycline
nlmeStruct
Nonlinear Mixed-Effects Structure
getResponse
Extract Response Variable from an Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
getCovariate.data.frame
Extract Data Frame Covariate
collapse
Collapse According to Groups
corSymm
General Correlation Structure
corCAR1
Continuous AR(1) Correlation Structure
gnls
Fit Nonlinear Model Using Generalized Least Squares
logDet.corStruct
Extract corStruct Log-Determinant
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
getGroups.gls
Extract gls Object Groups
getGroups.varFunc
Extract varFunc Groups
glsStruct
Generalized Least Squares Structure
getCovariate.varFunc
Extract varFunc Covariate
recalc.corStruct
Recalculate for corStruct Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
groupedData
Construct a groupedData Object
coef.modelStruct
Extract modelStruct Object Coefficients
Rail
Evaluation of Stress in Railway Rails
anova.lme
Compare Likelihoods of Fitted Objects
pdConstruct
Construct pdMat Objects
corGaus
Gaussian Correlation Structure
corFactor
Factor of a Correlation Matrix
asTable
Convert groupedData to a matrix
pdDiag
Diagonal Positive-Definite Matrix
pairs.lmList
Pairs Plot of an lmList Object
balancedGrouped
Create a groupedData object from a matrix
intervals
Confidence Intervals on Coefficients
corLin
Linear Correlation Structure
recalc.reStruct
Recalculate for an reStruct Object
as.matrix.pdMat
Matrix of a pdMat Object
getGroups
Extract Grouping Factors from an Object
getCovariate
Extract Covariate from an Object
formula.pdBlocked
Extract pdBlocked Formula
intervals.lmList
Confidence Intervals on lmList Coefficients
pdClasses
Positive-Definite Matrix Classes
glsObject
Fitted gls Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
predict.lme
Predictions from an lme Object
fitted.lme
Extract lme Fitted Values
varWeights
Extract Variance Function Weights
logDet.pdMat
Extract Log-Determinant from a pdMat Object
needUpdate
Check if Update is Needed
as.matrix.corStruct
Matrix of a corStruct Object
lmeObject
Fitted lme Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdNatural
General Positive-Definite Matrix in Natural Parametrization
nlmeControl
Control Values for nlme Fit
residuals.gnlsStruct
Calculate gnlsStruct Residuals
nlmeObject
Fitted nlme Object
pooledSD
Extract Pooled Standard Deviation
pdConstruct.pdBlocked
Construct pdBlocked Objects
getData.lmList
Extract lmList Object Data
pdLogChol
General Positive-Definite Matrix
pdSymm
General Positive-Definite Matrix
corFactor.corStruct
Factor of a corStruct Object Matrix
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
plot.nmGroupedData
Plot an nmGroupedData Object
isInitialized
Check if Object is Initialized
plot.lmList
Plot an lmList Object
ranef.lmList
Extract lmList Random Effects
quinModel
Model function for the Quinidine data
predict.lmList
Predictions from an lmList Object
recalc
Recalculate Condensed Linear Model Object
logLik.corStruct
Extract corStruct Log-Likelihood
random.effects
Extract Random Effects
corMatrix.corStruct
Matrix of a corStruct Object
plot.gls
Plot a gls Object
solve.reStruct
Apply Solve to an reStruct Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
varFunc
Variance Function Structure
summary.lme
Summarize an lme Object
getData
Extract Data from an Object
intervals.gls
Confidence Intervals on gls Parameters
varPower
Power Variance Function
predict.gls
Predictions from a gls Object
varConstPower
Constant Plus Power Variance Function
lme
Linear Mixed-Effects Models
intervals.lme
Confidence Intervals on lme Parameters
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
varIdent
Constant Variance Function
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
varExp
Exponential Variance Function
logLik.lme
Log-Likelihood of an lme Object
summary.pdMat
Summarize a pdMat Object
residuals.glsStruct
Calculate glsStruct Residuals
lmeControl
Control Values for lme Fit
logDet.reStruct
Extract reStruct Log-Determinants
nlsList.selfStart
nlsList Fit from a selfStart Function
plot.Variogram
Plot a Variogram Object
print.varFunc
Print a varFunc Object
summary.corStruct
Summarize a corStruct Object
splitFormula
Split a Formula
summary.varFunc
Summarize varFunc Object
augPred
Augmented Predictions
Initialize
Initialize Object
Glucose
Glucose levels over time
compareFits
Compare Fitted Objects
fitted.lmList
Extract lmList Fitted Values
lmList
List of lm Objects with a Common Model
Matrix.pdMat
Assign Matrix to a pdMat Object
Milk
Protein content of cows' milk
logLik.reStruct
Calculate reStruct Log-Likelihood
coef.gnls
Extract gnls Coefficients
comparePred
Compare Predictions
corExp
Exponential Correlation Structure
logLik.varFunc
Extract varFunc logLik
pairs.lme
Pairs Plot of an lme Object
isBalanced
Check a Design for Balance
plot.nfnGroupedData
Plot an nfnGroupedData Object
gsummary
Summarize by Groups
lme.groupedData
LME fit from groupedData Object
recalc.varFunc
Recalculate for varFunc Object
summary.gls
Summarize a gls Object
pairs.compareFits
Pairs Plot of compareFits Object
Coef
Assign Values to Coefficients
corCompSymm
Compound Symmetry Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
formula.pdMat
Extract pdMat Formula
getGroups.lmList
Extract lmList Object Groups
Dim.corSpatial
Dimensions of a corSpatial Object
getGroups.lme
Extract lme Object Groups
Covariate
Assign Covariate Values
Dim.corStruct
Dimensions of a corStruct Object
Initialize.reStruct
Initialize reStruct Object
plot.ranef.lme
Plot a ranef.lme Object
print.summary.pdMat
Print a summary.pdMat Object
Initialize.lmeStruct
Initialize an lmeStruct Object
predict.gnls
Predictions from a gnls Object
Names
Names Associated with an Object
Spruce
Growth of Spruce Trees
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
getData.gls
Extract gls Object Data
corARMA
ARMA(p,q) Correlation Structure
ranef.lme
Extract lme Random Effects
Orthodont
Growth curve data on an orthdontic measurement
Pixel
X-ray pixel intensities over time
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
Matrix.reStruct
Assign reStruct Matrices
fixef.lmList
Extract lmList Fixed Effects
coef.reStruct
reStruct Object Coefficients
residuals.lmeStruct
Calculate lmeStruct Residuals
update.modelStruct
Update a modelStruct Object
Phenobarb
Phenobarbitol Kinetics
corSpher
Spherical Correlation Structure
gapply
Apply a Function by Groups
nlme
Nonlinear Mixed-Effects Models
summary.modelStruct
Summarize a modelStruct Object
lmeStruct
Linear Mixed-Effects Structure
recalc.modelStruct
Recalculate for a modelStruct Object
summary.nlsList
Summarize an nlsList Object
phenoModel
Model function for the Phenobarb data
gnlsObject
Fitted gnls Object
lmList.groupedData
lmList Fit from a groupedData Object
getGroups.corStruct
Extract corStruct Groups
plot.intervals.lmList
Plot lmList Confidence Intervals
residuals.lmList
Extract lmList Residuals
glsControl
Control Values for gls Fit
PBG
Effect of Phenylbiguanide on Blood Pressure
lme.lmList
LME fit from lmList Object
nlsList
List of nls Objects with a Common Model
predict.nlme
Predictions from an nlme Object
VarCorr
Extract variance and correlation components
summary.lmList
Summarize an lmList Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
plot.compareFits
Plot a compareFits Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getResponseFormula
Extract Formula Specifying Response Variable
Cefamandole
Pharmacokinetics of Cefamandole
update.varFunc
Update varFunc Object
varFixed
Fixed Variance Function
logDet
Extract the Logarithm of the Determinant
model.matrix.reStruct
reStruct Model Matrix
pdBlocked
Positive-Definite Block Diagonal Matrix
varWeights.glsStruct
Variance Weights for glsStruct Object
Names.reStruct
Names of an reStruct Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Wafer
Modeling of Analog MOS Circuits
getGroupsFormula
Extract Grouping Formula
gnlsStruct
Generalized Nonlinear Least Squares Structure
logLik.gnls
Log-Likelihood of a gnls Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
getVarCov
Extract variance-covariance matrix
lmeScale
Scale for lme Optimization
plot.ACF
Plot an ACF Object
plot.lme
Plot an lme or nls object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
plot.augPred
Plot an augPred Object
residuals.lme
Extract lme Residuals
ACF
Autocorrelation Function
getGroups.data.frame
Extract Groups from a Data Frame
getCovariateFormula
Extract Covariates Formula
pdMat
Positive-Definite Matrix
simulate.lme
Simulate Results from
lme
Models
Names.pdMat
Names of a pdMat Object
varComb
Combination of Variance Functions
Fatigue
Cracks caused by metal fatigue
IGF
Radioimmunoassay of IGF-I Protein
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
residuals.gls
Extract gls Residuals
[.pdMat
Subscript a pdMat Object
MathAchieve
Mathematics achievement scores
fixed.effects
Extract Fixed Effects
Machines
Productivity Scores for Machines and Workers
reStruct
Random Effects Structure
bdf
Language scores
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
plot.ranef.lmList
Plot a ranef.lmList Object
coef.varFunc
varFunc Object Coefficients
varClasses
Variance Function Classes