nlme v3.1-86

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Linear and Nonlinear Mixed Effects Models

Fit and compare Gaussian linear and nonlinear mixed-effects models.

Functions in nlme

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

Date 2007-10-04
Priority recommended
LazyLoad yes
LazyData yes
License GPL (>=2)
Packaged Thu Oct 4 23:25:21 2007; hornik

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