nlme v3.1-131

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

Date 2017-02-06
Priority recommended
LazyData yes
ByteCompile yes
Encoding UTF-8
License GPL (>= 2) | file LICENCE
BugReports https://bugs.r-project.org
NeedsCompilation yes
Packaged 2017-02-06 10:56:42 UTC; maechler
Repository CRAN
Date/Publication 2017-02-06 21:34:58

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