nlme v3.1-1

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

Functions in nlme

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