nlme v3.1-148

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

Date 2020-05-13
Priority recommended
Contact see 'MailingList'
LazyData yes
ByteCompile yes
Encoding UTF-8
License GPL (>= 2) | file LICENCE
BugReports https://bugs.r-project.org
MailingList R-help@r-project.org
URL https://svn.r-project.org/R-packages/trunk/nlme
NeedsCompilation yes
Packaged 2020-05-13 08:42:56 UTC; maechler
Repository CRAN
Date/Publication 2020-05-24 00:40:02 UTC

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