nlme v3.1-141

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

Date 2019-08-01
Priority recommended
LazyData yes
ByteCompile yes
Encoding UTF-8
License GPL (>= 2) | file LICENCE
BugReports https://bugs.r-project.org
URL https://svn.r-project.org/R-packages/trunk/nlme
NeedsCompilation yes
Packaged 2019-08-01 03:39:13 UTC; hornik
Repository CRAN
Date/Publication 2019-08-01 06:04:26 UTC

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