nlme v3.1-137

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

Date 2018-04-07
Priority recommended
LazyData yes
ByteCompile yes
Encoding UTF-8
License GPL (>= 2) | file LICENCE
BugReports https://bugs.r-project.org
NeedsCompilation yes
Packaged 2018-04-07 08:11:41 UTC; ripley
Repository CRAN
Date/Publication 2018-04-07 12:20:47 UTC

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