nlme v3.1-145

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

Date 2020-03-03
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 2020-03-03 19:40:47 UTC; ripley
Repository CRAN
Date/Publication 2020-03-04 13:37:57 UTC

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