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nlme (version 3.1-118)
Linear and Nonlinear Mixed Effects Models
Description
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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3.1-2 (1999/12/23)
3.1-1
Install
install.packages('nlme')
Monthly Downloads
62,596
Version
3.1-118
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
October 7th, 2014
Functions in nlme (3.1-118)
Search all functions
Glucose
Glucose levels over time
Initialize.corStruct
Initialize corStruct Object
Soybean
Growth of soybean plants
Orthodont
Growth curve data on an orthdontic measurement
corNatural
General correlation in natural parameterization
Coef
Assign Values to Coefficients
getGroups.gls
Extract gls Object Groups
Dim.corStruct
Dimensions of a corStruct Object
getResponseFormula
Extract Formula Specifying Response Variable
Dim.pdMat
Dimensions of a pdMat Object
logLik.corStruct
Extract corStruct Log-Likelihood
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
plot.augPred
Plot an augPred Object
Tetracycline2
Pharmacokinetics of tetracycline
Relaxin
Assay for Relaxin
Assay
Bioassay on Cell Culture Plate
as.matrix.reStruct
Matrices of an reStruct Object
Initialize
Initialize Object
MathAchSchool
School demographic data for MathAchieve
Dim.corSpatial
Dimensions of a corSpatial Object
coef.corStruct
Coefficients of a corStruct Object
BodyWeight
Rat weight over time for different diets
Initialize.glsStruct
Initialize a glsStruct Object
ACF
Autocorrelation Function
Initialize.varFunc
Initialize varFunc Object
Matrix
Assign Matrix Values
corFactor
Factor of a Correlation Matrix
corARMA
ARMA(p,q) Correlation Structure
asTable
Convert groupedData to a matrix
Dim
Extract Dimensions from an Object
Variogram
Calculate Semi-variogram
Cefamandole
Pharmacokinetics of Cefamandole
Matrix.pdMat
Assign Matrix to a pdMat Object
isInitialized
Check if Object is Initialized
Meat
Tenderness of meat
as.matrix.corStruct
Matrix of a corStruct Object
PBG
Effect of Phenylbiguanide on Blood Pressure
ACF.gls
Autocorrelation Function for gls Residuals
ranef.lmList
Extract lmList Random Effects
compareFits
Compare Fitted Objects
[.pdMat
Subscript a pdMat Object
Machines
Productivity Scores for Machines and Workers
fitted.glsStruct
Calculate glsStruct Fitted Values
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
Fatigue
Cracks caused by metal fatigue
residuals.glsStruct
Calculate glsStruct Residuals
Rail
Evaluation of Stress in Railway Rails
Quinidine
Quinidine Kinetics
Names
Names Associated with an Object
corLin
Linear Correlation Structure
collapse.groupedData
Collapse a groupedData Object
coef.modelStruct
Extract modelStruct Object Coefficients
summary.lme
Summarize an lme Object
corCAR1
Continuous AR(1) Correlation Structure
gls-internal
Auxiliary functions used by gls
fitted.lme
Extract lme Fitted Values
gnlsControl
Control Values for gnls Fit
as.matrix.pdMat
Matrix of a pdMat Object
Oxide
Variability in Semiconductor Manufacturing
formula.reStruct
Extract reStruct Object Formula
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
comparePred
Compare Predictions
anova.gls
Compare Likelihoods of Fitted Objects
Glucose2
Glucose Levels Following Alcohol Ingestion
gnls
Fit Nonlinear Model Using Generalized Least Squares
groupedData
Construct a groupedData Object
intervals
Confidence Intervals on Coefficients
fitted.lmList
Extract lmList Fitted Values
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
pairs.lmList
Pairs Plot of an lmList Object
getCovariate.data.frame
Extract Data Frame Covariate
getGroups.lmList
Extract lmList Object Groups
Ovary
Counts of Ovarian Follicles
corSpher
Spherical Correlation Structure
summary.corStruct
Summarize a corStruct Object
intervals.lmList
Confidence Intervals on lmList Coefficients
corAR1
AR(1) Correlation Structure
plot.gls
Plot a gls Object
nlmeControl
Control Values for nlme Fit
logLik.glsStruct
Log-Likelihood of a glsStruct Object
model.matrix.reStruct
reStruct Model Matrix
corGaus
Gaussian Correlation Structure
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
corSpatial
Spatial Correlation Structure
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
gnlsObject
Fitted gnls Object
lme
Linear Mixed-Effects Models
predict.lme
Predictions from an lme Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
getGroups.data.frame
Extract Groups from a Data Frame
Names.formula
Extract Names from a formula
nlme
Nonlinear Mixed-Effects Models
lmeControl
Control Values for lme Fit
pdNatural
General Positive-Definite Matrix in Natural Parametrization
coef.pdMat
pdMat Object Coefficients
pdConstruct.pdBlocked
Construct pdBlocked Objects
corCompSymm
Compound Symmetry Correlation Structure
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdIdent
Multiple of the Identity Positive-Definite Matrix
qqnorm.gls
Normal Plot of Residuals from a gls Object
phenoModel
Model function for the Phenobarb data
getGroups.varFunc
Extract varFunc Groups
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
quinModel
Model function for the Quinidine data
residuals.lmList
Extract lmList Residuals
Covariate
Assign Covariate Values
pdDiag
Diagonal Positive-Definite Matrix
Covariate.varFunc
Assign varFunc Covariate
formula.pdMat
Extract pdMat Formula
MathAchieve
Mathematics achievement scores
getVarCov
Extract variance-covariance matrix
Wheat
Yields by growing conditions
Initialize.reStruct
Initialize reStruct Object
Dialyzer
High-Flux Hemodialyzer
recalc.modelStruct
Recalculate for a modelStruct Object
corMatrix
Extract Correlation Matrix
Gun
Methods for firing naval guns
RatPupWeight
The weight of rat pups
isBalanced
Check a Design for Balance
lmeStruct
Linear Mixed-Effects Structure
needUpdate
Check if Update is Needed
plot.Variogram
Plot a Variogram Object
Oats
Split-plot Experiment on Varieties of Oats
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
recalc
Recalculate Condensed Linear Model Object
logLik.lmList
Log-Likelihood of an lmList Object
intervals.gls
Confidence Intervals on gls Parameters
residuals.gnlsStruct
Calculate gnlsStruct Residuals
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
Names.pdBlocked
Names of a pdBlocked Object
varClasses
Variance Function Classes
Muscle
Contraction of heart muscle sections
Remifentanil
Pharmacokinetics of remifentanil
Initialize.lmeStruct
Initialize an lmeStruct Object
Milk
Protein content of cows' milk
asOneFormula
Combine Formulas of a Set of Objects
coef.lme
Extract lme Coefficients
pdSymm
General Positive-Definite Matrix
nlmeObject
Fitted nlme Object
residuals.lmeStruct
Calculate lmeStruct Residuals
getCovariate.varFunc
Extract varFunc Covariate
Pixel
X-ray pixel intensities over time
coef.gnls
Extract gnls Coefficients
summary.pdMat
Summarize a pdMat Object
Tetracycline1
Pharmacokinetics of tetracycline
Wheat2
Wheat Yield Trials
corSymm
General Correlation Structure
coef.reStruct
reStruct Object Coefficients
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
recalc.corStruct
Recalculate for corStruct Object
balancedGrouped
Create a groupedData object from a matrix
getGroups
Extract Grouping Factors from an Object
pooledSD
Extract Pooled Standard Deviation
augPred
Augmented Predictions
corClasses
Correlation Structure Classes
glsControl
Control Values for gls Fit
ranef.lme
Extract lme Random Effects
ergoStool
Ergometrics experiment with stool types
varFixed
Fixed Variance Function
IGF
Radioimmunoassay of IGF-I Protein
Matrix.reStruct
Assign reStruct Matrices
collapse
Collapse According to Groups
Spruce
Growth of Spruce Trees
VarCorr
Extract variance and correlation components
plot.lme
Plot an lme or nls object
recalc.varFunc
Recalculate for varFunc Object
random.effects
Extract Random Effects
getData.gls
Extract gls Object Data
corFactor.corStruct
Factor of a corStruct Object Matrix
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
predict.lmList
Predictions from an lmList Object
plot.intervals.lmList
Plot lmList Confidence Intervals
fdHess
Finite difference Hessian
getGroups.corStruct
Extract corStruct Groups
fixed.effects
Extract Fixed Effects
splitFormula
Split a Formula
corRatio
Rational Quadratic Correlation Structure
varWeights.glsStruct
Variance Weights for glsStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varConstPower
Constant Plus Power Variance Function
getData
Extract Data from an Object
fixef.lmList
Extract lmList Fixed Effects
getCovariateFormula
Extract Covariates Formula
corMatrix.corStruct
Matrix of a corStruct Object
Wafer
Modeling of Analog MOS Circuits
varExp
Exponential Variance Function
gls
Fit Linear Model Using Generalized Least Squares
lmeObject
Fitted lme Object
varWeights
Extract Variance Function Weights
intervals.lme
Confidence Intervals on lme Parameters
getGroups.lme
Extract lme Object Groups
Names.pdMat
Names of a pdMat Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
glsStruct
Generalized Least Squares Structure
glsObject
Fitted gls Object
getGroupsFormula
Extract Grouping Formula
Variogram.default
Calculate Semi-variogram
gnlsStruct
Generalized Nonlinear Least Squares Structure
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
getData.lmList
Extract lmList Object Data
summary.varFunc
Summarize varFunc Object
logLik.lme
Log-Likelihood of an lme Object
formula.pdBlocked
Extract pdBlocked Formula
getResponse
Extract Response Variable from an Object
pdMat
Positive-Definite Matrix
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.lmeStruct
Calculate lmeStruct Fitted Values
gapply
Apply a Function by Groups
nlmeStruct
Nonlinear Mixed-Effects Structure
lmList
List of lm Objects with a Common Model
plot.nfnGroupedData
Plot an nfnGroupedData Object
lme.groupedData
LME fit from groupedData Object
getCovariate
Extract Covariate from an Object
print.varFunc
Print a varFunc Object
pdBlocked
Positive-Definite Block Diagonal Matrix
logDet.corStruct
Extract corStruct Log-Determinant
solve.reStruct
Apply Solve to an reStruct Object
pairs.compareFits
Pairs Plot of compareFits Object
coef.lmList
Extract lmList Coefficients
logDet
Extract the Logarithm of the Determinant
logLik.reStruct
Calculate reStruct Log-Likelihood
summary.gls
Summarize a gls Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
coef.varFunc
varFunc Object Coefficients
nlsList.selfStart
nlsList Fit from a selfStart Function
pdClasses
Positive-Definite Matrix Classes
lme.lmList
LME fit from lmList Object
predict.gls
Predictions from a gls Object
pdLogChol
General Positive-Definite Matrix
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
plot.lmList
Plot an lmList Object
update.modelStruct
Update a modelStruct Object
plot.nmGroupedData
Plot an nmGroupedData Object
plot.nffGroupedData
Plot an nffGroupedData Object
nlme.nlsList
NLME fit from nlsList Object
recalc.reStruct
Recalculate for an reStruct Object
Oxboys
Heights of Boys in Oxford
print.summary.pdMat
Print a summary.pdMat Object
residuals.lme
Extract lme Residuals
Phenobarb
Phenobarbitol Kinetics
predict.gnls
Predictions from a gnls Object
predict.nlme
Predictions from an nlme Object
residuals.gls
Extract gls Residuals
update.varFunc
Update varFunc Object
varComb
Combination of Variance Functions
Gasoline
Refinery yield of gasoline
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
gsummary
Summarize by Groups
varIdent
Constant Variance Function
simulate.lme
Simulate Results from
lme
Models
varPower
Power Variance Function
summary.lmList
Summarize an lmList Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
getData.lme
Extract lme Object Data
logLik.varFunc
Extract varFunc logLik
varFunc
Variance Function Structure
Earthquake
Earthquake Intensity
nlsList
List of nls Objects with a Common Model
pdConstruct
Construct pdMat Objects
Names.reStruct
Names of an reStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
allCoef
Extract Coefficients from a Set of Objects
corExp
Exponential Correlation Structure
logDet.pdMat
Extract Log-Determinant from a pdMat Object
getCovariate.corStruct
Extract corStruct Object Covariate
lmList.groupedData
lmList Fit from a groupedData Object
plot.ACF
Plot an ACF Object
plot.ranef.lme
Plot a ranef.lme Object
plot.compareFits
Plot a compareFits Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
logLik.gnls
Log-Likelihood of a gnls Object
LDEsysMat
Generate system matrix for LDEs
plot.ranef.lmList
Plot a ranef.lmList Object
bdf
Language scores
ACF.lme
Autocorrelation Function for lme Residuals
Nitrendipene
Assay of nitrendipene
reStruct
Random Effects Structure
summary.nlsList
Summarize an nlsList Object
logDet.reStruct
Extract reStruct Log-Determinants
pairs.lme
Pairs Plot of an lme Object
summary.modelStruct
Summarize a modelStruct Object