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nlme (version 3.1-99)
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
139,641
Version
3.1-99
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
February 25th, 2011
Functions in nlme (3.1-99)
Search all functions
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
plot.nmGroupedData
Plot an nmGroupedData Object
pdBlocked
Positive-Definite Block Diagonal Matrix
Covariate.varFunc
Assign varFunc Covariate
Assay
Bioassay on Cell Culture Plate
BodyWeight
Rat weight over time for different diets
ACF
Autocorrelation Function
Coef
Assign Values to Coefficients
coef.gnls
Extract gnls Coefficients
getGroups.lmList
Extract lmList Object Groups
gapply
Apply a Function by Groups
Wheat
Yields by growing conditions
BIC
Bayesian Information Criterion
Initialize
Initialize Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Oxide
Variability in Semiconductor Manufacturing
Earthquake
Earthquake Intensity
Matrix.pdMat
Assign Matrix to a pdMat Object
as.matrix.reStruct
Matrices of an reStruct Object
Names
Names Associated with an Object
isInitialized
Check if Object is Initialized
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Milk
Protein content of cows' milk
corLin
Linear Correlation Structure
Phenobarb
Phenobarbitol Kinetics
Dim.pdMat
Dimensions of a pdMat Object
Glucose
Glucose levels over time
[.pdMat
Subscript a pdMat Object
Initialize.reStruct
Initialize reStruct Object
getGroups.gls
Extract gls Object Groups
corMatrix
Extract Correlation Matrix
Matrix.reStruct
Assign reStruct Matrices
Muscle
Contraction of heart muscle sections
Names.formula
Extract Names from a formula
nlmeStruct
Nonlinear Mixed-Effects Structure
allCoef
Extract Coefficients from a Set of Objects
as.matrix.pdMat
Matrix of a pdMat Object
MathAchSchool
School demographic data for MathAchieve
Remifentanil
Pharmacokinetics of remifentanil
corExp
Exponential Correlation Structure
Cefamandole
Pharmacokinetics of Cefamandole
groupedData
Construct a groupedData Object
Names.pdBlocked
Names of a pdBlocked Object
Matrix
Assign Matrix Values
Fatigue
Cracks caused by metal fatigue
Initialize.varFunc
Initialize varFunc Object
getGroups
Extract Grouping Factors from an Object
anova.lme
Compare Likelihoods of Fitted Objects
corCAR1
Continuous AR(1) Correlation Structure
Tetracycline2
Pharmacokinetics of tetracycline
Soybean
Growth of soybean plants
MathAchieve
Mathematics achievement scores
corRatio
Rational Quadratic Correlation Structure
Covariate
Assign Covariate Values
Wheat2
Wheat Yield Trials
asOneFormula
Combine Formulas of a Set of Objects
collapse.groupedData
Collapse a groupedData Object
fdHess
Finite difference Hessian
Dim.corStruct
Dimensions of a corStruct Object
formula.reStruct
Extract reStruct Object Formula
Gun
Methods for firing naval guns
corFactor
Factor of a Correlation Matrix
nlme.nlsList
NLME fit from nlsList Object
Names.pdMat
Names of a pdMat Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Spruce
Growth of Spruce Trees
Dialyzer
High-Flux Hemodialyzer
compareFits
Compare Fitted Objects
RatPupWeight
The weight of rat pups
corFactor.corStruct
Factor of a corStruct Object Matrix
pdDiag
Diagonal Positive-Definite Matrix
gsummary
Summarize by Groups
corARMA
ARMA(p,q) Correlation Structure
Oats
Split-plot Experiment on Varieties of Oats
Variogram.default
Calculate Semi-variogram
bdf
Language scores
Orthodont
Growth curve data on an orthdontic measurement
coef.lmList
Extract lmList Coefficients
Gasoline
Refinery yield of gasoline
Initialize.glsStruct
Initialize a glsStruct Object
corGaus
Gaussian Correlation Structure
coef.reStruct
reStruct Object Coefficients
coef.varFunc
varFunc Object Coefficients
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
collapse
Collapse According to Groups
corClasses
Correlation Structure Classes
fixef.lmList
Extract lmList Fixed Effects
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
ACF.gls
Autocorrelation Function for gls Residuals
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
Wafer
Modeling of Analog MOS Circuits
formula.pdBlocked
Extract pdBlocked Formula
Machines
Productivity Scores for Machines and Workers
Tetracycline1
Pharmacokinetics of tetracycline
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
getGroups.data.frame
Extract Groups from a Data Frame
ACF.lme
Autocorrelation Function for lme Residuals
augPred
Augmented Predictions
getData.lme
Extract lme Object Data
Nitrendipene
Assay of nitrendipene
Variogram
Calculate Semi-variogram
getGroups.corStruct
Extract corStruct Groups
getGroupsFormula
Extract Grouping Formula
logDet.corStruct
Extract corStruct Log-Determinant
Names.reStruct
Names of an reStruct Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
getResponse
Extract Response Variable from an Object
Initialize.corStruct
Initialize corStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
getCovariate
Extract Covariate from an Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
Rail
Evaluation of Stress in Railway Rails
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
gnlsControl
Control Values for gnls Fit
pdIdent
Multiple of the Identity Positive-Definite Matrix
predict.lmList
Predictions from an lmList Object
corSpatial
Spatial Correlation Structure
corCompSymm
Compound Symmetry Correlation Structure
intervals.lme
Confidence Intervals on lme Parameters
lmList
List of lm Objects with a Common Model
random.effects
Extract Random Effects
getData
Extract Data from an Object
pairs.lme
Pairs Plot of an lme Object
Dim.corSpatial
Dimensions of a corSpatial Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getGroups.varFunc
Extract varFunc Groups
pdConstruct.pdBlocked
Construct pdBlocked Objects
logLik.glsStruct
Log-Likelihood of a glsStruct Object
isBalanced
Check a Design for Balance
lmeStruct
Linear Mixed-Effects Structure
residuals.lmList
Extract lmList Residuals
fitted.glsStruct
Calculate glsStruct Fitted Values
lmeControl
Control Values for lme Fit
residuals.glsStruct
Calculate glsStruct Residuals
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdSymm
General Positive-Definite Matrix
Ovary
Counts of Ovarian Follicles
plot.gls
Plot a gls Object
plot.Variogram
Plot a Variogram Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
corNatural
General correlation in natural parameterization
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
lmList.groupedData
lmList Fit from a groupedData Object
lmeScale
Scale for lme Optimization
PBG
Effect of Phenylbiguanide on Blood Pressure
getCovariateFormula
Extract Covariates Formula
Dim
Extract Dimensions from an Object
getResponseFormula
Extract Formula Specifying Response Variable
plot.compareFits
Plot a compareFits Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Oxboys
Heights of Boys in Oxford
logDet.reStruct
Extract reStruct Log-Determinants
getVarCov
Extract variance-covariance matrix
corMatrix.corStruct
Matrix of a corStruct Object
summary.lmList
Summarize an lmList Object
residuals.gls
Extract gls Residuals
lmeObject
Fitted lme Object
pdConstruct
Construct pdMat Objects
Quinidine
Quinidine Kinetics
getData.lmList
Extract lmList Object Data
recalc
Recalculate Condensed Linear Model Object
nlmeControl
Control Values for nlme Fit
pairs.compareFits
Pairs Plot of compareFits Object
pdClasses
Positive-Definite Matrix Classes
summary.modelStruct
Summarize a modelStruct Object
getCovariate.corStruct
Extract corStruct Object Covariate
gnls
Fit Nonlinear Model Using Generalized Least Squares
summary.lme
Summarize an lme Object
intervals.lmList
Confidence Intervals on lmList Coefficients
logLik.reStruct
Calculate reStruct Log-Likelihood
coef.corStruct
Coefficients of a corStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
summary.pdMat
Summarize a pdMat Object
lme
Linear Mixed-Effects Models
intervals
Confidence Intervals on Coefficients
summary.gls
Summarize a gls Object
gls
Fit Linear Model Using Generalized Least Squares
pairs.lmList
Pairs Plot of an lmList Object
plot.lme
Plot an lme or nls object
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.ranef.lme
Plot a ranef.lme Object
glsObject
Fitted gls Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
VarCorr
Extract variance and correlation components
logDet
Extract the Logarithm of the Determinant
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
recalc.varFunc
Recalculate for varFunc Object
recalc.corStruct
Recalculate for corStruct Object
plot.ranef.lmList
Plot a ranef.lmList Object
logLik.varFunc
Extract varFunc logLik
glsStruct
Generalized Least Squares Structure
nlsList.selfStart
nlsList Fit from a selfStart Function
update.varFunc
Update varFunc Object
varWeights
Extract Variance Function Weights
pooledSD
Extract Pooled Standard Deviation
logLik.corStruct
Extract corStruct Log-Likelihood
corSymm
General Correlation Structure
simulate.lme
Simulate results from lme models
IGF
Radioimmunoassay of IGF-I Protein
ergoStool
Ergometrics experiment with stool types
recalc.modelStruct
Recalculate for a modelStruct Object
lme.groupedData
LME fit from groupedData Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
predict.gls
Predictions from a gls Object
Initialize.lmeStruct
Initialize an lmeStruct Object
fitted.lme
Extract lme Fitted Values
pdMat
Positive-Definite Matrix
getGroups.lme
Extract lme Object Groups
fixed.effects
Extract Fixed Effects
splitFormula
Split a Formula
comparePred
Compare Predictions
nlmeObject
Fitted nlme Object
ranef.lmList
Extract lmList Random Effects
pdNatural
General Positive-Definite Matrix in Natural Parametrization
formula.pdMat
Extract pdMat Formula
reStruct
Random Effects Structure
varConstPower
Constant Plus Power Variance Function
summary.corStruct
Summarize a corStruct Object
varClasses
Variance Function Classes
intervals.gls
Confidence Intervals on gls Parameters
Meat
Tenderness of meat
logLik.lmList
Log-Likelihood of an lmList Object
print.varFunc
Print a varFunc Object
varPower
Power Variance Function
quinModel
Model function for the Quinidine data
getCovariate.varFunc
Extract varFunc Covariate
update.modelStruct
Update a modelStruct Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
varComb
Combination of Variance Functions
plot.augPred
Plot an augPred Object
summary.varFunc
Summarize varFunc Object
residuals.lmeStruct
Calculate lmeStruct Residuals
getCovariate.data.frame
Extract Data Frame Covariate
residuals.lme
Extract lme Residuals
getData.gls
Extract gls Object Data
varExp
Exponential Variance Function
plot.lmList
Plot an lmList Object
varIdent
Constant Variance Function
lme.lmList
LME fit from lmList Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
predict.lme
Predictions from an lme Object
solve.reStruct
Apply Solve to an reStruct Object
pdLogChol
General Positive-Definite Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
ranef.lme
Extract lme Random Effects
model.matrix.reStruct
reStruct Model Matrix
varFixed
Fixed Variance Function
logLik.lme
Log-Likelihood of an lme Object
predict.gnls
Predictions from a gnls Object
varFunc
Variance Function Structure
anova.gls
Compare Likelihoods of Fitted Objects
needUpdate
Check if Update is Needed
varWeights.glsStruct
Variance Weights for glsStruct Object
print.summary.pdMat
Print a summary.pdMat Object
nlme
Nonlinear Mixed-Effects Models
nlsList
List of nls Objects with a Common Model
recalc.reStruct
Recalculate for an reStruct Object
LDEsysMat
Generate system matrix for LDEs
Pixel
X-ray pixel intensities over time
plot.ACF
Plot an ACF Object
phenoModel
Model function for the Phenobarb data
fitted.lmList
Extract lmList Fitted Values
asTable
Convert groupedData to a matrix
summary.nlsList
Summarize an nlsList Object
gnlsObject
Fitted gnls Object
plot.nffGroupedData
Plot an nffGroupedData Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
glsControl
Control Values for gls Fit
predict.nlme
Predictions from an nlme Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
corAR1
AR(1) Correlation Structure
coef.modelStruct
Extract modelStruct Object Coefficients
corSpher
Spherical Correlation Structure
coef.lme
Extract lme Coefficients
Relaxin
Assay for Relaxin
balancedGrouped
Create a groupedData object from a matrix
Variogram.corExp
Calculate Semi-variogram for a corExp Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
coef.pdMat
pdMat Object Coefficients