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nlme (version 3.1-96)
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
3.1-96
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
October 15th, 2009
Functions in nlme (3.1-96)
Search all functions
Variogram
Calculate Semi-variogram
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
getData
Extract Data from an Object
Wheat
Yields by growing conditions
BIC.logLik
BIC of a logLik Object
Dialyzer
High-Flux Hemodialyzer
Gasoline
Refinery yield of gasoline
Dim.corStruct
Dimensions of a corStruct Object
Dim.pdMat
Dimensions of a pdMat Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Dim.corSpatial
Dimensions of a corSpatial Object
summary.lme
Summarize an lme Object
Meat
Tenderness of meat
Matrix.reStruct
Assign reStruct Matrices
Glucose2
Glucose Levels Following Alcohol Ingestion
Fatigue
Cracks caused by metal fatigue
Covariate.varFunc
Assign varFunc Covariate
IGF
Radioimmunoassay of IGF-I Protein
Milk
Protein content of cows' milk
allCoef
Extract Coefficients from a Set of Objects
Names.pdBlocked
Names of a pdBlocked Object
Oxboys
Heights of Boys in Oxford
ACF
Autocorrelation Function
Ovary
Counts of Ovarian Follicles
RatPupWeight
The weight of rat pups
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
corFactor.corStruct
Factor of a corStruct Object Matrix
LDEsysMat
Generate system matrix for LDEs
getResponse
Extract Response Variable from an Object
Wafer
Modeling of Analog MOS Circuits
BodyWeight
Rat weight over time for different diets
Names
Names Associated with an Object
Gun
Methods for firing naval guns
glsStruct
Generalized Least Squares Structure
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
summary.modelStruct
Summarize a modelStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
collapse.groupedData
Collapse a groupedData Object
anova.lme
Compare Likelihoods of Fitted Objects
corRatio
Rational Quadratic Correlation Structure
Earthquake
Earthquake Intensity
Coef
Assign Values to Coefficients
Variogram.default
Calculate Semi-variogram
ACF.gls
Autocorrelation Function for gls Residuals
Tetracycline2
Pharmacokinetics of tetracycline
Rail
Evaluation of Stress in Railway Rails
Oxide
Variability in Semiconductor Manufacturing
Matrix
Assign Matrix Values
Cefamandole
Pharmacokinetics of Cefamandole
coef.corStruct
Coefficients of a corStruct Object
Assay
Bioassay on Cell Culture Plate
Soybean
Growth of soybean plants
logLik.reStruct
Calculate reStruct Log-Likelihood
PBG
Effect of Phenylbiguanide on Blood Pressure
Remifentanil
Pharmacokinetics of remifentanil
Initialize.glsStruct
Initialize a glsStruct Object
varComb
Combination of Variance Functions
Quinidine
Quinidine Kinetics
MathAchSchool
School demographic data for MathAchieve
Oats
Split-plot Experiment on Varieties of Oats
as.matrix.reStruct
Matrices of an reStruct Object
varClasses
Variance Function Classes
getGroups
Extract Grouping Factors from an Object
ACF.lme
Autocorrelation Function for lme Residuals
Orthodont
Growth curve data on an orthdontic measurement
Machines
Productivity Scores for Machines and Workers
coef.lmList
Extract lmList Coefficients
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
Initialize.reStruct
Initialize reStruct Object
fixed.effects
Extract Fixed Effects
splitFormula
Split a Formula
varPower
Power Variance Function
recalc.varFunc
Recalculate for varFunc Object
getData.lme
Extract lme Object Data
getResponseFormula
Extract Formula Specifying Response Variable
Initialize
Initialize Object
Dim
Extract Dimensions from an Object
fixef.lmList
Extract lmList Fixed Effects
Tetracycline1
Pharmacokinetics of tetracycline
getCovariate.corStruct
Extract corStruct Object Covariate
fdHess
Finite difference Hessian
corARMA
ARMA(p,q) Correlation Structure
formula.pdMat
Extract pdMat Formula
VarCorr
Extract variance and correlation components
summary.corStruct
Summarize a corStruct Object
getGroups.lme
Extract lme Object Groups
collapse
Collapse According to Groups
residuals.lmList
Extract lmList Residuals
getCovariate.data.frame
Extract Data Frame Covariate
varExp
Exponential Variance Function
coef.modelStruct
Extract modelStruct Object Coefficients
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
Names.formula
Extract Names from a formula
Wheat2
Wheat Yield Trials
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Spruce
Growth of Spruce Trees
getGroups.varFunc
Extract varFunc Groups
Relaxin
Assay for Relaxin
comparePred
Compare Predictions
getCovariate.varFunc
Extract varFunc Covariate
Muscle
Contraction of heart muscle sections
logLik.lmList
Log-Likelihood of an lmList Object
varFunc
Variance Function Structure
lmList.groupedData
lmList Fit from a groupedData Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Covariate
Assign Covariate Values
getCovariateFormula
Extract Covariates Formula
summary.pdMat
Summarize a pdMat Object
update.varFunc
Update varFunc Object
getGroupsFormula
Extract Grouping Formula
coef.gnls
Extract gnls Coefficients
as.matrix.pdMat
Matrix of a pdMat Object
corSymm
General Correlation Structure
augPred
Augmented Predictions
getGroups.data.frame
Extract Groups from a Data Frame
asTable
Convert groupedData to a matrix
getData.gls
Extract gls Object Data
coef.lme
Extract lme Coefficients
corCompSymm
Compound Symmetry Correlation Structure
compareFits
Compare Fitted Objects
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
update.modelStruct
Update a modelStruct Object
residuals.lme
Extract lme Residuals
[.pdMat
Subscript a pdMat Object
summary.varFunc
Summarize varFunc Object
ergoStool
Ergometrics experiment with stool types
Initialize.corStruct
Initialize corStruct Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
residuals.glsStruct
Calculate glsStruct Residuals
print.varFunc
Print a varFunc Object
Pixel
X-ray pixel intensities over time
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Nitrendipene
Assay of nitrendipene
quinModel
Model function for the Quinidine data
coef.pdMat
pdMat Object Coefficients
plot.augPred
Plot an augPred Object
varWeights
Extract Variance Function Weights
simulate.lme
Simulate results from lme models
logLik.gnls
Log-Likelihood of a gnls Object
recalc.corStruct
Recalculate for corStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corGaus
Gaussian Correlation Structure
getGroups.corStruct
Extract corStruct Groups
coef.varFunc
varFunc Object Coefficients
plot.ACF
Plot an ACF Object
corLin
Linear Correlation Structure
MathAchieve
Mathematics achievement scores
Names.pdMat
Names of a pdMat Object
logLik.lme
Log-Likelihood of an lme Object
Initialize.varFunc
Initialize varFunc Object
summary.nlsList
Summarize an nlsList Object
predict.lmList
Predictions from an lmList Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
varConstPower
Constant Plus Power Variance Function
logLik.glsStruct
Log-Likelihood of a glsStruct Object
coef.reStruct
reStruct Object Coefficients
Matrix.pdMat
Assign Matrix to a pdMat Object
logDet
Extract the Logarithm of the Determinant
summary.lmList
Summarize an lmList Object
solve.reStruct
Apply Solve to an reStruct Object
Glucose
Glucose levels over time
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
bdf
Language scores
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
print.summary.pdMat
Print a summary.pdMat Object
recalc
Recalculate Condensed Linear Model Object
residuals.lmeStruct
Calculate lmeStruct Residuals
Initialize.lmeStruct
Initialize an lmeStruct Object
plot.ranef.lme
Plot a ranef.lme Object
needUpdate
Check if Update is Needed
Phenobarb
Phenobarbitol Kinetics
recalc.reStruct
Recalculate for an reStruct Object
corExp
Exponential Correlation Structure
corMatrix.corStruct
Matrix of a corStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getData.lmList
Extract lmList Object Data
varFixed
Fixed Variance Function
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
plot.lme
Plot an lme or nls object
glsObject
Fitted gls Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
nlmeStruct
Nonlinear Mixed-Effects Structure
lmeStruct
Linear Mixed-Effects Structure
anova.gls
Compare Likelihoods of Fitted Objects
BIC
Bayesian Information Criterion
lme.groupedData
LME fit from groupedData Object
formula.reStruct
Extract reStruct Object Formula
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
fitted.lmList
Extract lmList Fitted Values
getGroups.lmList
Extract lmList Object Groups
Names.reStruct
Names of an reStruct Object
nlsList.selfStart
nlsList Fit from a selfStart Function
fitted.lme
Extract lme Fitted Values
plot.ranef.lmList
Plot a ranef.lmList Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
Variogram.corLin
Calculate Semi-variogram for a corLin Object
summary.gls
Summarize a gls Object
getGroups.gls
Extract gls Object Groups
fitted.glsStruct
Calculate glsStruct Fitted Values
logLik.corStruct
Extract corStruct Log-Likelihood
pdClasses
Positive-Definite Matrix Classes
gapply
Apply a Function by Groups
intervals.lmList
Confidence Intervals on lmList Coefficients
gnlsControl
Control Values for gnls Fit
corSpher
Spherical Correlation Structure
corMatrix
Extract Correlation Matrix
isBalanced
Check a Design for Balance
plot.intervals.lmList
Plot lmList Confidence Intervals
gls
Fit Linear Model Using Generalized Least Squares
logDet.corStruct
Extract corStruct Log-Determinant
nlmeControl
Control Values for nlme Fit
plot.compareFits
Plot a compareFits Object
predict.gnls
Predictions from a gnls Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
pdMat
Positive-Definite Matrix
as.matrix.corStruct
Matrix of a corStruct Object
glsControl
Control Values for gls Fit
ranef.lme
Extract lme Random Effects
lmeObject
Fitted lme Object
predict.lme
Predictions from an lme Object
plot.Variogram
Plot a Variogram Object
phenoModel
Model function for the Phenobarb data
intervals.lme
Confidence Intervals on lme Parameters
pdSymm
General Positive-Definite Matrix
pdDiag
Diagonal Positive-Definite Matrix
corAR1
AR(1) Correlation Structure
corClasses
Correlation Structure Classes
asOneFormula
Combine Formulas of a Set of Objects
corCAR1
Continuous AR(1) Correlation Structure
nlmeObject
Fitted nlme Object
nlme.nlsList
NLME fit from nlsList Object
intervals.gls
Confidence Intervals on gls Parameters
residuals.gls
Extract gls Residuals
getVarCov
Extract variance-covariance matrix
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
plot.nfnGroupedData
Plot an nfnGroupedData Object
pairs.compareFits
Pairs Plot of compareFits Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
logDet.reStruct
Extract reStruct Log-Determinants
pdLogChol
General Positive-Definite Matrix
pairs.lme
Pairs Plot of an lme Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdConstruct.pdBlocked
Construct pdBlocked Objects
gsummary
Summarize by Groups
pdBlocked
Positive-Definite Block Diagonal Matrix
residuals.nlmeStruct
Calculate nlmeStruct Residuals
lmeScale
Scale for lme Optimization
balancedGrouped
Create a groupedData object from a matrix
model.matrix.reStruct
reStruct Model Matrix
nlsList
List of nls Objects with a Common Model
plot.nffGroupedData
Plot an nffGroupedData Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
logLik.varFunc
Extract varFunc logLik
pairs.lmList
Pairs Plot of an lmList Object
formula.pdBlocked
Extract pdBlocked Formula
varIdent
Constant Variance Function
plot.nmGroupedData
Plot an nmGroupedData Object
getCovariate
Extract Covariate from an Object
pdConstruct
Construct pdMat Objects
residuals.gnlsStruct
Calculate gnlsStruct Residuals
gnlsObject
Fitted gnls Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
predict.nlme
Predictions from an nlme Object
corNatural
General correlation in natural parameterization
lmList
List of lm Objects with a Common Model
predict.gls
Predictions from a gls Object
random.effects
Extract Random Effects
lmeControl
Control Values for lme Fit
groupedData
Construct a groupedData Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
intervals
Confidence Intervals on Coefficients
corSpatial
Spatial Correlation Structure
corFactor
Factor of a Correlation Matrix
isInitialized
Check if Object is Initialized
lme
Linear Mixed-Effects Models
pooledSD
Extract Pooled Standard Deviation
nlme
Nonlinear Mixed-Effects Models
ranef.lmList
Extract lmList Random Effects
reStruct
Random Effects Structure
pdNatural
General Positive-Definite Matrix in Natural Parametrization
lme.lmList
LME fit from lmList Object
plot.lmList
Plot an lmList Object
plot.gls
Plot a gls Object