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nlme (version 3.1-83)
Linear and Nonlinear Mixed Effects Models
Description
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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Install
install.packages('nlme')
Monthly Downloads
98,563
Version
3.1-83
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
June 13th, 2007
Functions in nlme (3.1-83)
Search functions
getGroupsFormula
Extract Grouping Formula
pdConstruct
Construct pdMat Objects
intervals.lmList
Confidence Intervals on lmList Coefficients
ACF.gls
Autocorrelation Function for gls Residuals
balancedGrouped
Create a groupedData object from a matrix
asTable
Convert groupedData to a matrix
plot.ACF
Plot an ACF Object
recalc.varFunc
Recalculate for varFunc Object
simulate.lme
Simulate results from lme models
residuals.nlmeStruct
Calculate nlmeStruct Residuals
varConstPower
Constant Plus Power Variance Function
pooledSD
Extract Pooled Standard Deviation
residuals.gnlsStruct
Calculate gnlsStruct Residuals
summary.pdMat
Summarize a pdMat Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
intervals.gls
Confidence Intervals on gls Parameters
ACF.lme
Autocorrelation Function for lme Residuals
Coef
Assign Values to Coefficients
coef.varFunc
varFunc Object Coefficients
coef.pdMat
pdMat Object Coefficients
corGaus
Gaussian Correlation Structure
fixed.effects
Extract Fixed Effects
collapse
Collapse According to Groups
ACF
Autocorrelation Function
coef.reStruct
reStruct Object Coefficients
glsObject
Fitted gls Object
needUpdate
Check if Update is Needed
varWeights
Extract Variance Function Weights
gapply
Apply a Function by Groups
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
getCovariate
Extract Covariate from an Object
Covariate
Assign Covariate Values
plot.gls
Plot a gls Object
residuals.gls
Extract gls Residuals
recalc.corStruct
Recalculate for corStruct Object
varExp
Exponential Variance Function
update.varFunc
Update varFunc Object
getResponseFormula
Extract Formula Specifying Response Variable
lmeScale
Scale for lme Optimization
glsControl
Control Values for gls Fit
compareFits
Compare Fitted Objects
corFactor
Factor of a Correlation Matrix
fixef.lmList
Extract lmList Fixed Effects
corNatural
General correlation in natural parameterization
isInitialized
Check if Object is Initialized
pdSymm
General Positive-Definite Matrix
summary.lmList
Summarize an lmList Object
getCovariate.varFunc
Extract varFunc Covariate
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
formula.reStruct
Extract reStruct Object Formula
getCovariate.corStruct
Extract corStruct Object Covariate
formula.pdMat
Extract pdMat Formula
recalc
Recalculate Condensed Linear Model Object
getCovariateFormula
Extract Covariates Formula
coef.gnls
Extract gnls Coefficients
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getGroups
Extract Grouping Factors from an Object
coef.lmList
Extract lmList Coefficients
Dim.pdMat
Dimensions of a pdMat Object
splitFormula
Split a Formula
Initialize
Initialize Object
solve.reStruct
Apply Solve to an reStruct Object
pdDiag
Diagonal Positive-Definite Matrix
varComb
Combination of Variance Functions
pairs.compareFits
Pairs Plot of compareFits Object
getData.lmList
Extract lmList Object Data
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
varFunc
Variance Function Structure
pairs.lmList
Pairs Plot of an lmList Object
predict.nlme
Predictions from an nlme Object
corCompSymm
Compound Symmetry Correlation Structure
print.varFunc
Print a varFunc Object
getData
Extract Data from an Object
getData.gls
Extract gls Object Data
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
residuals.lmeStruct
Calculate lmeStruct Residuals
[.pdMat
Subscript a pdMat Object
coef.lme
Extract lme Coefficients
Dim.corStruct
Dimensions of a corStruct Object
residuals.lmList
Extract lmList Residuals
varIdent
Constant Variance Function
gnlsObject
Fitted gnls Object
predict.lmList
Predictions from an lmList Object
recalc.modelStruct
Recalculate for a modelStruct Object
summary.gls
Summarize a gls Object
BIC.logLik
BIC of a logLik Object
glsStruct
Generalized Least Squares Structure
getGroups.gls
Extract gls Object Groups
getData.lme
Extract lme Object Data
getGroups.lme
Extract lme Object Groups
getGroups.varFunc
Extract varFunc Groups
getVarCov
Extract variance-covariance matrix
intervals
Confidence Intervals on Coefficients
predict.lme
Predictions from an lme Object
predict.gls
Predictions from a gls Object
phenoModel
Model function for the Phenobarb data
Names.pdMat
Names of a pdMat Object
lme.groupedData
LME fit from groupedData Object
gls
Fit Linear Model Using Generalized Least Squares
isBalanced
Check a Design for Balance
residuals.glsStruct
Calculate glsStruct Residuals
predict.gnls
Predictions from a gnls Object
fitted.glsStruct
Calculate glsStruct Fitted Values
fitted.lmList
Extract lmList Fitted Values
corARMA
ARMA(p,q) Correlation Structure
lmList.groupedData
lmList Fit from a groupedData Object
corCAR1
Continuous AR(1) Correlation Structure
Initialize.varFunc
Initialize varFunc Object
quinModel
Model function for the Quinidine data
intervals.lme
Confidence Intervals on lme Parameters
LDEsysMat
Generate system matrix for LDEs
varClasses
Variance Function Classes
nlmeControl
Control Values for nlme Fit
residuals.lme
Extract lme Residuals
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corAR1
AR(1) Correlation Structure
getCovariate.data.frame
Extract Data Frame Covariate
reStruct
Random Effects Structure
corSymm
General Correlation Structure
coef.corStruct
Coefficients of a corStruct Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
nlsList
List of nls Objects with a Common Model
BIC
Bayesian Information Criterion
logLik.varFunc
Extract varFunc logLik
gsummary
Summarize by Groups
gnls
Fit Nonlinear Model Using Generalized Least Squares
lmeControl
Control Values for lme Fit
gnlsStruct
Generalized Nonlinear Least Squares Structure
Matrix
Assign Matrix Values
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Initialize.corStruct
Initialize corStruct Object
ranef.lme
Extract lme Random Effects
getGroups.lmList
Extract lmList Object Groups
Dim.corSpatial
Dimensions of a corSpatial Object
summary.corStruct
Summarize a corStruct Object
gnlsControl
Control Values for gnls Fit
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
varPower
Power Variance Function
random.effects
Extract Random Effects
summary.nlsList
Summarize an nlsList Object
corExp
Exponential Correlation Structure
formula.pdBlocked
Extract pdBlocked Formula
getGroups.corStruct
Extract corStruct Groups
corSpher
Spherical Correlation Structure
ranef.lmList
Extract lmList Random Effects
recalc.reStruct
Recalculate for an reStruct Object
Initialize.glsStruct
Initialize a glsStruct Object
coef.modelStruct
Extract modelStruct Object Coefficients
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
pdLogChol
General Positive-Definite Matrix
Names.reStruct
Names of an reStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
corFactor.corStruct
Factor of a corStruct Object Matrix
comparePred
Compare Predictions
logDet.pdMat
Extract Log-Determinant from a pdMat Object
lmList
List of lm Objects with a Common Model
nlme
Nonlinear Mixed-Effects Models
nlmeObject
Fitted nlme Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
print.summary.pdMat
Print a summary.pdMat Object
collapse.groupedData
Collapse a groupedData Object
plot.intervals.lmList
Plot lmList Confidence Intervals
pdClasses
Positive-Definite Matrix Classes
plot.Variogram
Plot a Variogram Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
logLik.reStruct
Calculate reStruct Log-Likelihood
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
qqnorm.gls
Normal Plot of Residuals from a gls Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
summary.modelStruct
Summarize a modelStruct Object
Initialize.reStruct
Initialize reStruct Object
corMatrix.corStruct
Matrix of a corStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
allCoef
Extract Coefficients from a Set of Objects
corLin
Linear Correlation Structure
logDet.reStruct
Extract reStruct Log-Determinants
Variogram.corLin
Calculate Semi-variogram for a corLin Object
corClasses
Correlation Structure Classes
Variogram.default
Calculate Semi-variogram
nlme.nlsList
NLME fit from nlsList Object
Initialize.lmeStruct
Initialize an lmeStruct Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
Dim
Extract Dimensions from an Object
plot.lmList
Plot an lmList Object
corRatio
Rational Quadratic Correlation Structure
summary.lme
Summarize an lme Object
plot.nmGroupedData
Plot an nmGroupedData Object
Matrix.reStruct
Assign reStruct Matrices
summary.varFunc
Summarize varFunc Object
lmeStruct
Linear Mixed-Effects Structure
Covariate.varFunc
Assign varFunc Covariate
corSpatial
Spatial Correlation Structure
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdBlocked
Positive-Definite Block Diagonal Matrix
logLik.gnls
Log-Likelihood of a gnls Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
logDet
Extract the Logarithm of the Determinant
lmeObject
Fitted lme Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
as.matrix.pdMat
Matrix of a pdMat Object
augPred
Augmented Predictions
corMatrix
Extract Correlation Matrix
logDet.corStruct
Extract corStruct Log-Determinant
getResponse
Extract Response Variable from an Object
groupedData
Construct a groupedData Object
pdMat
Positive-Definite Matrix
asOneFormula
Combine Formulas of a Set of Objects
plot.nfnGroupedData
Plot an nfnGroupedData Object
nlmeStruct
Nonlinear Mixed-Effects Structure
as.matrix.corStruct
Matrix of a corStruct Object
plot.ranef.lmList
Plot a ranef.lmList Object
fdHess
Finite difference Hessian
logLik.glsStruct
Log-Likelihood of a glsStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
lme
Linear Mixed-Effects Models
nlsList.selfStart
nlsList Fit from a selfStart Function
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pairs.lme
Pairs Plot of an lme Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
logLik.lme
Log-Likelihood of an lme Object
varFixed
Fixed Variance Function
update.modelStruct
Update a modelStruct Object
anova.gls
Compare Likelihoods of Fitted Objects
Variogram
Calculate Semi-variogram
pdFactor
Square-Root Factor of a Positive-Definite Matrix
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
plot.compareFits
Plot a compareFits Object
fitted.lme
Extract lme Fitted Values
plot.ranef.lme
Plot a ranef.lme Object
model.matrix.reStruct
reStruct Model Matrix
plot.lme
Plot an lme or nls object
plot.augPred
Plot an augPred Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Matrix.pdMat
Assign Matrix to a pdMat Object
VarCorr
Extract variance and correlation components
Names.pdBlocked
Names of a pdBlocked Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
lme.lmList
LME fit from lmList Object
Names
Names Associated with an Object
Names.formula
Extract Names from a formula
as.matrix.reStruct
Matrices of an reStruct Object
logLik.corStruct
Extract corStruct Log-Likelihood
BodyWeight
Rat weight over time for different diets
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Relaxin
Assay for Relaxin
MathAchieve
Mathematics achievement scores
Fatigue
Cracks caused by metal fatigue
Muscle
Contraction of heart muscle sections
Gasoline
Refinery yield of gasoline
Meat
Tenderness of meat
Oxboys
Heights of Boys in Oxford
MathAchSchool
School demographic data for MathAchieve
Milk
Protein content of cows' milk
Soybean
Growth of soybean plants
Remifentanil
Pharmacokinetics of remifentanil
Nitrendipene
Assay of nitrendipene
Quinidine
Quinidine Kinetics
Machines
Productivity Scores for Machines and Workers
bdf
Language scores
Earthquake
Earthquake Intensity
Dialyzer
High-Flux Hemodialyzer
Ovary
Counts of Ovarian Follicles
Gun
Methods for firing naval guns
RatPupWeight
The weight of rat pups
Wheat2
Wheat Yield Trials
IGF
Radioimmunoassay of IGF-I Protein
Glucose2
Glucose Levels Following Alcohol Ingestion
Oats
Split-plot Experiment on Varieties of Oats
Cefamandole
Pharmacokinetics of Cefamandole
Phenobarb
Phenobarbitol Kinetics
Glucose
Glucose levels over time
Rail
Evaluation of Stress in Railway Rails
PBG
Effect of Phenylbiguanide on Blood Pressure
Tetracycline1
Pharmacokinetics of tetracycline
Tetracycline2
Pharmacokinetics of tetracycline
ergoStool
Ergometrics experiment with stool types
Assay
Bioassay on Cell Culture Plate
Spruce
Growth of Spruce Trees
Oxide
Variability in Semiconductor Manufacturing
Orthodont
Growth curve data on an orthdontic measurement
Wafer
Modeling of Analog MOS Circuits
Pixel
X-ray pixel intensities over time
Wheat
Yields by growing conditions