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nlme (version 3.1-84)
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
83,497
Version
3.1-84
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
July 27th, 2007
Functions in nlme (3.1-84)
Search functions
ACF.gls
Autocorrelation Function for gls Residuals
Initialize.reStruct
Initialize reStruct Object
varComb
Combination of Variance Functions
augPred
Augmented Predictions
pdBlocked
Positive-Definite Block Diagonal Matrix
summary.pdMat
Summarize a pdMat Object
plot.Variogram
Plot a Variogram Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
summary.modelStruct
Summarize a modelStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
pairs.compareFits
Pairs Plot of compareFits Object
as.matrix.reStruct
Matrices of an reStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
Matrix.reStruct
Assign reStruct Matrices
pdClasses
Positive-Definite Matrix Classes
pdDiag
Diagonal Positive-Definite Matrix
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
ACF
Autocorrelation Function
corSpatial
Spatial Correlation Structure
VarCorr
Extract variance and correlation components
varFunc
Variance Function Structure
Initialize.lmeStruct
Initialize an lmeStruct Object
predict.lme
Predictions from an lme Object
varExp
Exponential Variance Function
varWeights
Extract Variance Function Weights
summary.varFunc
Summarize varFunc Object
corFactor.corStruct
Factor of a corStruct Object Matrix
Names
Names Associated with an Object
residuals.lme
Extract lme Residuals
Initialize.glsStruct
Initialize a glsStruct Object
coef.reStruct
reStruct Object Coefficients
[.pdMat
Subscript a pdMat Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
update.modelStruct
Update a modelStruct Object
Initialize.varFunc
Initialize varFunc Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
Variogram.default
Calculate Semi-variogram
corMatrix.corStruct
Matrix of a corStruct Object
varClasses
Variance Function Classes
pdNatural
General Positive-Definite Matrix in Natural Parametrization
logLik.lme
Log-Likelihood of an lme Object
corCAR1
Continuous AR(1) Correlation Structure
compareFits
Compare Fitted Objects
varFixed
Fixed Variance Function
residuals.gls
Extract gls Residuals
ranef.lmList
Extract lmList Random Effects
Initialize
Initialize Object
Names.reStruct
Names of an reStruct Object
corARMA
ARMA(p,q) Correlation Structure
plot.ACF
Plot an ACF Object
BIC.logLik
BIC of a logLik Object
Dim
Extract Dimensions from an Object
residuals.lmList
Extract lmList Residuals
recalc.corStruct
Recalculate for corStruct Object
formula.pdMat
Extract pdMat Formula
logDet.pdMat
Extract Log-Determinant from a pdMat Object
random.effects
Extract Random Effects
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
corAR1
AR(1) Correlation Structure
residuals.lmeStruct
Calculate lmeStruct Residuals
corSymm
General Correlation Structure
corCompSymm
Compound Symmetry Correlation Structure
corFactor
Factor of a Correlation Matrix
coef.varFunc
varFunc Object Coefficients
ACF.lme
Autocorrelation Function for lme Residuals
LDEsysMat
Generate system matrix for LDEs
recalc.varFunc
Recalculate for varFunc Object
formula.pdBlocked
Extract pdBlocked Formula
summary.corStruct
Summarize a corStruct Object
nlmeObject
Fitted nlme Object
anova.gls
Compare Likelihoods of Fitted Objects
fixef.lmList
Extract lmList Fixed Effects
nlmeStruct
Nonlinear Mixed-Effects Structure
getVarCov
Extract variance-covariance matrix
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Coef
Assign Values to Coefficients
summary.lme
Summarize an lme Object
isInitialized
Check if Object is Initialized
pairs.lmList
Pairs Plot of an lmList Object
update.varFunc
Update varFunc Object
coef.lme
Extract lme Coefficients
fitted.glsStruct
Calculate glsStruct Fitted Values
getCovariate.varFunc
Extract varFunc Covariate
Dim.corStruct
Dimensions of a corStruct Object
Covariate
Assign Covariate Values
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
corExp
Exponential Correlation Structure
Variogram.corLin
Calculate Semi-variogram for a corLin Object
print.summary.pdMat
Print a summary.pdMat Object
lme
Linear Mixed-Effects Models
pooledSD
Extract Pooled Standard Deviation
recalc.reStruct
Recalculate for an reStruct Object
corMatrix
Extract Correlation Matrix
coef.gnls
Extract gnls Coefficients
nlsList
List of nls Objects with a Common Model
plot.nffGroupedData
Plot an nffGroupedData Object
summary.nlsList
Summarize an nlsList Object
asTable
Convert groupedData to a matrix
getData.gls
Extract gls Object Data
coef.corStruct
Coefficients of a corStruct Object
getData
Extract Data from an Object
pdMat
Positive-Definite Matrix
getGroups.lme
Extract lme Object Groups
pairs.lme
Pairs Plot of an lme Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
glsStruct
Generalized Least Squares Structure
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
nlsList.selfStart
nlsList Fit from a selfStart Function
getData.lme
Extract lme Object Data
fixed.effects
Extract Fixed Effects
qqnorm.gls
Normal Plot of Residuals from a gls Object
plot.ranef.lme
Plot a ranef.lme Object
recalc
Recalculate Condensed Linear Model Object
isBalanced
Check a Design for Balance
getGroups.varFunc
Extract varFunc Groups
getResponseFormula
Extract Formula Specifying Response Variable
varPower
Power Variance Function
pdConstruct
Construct pdMat Objects
plot.nfnGroupedData
Plot an nfnGroupedData Object
summary.gls
Summarize a gls Object
recalc.modelStruct
Recalculate for a modelStruct Object
getGroups.corStruct
Extract corStruct Groups
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
formula.reStruct
Extract reStruct Object Formula
gls
Fit Linear Model Using Generalized Least Squares
logDet
Extract the Logarithm of the Determinant
getGroups.lmList
Extract lmList Object Groups
collapse.groupedData
Collapse a groupedData Object
varIdent
Constant Variance Function
glsObject
Fitted gls Object
predict.lmList
Predictions from an lmList Object
getCovariate
Extract Covariate from an Object
corRatio
Rational Quadratic Correlation Structure
reStruct
Random Effects Structure
solve.reStruct
Apply Solve to an reStruct Object
plot.ranef.lmList
Plot a ranef.lmList Object
quinModel
Model function for the Quinidine data
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.lmeStruct
Calculate lmeStruct Fitted Values
logLik.gnls
Log-Likelihood of a gnls Object
logLik.corStruct
Extract corStruct Log-Likelihood
splitFormula
Split a Formula
pdIdent
Multiple of the Identity Positive-Definite Matrix
corGaus
Gaussian Correlation Structure
predict.gls
Predictions from a gls Object
getGroups
Extract Grouping Factors from an Object
collapse
Collapse According to Groups
Initialize.corStruct
Initialize corStruct Object
plot.compareFits
Plot a compareFits Object
varConstPower
Constant Plus Power Variance Function
pdLogChol
General Positive-Definite Matrix
Matrix.pdMat
Assign Matrix to a pdMat Object
nlme
Nonlinear Mixed-Effects Models
pdSymm
General Positive-Definite Matrix
gnlsControl
Control Values for gnls Fit
allCoef
Extract Coefficients from a Set of Objects
as.matrix.pdMat
Matrix of a pdMat Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Matrix
Assign Matrix Values
asOneFormula
Combine Formulas of a Set of Objects
Names.pdBlocked
Names of a pdBlocked Object
Names.pdMat
Names of a pdMat Object
plot.lme
Plot an lme or nls object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
needUpdate
Check if Update is Needed
print.varFunc
Print a varFunc Object
coef.pdMat
pdMat Object Coefficients
plot.augPred
Plot an augPred Object
logLik.varFunc
Extract varFunc logLik
glsControl
Control Values for gls Fit
residuals.gnlsStruct
Calculate gnlsStruct Residuals
Covariate.varFunc
Assign varFunc Covariate
Dim.pdMat
Dimensions of a pdMat Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
plot.lmList
Plot an lmList Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
lmeControl
Control Values for lme Fit
predict.gnls
Predictions from a gnls Object
Dim.corSpatial
Dimensions of a corSpatial Object
simulate.lme
Simulate results from lme models
plot.nmGroupedData
Plot an nmGroupedData Object
nlmeControl
Control Values for nlme Fit
coef.lmList
Extract lmList Coefficients
Names.formula
Extract Names from a formula
fitted.lmList
Extract lmList Fitted Values
predict.nlme
Predictions from an nlme Object
plot.intervals.lmList
Plot lmList Confidence Intervals
summary.lmList
Summarize an lmList Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
comparePred
Compare Predictions
BIC
Bayesian Information Criterion
phenoModel
Model function for the Phenobarb data
Variogram
Calculate Semi-variogram
anova.lme
Compare Likelihoods of Fitted Objects
corLin
Linear Correlation Structure
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
corClasses
Correlation Structure Classes
corSpher
Spherical Correlation Structure
coef.modelStruct
Extract modelStruct Object Coefficients
nlme.nlsList
NLME fit from nlsList Object
gsummary
Summarize by Groups
ranef.lme
Extract lme Random Effects
residuals.nlmeStruct
Calculate nlmeStruct Residuals
plot.gls
Plot a gls Object
model.matrix.reStruct
reStruct Model Matrix
pdFactor
Square-Root Factor of a Positive-Definite Matrix
balancedGrouped
Create a groupedData object from a matrix
gapply
Apply a Function by Groups
getCovariateFormula
Extract Covariates Formula
lmeObject
Fitted lme Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
getCovariate.data.frame
Extract Data Frame Covariate
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
lmList
List of lm Objects with a Common Model
lme.lmList
LME fit from lmList Object
lmeStruct
Linear Mixed-Effects Structure
logLik.lmList
Log-Likelihood of an lmList Object
getGroups.gls
Extract gls Object Groups
intervals.lme
Confidence Intervals on lme Parameters
getCovariate.corStruct
Extract corStruct Object Covariate
intervals.gls
Confidence Intervals on gls Parameters
lmList.groupedData
lmList Fit from a groupedData Object
intervals.lmList
Confidence Intervals on lmList Coefficients
lmeScale
Scale for lme Optimization
getGroupsFormula
Extract Grouping Formula
logDet.corStruct
Extract corStruct Log-Determinant
intervals
Confidence Intervals on Coefficients
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
gnlsObject
Fitted gnls Object
groupedData
Construct a groupedData Object
getResponse
Extract Response Variable from an Object
getData.lmList
Extract lmList Object Data
logDet.reStruct
Extract reStruct Log-Determinants
fitted.lme
Extract lme Fitted Values
lme.groupedData
LME fit from groupedData Object
corNatural
General correlation in natural parameterization
fdHess
Finite difference Hessian
gnls
Fit Nonlinear Model Using Generalized Least Squares
gnlsStruct
Generalized Nonlinear Least Squares Structure
Glucose2
Glucose Levels Following Alcohol Ingestion
Gasoline
Refinery yield of gasoline
Ovary
Counts of Ovarian Follicles
Oxboys
Heights of Boys in Oxford
RatPupWeight
The weight of rat pups
Assay
Bioassay on Cell Culture Plate
Relaxin
Assay for Relaxin
Tetracycline2
Pharmacokinetics of tetracycline
Cefamandole
Pharmacokinetics of Cefamandole
Dialyzer
High-Flux Hemodialyzer
Wheat2
Wheat Yield Trials
Glucose
Glucose levels over time
Nitrendipene
Assay of nitrendipene
Soybean
Growth of soybean plants
Meat
Tenderness of meat
Gun
Methods for firing naval guns
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Quinidine
Quinidine Kinetics
bdf
Language scores
Oxide
Variability in Semiconductor Manufacturing
Oats
Split-plot Experiment on Varieties of Oats
BodyWeight
Rat weight over time for different diets
Rail
Evaluation of Stress in Railway Rails
Orthodont
Growth curve data on an orthdontic measurement
Earthquake
Earthquake Intensity
Milk
Protein content of cows' milk
Remifentanil
Pharmacokinetics of remifentanil
Spruce
Growth of Spruce Trees
Pixel
X-ray pixel intensities over time
Machines
Productivity Scores for Machines and Workers
MathAchieve
Mathematics achievement scores
Phenobarb
Phenobarbitol Kinetics
ergoStool
Ergometrics experiment with stool types
MathAchSchool
School demographic data for MathAchieve
Fatigue
Cracks caused by metal fatigue
Wheat
Yields by growing conditions
IGF
Radioimmunoassay of IGF-I Protein
Muscle
Contraction of heart muscle sections
PBG
Effect of Phenylbiguanide on Blood Pressure
Tetracycline1
Pharmacokinetics of tetracycline
Wafer
Modeling of Analog MOS Circuits