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nlme (version 3.1-105)
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
3.1-105
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
October 11th, 2012
Functions in nlme (3.1-105)
Search functions
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Dim.corSpatial
Dimensions of a corSpatial Object
corCAR1
Continuous AR(1) Correlation Structure
Assay
Bioassay on Cell Culture Plate
Tetracycline1
Pharmacokinetics of tetracycline
Names
Names Associated with an Object
asTable
Convert groupedData to a matrix
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
comparePred
Compare Predictions
glsControl
Control Values for gls Fit
gnlsObject
Fitted gnls Object
augPred
Augmented Predictions
Names.reStruct
Names of an reStruct Object
getCovariate.data.frame
Extract Data Frame Covariate
gnlsStruct
Generalized Nonlinear Least Squares Structure
IGF
Radioimmunoassay of IGF-I Protein
corExp
Exponential Correlation Structure
Fatigue
Cracks caused by metal fatigue
Glucose2
Glucose Levels Following Alcohol Ingestion
Meat
Tenderness of meat
corRatio
Rational Quadratic Correlation Structure
needUpdate
Check if Update is Needed
Matrix.pdMat
Assign Matrix to a pdMat Object
balancedGrouped
Create a groupedData object from a matrix
fixed.effects
Extract Fixed Effects
Milk
Protein content of cows' milk
nlme
Nonlinear Mixed-Effects Models
logDet
Extract the Logarithm of the Determinant
pdLogChol
General Positive-Definite Matrix
Cefamandole
Pharmacokinetics of Cefamandole
corGaus
Gaussian Correlation Structure
Dim.pdMat
Dimensions of a pdMat Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
lme.lmList
LME fit from lmList Object
lme.groupedData
LME fit from groupedData Object
Dim
Extract Dimensions from an Object
PBG
Effect of Phenylbiguanide on Blood Pressure
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.corStruct
Extract corStruct Log-Likelihood
Glucose
Glucose levels over time
Oxide
Variability in Semiconductor Manufacturing
plot.lmList
Plot an lmList Object
BodyWeight
Rat weight over time for different diets
predict.gls
Predictions from a gls Object
Initialize.glsStruct
Initialize a glsStruct Object
ACF.lme
Autocorrelation Function for lme Residuals
summary.nlsList
Summarize an nlsList Object
Spruce
Growth of Spruce Trees
varWeights.glsStruct
Variance Weights for glsStruct Object
Machines
Productivity Scores for Machines and Workers
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
Matrix
Assign Matrix Values
coef.modelStruct
Extract modelStruct Object Coefficients
Rail
Evaluation of Stress in Railway Rails
Pixel
X-ray pixel intensities over time
lmeObject
Fitted lme Object
pdSymm
General Positive-Definite Matrix
summary.corStruct
Summarize a corStruct Object
coef.corStruct
Coefficients of a corStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
nlsList.selfStart
nlsList Fit from a selfStart Function
Dim.corStruct
Dimensions of a corStruct Object
as.matrix.reStruct
Matrices of an reStruct Object
lmList
List of lm Objects with a Common Model
Initialize.corStruct
Initialize corStruct Object
intervals.lmList
Confidence Intervals on lmList Coefficients
Wafer
Modeling of Analog MOS Circuits
varFunc
Variance Function Structure
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
Initialize
Initialize Object
summary.gls
Summarize a gls Object
as.matrix.corStruct
Matrix of a corStruct Object
getVarCov
Extract variance-covariance matrix
plot.ranef.lme
Plot a ranef.lme Object
Initialize.reStruct
Initialize reStruct Object
collapse.groupedData
Collapse a groupedData Object
corFactor.corStruct
Factor of a corStruct Object Matrix
anova.gls
Compare Likelihoods of Fitted Objects
varComb
Combination of Variance Functions
summary.lme
Summarize an lme Object
fdHess
Finite difference Hessian
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
pdNatural
General Positive-Definite Matrix in Natural Parametrization
anova.lme
Compare Likelihoods of Fitted Objects
Names.pdBlocked
Names of a pdBlocked Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
update.modelStruct
Update a modelStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
fitted.lmList
Extract lmList Fitted Values
Orthodont
Growth curve data on an orthdontic measurement
gnls
Fit Nonlinear Model Using Generalized Least Squares
gsummary
Summarize by Groups
logDet.corStruct
Extract corStruct Log-Determinant
Muscle
Contraction of heart muscle sections
coef.lme
Extract lme Coefficients
getGroups.lmList
Extract lmList Object Groups
fixef.lmList
Extract lmList Fixed Effects
pdMat
Positive-Definite Matrix
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
corARMA
ARMA(p,q) Correlation Structure
as.matrix.pdMat
Matrix of a pdMat Object
Oats
Split-plot Experiment on Varieties of Oats
summary.pdMat
Summarize a pdMat Object
getData
Extract Data from an Object
coef.varFunc
varFunc Object Coefficients
corCompSymm
Compound Symmetry Correlation Structure
Names.pdMat
Names of a pdMat Object
Matrix.reStruct
Assign reStruct Matrices
varClasses
Variance Function Classes
residuals.gnlsStruct
Calculate gnlsStruct Residuals
MathAchSchool
School demographic data for MathAchieve
recalc
Recalculate Condensed Linear Model Object
plot.ranef.lmList
Plot a ranef.lmList Object
predict.lmList
Predictions from an lmList Object
formula.pdBlocked
Extract pdBlocked Formula
corAR1
AR(1) Correlation Structure
recalc.reStruct
Recalculate for an reStruct Object
logDet.reStruct
Extract reStruct Log-Determinants
formula.reStruct
Extract reStruct Object Formula
getCovariate.corStruct
Extract corStruct Object Covariate
getCovariate
Extract Covariate from an Object
getGroups.lme
Extract lme Object Groups
varPower
Power Variance Function
Relaxin
Assay for Relaxin
Gun
Methods for firing naval guns
Covariate
Assign Covariate Values
Initialize.varFunc
Initialize varFunc Object
LDEsysMat
Generate system matrix for LDEs
Variogram.default
Calculate Semi-variogram
Coef
Assign Values to Coefficients
coef.reStruct
reStruct Object Coefficients
Initialize.lmeStruct
Initialize an lmeStruct Object
Variogram
Calculate Semi-variogram
ergoStool
Ergometrics experiment with stool types
gls
Fit Linear Model Using Generalized Least Squares
ACF.gls
Autocorrelation Function for gls Residuals
coef.gnls
Extract gnls Coefficients
Ovary
Counts of Ovarian Follicles
glsStruct
Generalized Least Squares Structure
VarCorr
Extract variance and correlation components
gapply
Apply a Function by Groups
getGroups.corStruct
Extract corStruct Groups
bdf
Language scores
MathAchieve
Mathematics achievement scores
Earthquake
Earthquake Intensity
Remifentanil
Pharmacokinetics of remifentanil
[.pdMat
Subscript a pdMat Object
ACF
Autocorrelation Function
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
groupedData
Construct a groupedData Object
lmeControl
Control Values for lme Fit
Names.formula
Extract Names from a formula
Tetracycline2
Pharmacokinetics of tetracycline
Gasoline
Refinery yield of gasoline
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Dialyzer
High-Flux Hemodialyzer
logLik.gnls
Log-Likelihood of a gnls Object
Phenobarb
Phenobarbitol Kinetics
Soybean
Growth of soybean plants
coef.pdMat
pdMat Object Coefficients
corFactor
Factor of a Correlation Matrix
residuals.lmList
Extract lmList Residuals
getResponse
Extract Response Variable from an Object
lmeStruct
Linear Mixed-Effects Structure
getGroups.data.frame
Extract Groups from a Data Frame
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
intervals.lme
Confidence Intervals on lme Parameters
plot.lme
Plot an lme or nls object
getData.lme
Extract lme Object Data
predict.nlme
Predictions from an nlme Object
pairs.compareFits
Pairs Plot of compareFits Object
lme
Linear Mixed-Effects Models
logLik.reStruct
Calculate reStruct Log-Likelihood
plot.nmGroupedData
Plot an nmGroupedData Object
corSpher
Spherical Correlation Structure
compareFits
Compare Fitted Objects
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
Wheat2
Wheat Yield Trials
lmeScale
Scale for lme Optimization
pdFactor
Square-Root Factor of a Positive-Definite Matrix
Variogram.corExp
Calculate Semi-variogram for a corExp Object
predict.gnls
Predictions from a gnls Object
summary.modelStruct
Summarize a modelStruct Object
coef.lmList
Extract lmList Coefficients
corLin
Linear Correlation Structure
fitted.lme
Extract lme Fitted Values
plot.compareFits
Plot a compareFits Object
isInitialized
Check if Object is Initialized
ranef.lme
Extract lme Random Effects
fitted.glsStruct
Calculate glsStruct Fitted Values
logLik.lme
Log-Likelihood of an lme Object
pairs.lme
Pairs Plot of an lme Object
getData.lmList
Extract lmList Object Data
corSpatial
Spatial Correlation Structure
getGroups.varFunc
Extract varFunc Groups
logLik.glsStruct
Log-Likelihood of a glsStruct Object
intervals.gls
Confidence Intervals on gls Parameters
getGroups.gls
Extract gls Object Groups
getGroups
Extract Grouping Factors from an Object
nlmeControl
Control Values for nlme Fit
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
model.matrix.reStruct
reStruct Model Matrix
pdClasses
Positive-Definite Matrix Classes
recalc.modelStruct
Recalculate for a modelStruct Object
corMatrix
Extract Correlation Matrix
plot.nffGroupedData
Plot an nffGroupedData Object
recalc.corStruct
Recalculate for corStruct Object
predict.lme
Predictions from an lme Object
plot.Variogram
Plot a Variogram Object
pooledSD
Extract Pooled Standard Deviation
residuals.lmeStruct
Calculate lmeStruct Residuals
plot.gls
Plot a gls Object
logLik.lmList
Log-Likelihood of an lmList Object
simulate.lme
Simulate Results from
lme
Models
plot.ACF
Plot an ACF Object
corClasses
Correlation Structure Classes
varExp
Exponential Variance Function
getCovariateFormula
Extract Covariates Formula
allCoef
Extract Coefficients from a Set of Objects
Wheat
Yields by growing conditions
quinModel
Model function for the Quinidine data
nlme.nlsList
NLME fit from nlsList Object
solve.reStruct
Apply Solve to an reStruct Object
nlmeStruct
Nonlinear Mixed-Effects Structure
varWeights
Extract Variance Function Weights
pairs.lmList
Pairs Plot of an lmList Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
residuals.lme
Extract lme Residuals
varWeights.lmeStruct
Variance Weights for lmeStruct Object
gnlsControl
Control Values for gnls Fit
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
varIdent
Constant Variance Function
getData.gls
Extract gls Object Data
plot.intervals.lmList
Plot lmList Confidence Intervals
summary.lmList
Summarize an lmList Object
logLik.varFunc
Extract varFunc logLik
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
isBalanced
Check a Design for Balance
nlmeObject
Fitted nlme Object
print.varFunc
Print a varFunc Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
plot.nfnGroupedData
Plot an nfnGroupedData Object
ranef.lmList
Extract lmList Random Effects
nlsList
List of nls Objects with a Common Model
random.effects
Extract Random Effects
update.varFunc
Update varFunc Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdDiag
Diagonal Positive-Definite Matrix
corMatrix.corStruct
Matrix of a corStruct Object
pdConstruct
Construct pdMat Objects
recalc.varFunc
Recalculate for varFunc Object
plot.augPred
Plot an augPred Object
phenoModel
Model function for the Phenobarb data
collapse
Collapse According to Groups
varFixed
Fixed Variance Function
getResponseFormula
Extract Formula Specifying Response Variable
residuals.glsStruct
Calculate glsStruct Residuals
summary.varFunc
Summarize varFunc Object
print.summary.pdMat
Print a summary.pdMat Object
residuals.gls
Extract gls Residuals
getGroupsFormula
Extract Grouping Formula
qqnorm.gls
Normal Plot of Residuals from a gls Object
varConstPower
Constant Plus Power Variance Function
intervals
Confidence Intervals on Coefficients
splitFormula
Split a Formula
formula.pdMat
Extract pdMat Formula
residuals.nlmeStruct
Calculate nlmeStruct Residuals
Quinidine
Quinidine Kinetics
RatPupWeight
The weight of rat pups
getCovariate.varFunc
Extract varFunc Covariate
corNatural
General correlation in natural parameterization
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
reStruct
Random Effects Structure
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Oxboys
Heights of Boys in Oxford
corSymm
General Correlation Structure
Covariate.varFunc
Assign varFunc Covariate
glsObject
Fitted gls Object
Nitrendipene
Assay of nitrendipene
pdBlocked
Positive-Definite Block Diagonal Matrix
lmList.groupedData
lmList Fit from a groupedData Object
asOneFormula
Combine Formulas of a Set of Objects