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nlme (version 3.1-110)
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
3.1-110
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
July 7th, 2013
Functions in nlme (3.1-110)
Search functions
BodyWeight
Rat weight over time for different diets
Coef
Assign Values to Coefficients
ACF.gls
Autocorrelation Function for gls Residuals
ACF
Autocorrelation Function
Assay
Bioassay on Cell Culture Plate
Covariate
Assign Covariate Values
Initialize.lmeStruct
Initialize an lmeStruct Object
Initialize.reStruct
Initialize reStruct Object
Initialize.varFunc
Initialize varFunc Object
LDEsysMat
Generate system matrix for LDEs
Matrix
Assign Matrix Values
Matrix.pdMat
Assign Matrix to a pdMat Object
MathAchSchool
School demographic data for MathAchieve
Machines
Productivity Scores for Machines and Workers
MathAchieve
Mathematics achievement scores
Muscle
Contraction of heart muscle sections
Matrix.reStruct
Assign reStruct Matrices
Initialize.glsStruct
Initialize a glsStruct Object
Fatigue
Cracks caused by metal fatigue
Gasoline
Refinery yield of gasoline
Rail
Evaluation of Stress in Railway Rails
Orthodont
Growth curve data on an orthdontic measurement
Phenobarb
Phenobarbitol Kinetics
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Names.pdBlocked
Names of a pdBlocked Object
Initialize
Initialize Object
Names.reStruct
Names of an reStruct Object
PBG
Effect of Phenylbiguanide on Blood Pressure
Dialyzer
High-Flux Hemodialyzer
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Dim.corStruct
Dimensions of a corStruct Object
Nitrendipene
Assay of nitrendipene
Milk
Protein content of cows' milk
Oxboys
Heights of Boys in Oxford
RatPupWeight
The weight of rat pups
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Meat
Tenderness of meat
Tetracycline2
Pharmacokinetics of tetracycline
Dim.corSpatial
Dimensions of a corSpatial Object
Earthquake
Earthquake Intensity
Oxide
Variability in Semiconductor Manufacturing
Names
Names Associated with an Object
Quinidine
Quinidine Kinetics
[.pdMat
Subscript a pdMat Object
Names.pdMat
Names of a pdMat Object
VarCorr
Extract variance and correlation components
Variogram.default
Calculate Semi-variogram
Names.formula
Extract Names from a formula
Ovary
Counts of Ovarian Follicles
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
IGF
Radioimmunoassay of IGF-I Protein
Cefamandole
Pharmacokinetics of Cefamandole
Wafer
Modeling of Analog MOS Circuits
Dim.pdMat
Dimensions of a pdMat Object
Covariate.varFunc
Assign varFunc Covariate
Gun
Methods for firing naval guns
Initialize.corStruct
Initialize corStruct Object
ACF.lme
Autocorrelation Function for lme Residuals
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram
Calculate Semi-variogram
coef.corStruct
Coefficients of a corStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
asTable
Convert groupedData to a matrix
asOneFormula
Combine Formulas of a Set of Objects
Remifentanil
Pharmacokinetics of remifentanil
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
balancedGrouped
Create a groupedData object from a matrix
Tetracycline1
Pharmacokinetics of tetracycline
Oats
Split-plot Experiment on Varieties of Oats
as.matrix.reStruct
Matrices of an reStruct Object
as.matrix.pdMat
Matrix of a pdMat Object
Pixel
X-ray pixel intensities over time
coef.lmList
Extract lmList Coefficients
Soybean
Growth of soybean plants
Wheat
Yields by growing conditions
anova.lme
Compare Likelihoods of Fitted Objects
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
coef.lme
Extract lme Coefficients
coef.gnls
Extract gnls Coefficients
bdf
Language scores
augPred
Augmented Predictions
coef.pdMat
pdMat Object Coefficients
Spruce
Growth of Spruce Trees
coef.reStruct
reStruct Object Coefficients
Wheat2
Wheat Yield Trials
coef.varFunc
varFunc Object Coefficients
collapse.groupedData
Collapse a groupedData Object
compareFits
Compare Fitted Objects
corARMA
ARMA(p,q) Correlation Structure
corAR1
AR(1) Correlation Structure
collapse
Collapse According to Groups
corExp
Exponential Correlation Structure
corCompSymm
Compound Symmetry Correlation Structure
corMatrix.corStruct
Matrix of a corStruct Object
corFactor
Factor of a Correlation Matrix
corMatrix
Extract Correlation Matrix
corFactor.corStruct
Factor of a corStruct Object Matrix
corCAR1
Continuous AR(1) Correlation Structure
corClasses
Correlation Structure Classes
corLin
Linear Correlation Structure
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corNatural
General correlation in natural parameterization
fitted.glsStruct
Calculate glsStruct Fitted Values
fitted.lmList
Extract lmList Fitted Values
fdHess
Finite difference Hessian
fitted.lme
Extract lme Fitted Values
corSpher
Spherical Correlation Structure
corRatio
Rational Quadratic Correlation Structure
fixed.effects
Extract Fixed Effects
gapply
Apply a Function by Groups
lme.groupedData
LME fit from groupedData Object
getResponseFormula
Extract Formula Specifying Response Variable
lmList.groupedData
lmList Fit from a groupedData Object
lme.lmList
LME fit from lmList Object
lmeControl
Control Values for lme Fit
glsStruct
Generalized Least Squares Structure
getCovariateFormula
Extract Covariates Formula
getGroups.varFunc
Extract varFunc Groups
logDet.corStruct
Extract corStruct Log-Determinant
groupedData
Construct a groupedData Object
gls
Fit Linear Model Using Generalized Least Squares
lmeScale
Scale for lme Optimization
getResponse
Extract Response Variable from an Object
lmList
List of lm Objects with a Common Model
getGroups.gls
Extract gls Object Groups
getGroups.corStruct
Extract corStruct Groups
getGroups
Extract Grouping Factors from an Object
getGroups.lmList
Extract lmList Object Groups
lmeStruct
Linear Mixed-Effects Structure
getVarCov
Extract variance-covariance matrix
logDet.reStruct
Extract reStruct Log-Determinants
logDet
Extract the Logarithm of the Determinant
formula.reStruct
Extract reStruct Object Formula
glsObject
Fitted gls Object
getGroupsFormula
Extract Grouping Formula
getData.lmList
Extract lmList Object Data
logDet.pdMat
Extract Log-Determinant from a pdMat Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
lme
Linear Mixed-Effects Models
lmeObject
Fitted lme Object
logLik.gnls
Log-Likelihood of a gnls Object
model.matrix.reStruct
reStruct Model Matrix
logLik.corStruct
Extract corStruct Log-Likelihood
logLik.lme
Log-Likelihood of an lme Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
logLik.varFunc
Extract varFunc logLik
nlme
Nonlinear Mixed-Effects Models
nlmeStruct
Nonlinear Mixed-Effects Structure
nlmeObject
Fitted nlme Object
pairs.lme
Pairs Plot of an lme Object
needUpdate
Check if Update is Needed
pdConstruct
Construct pdMat Objects
pdClasses
Positive-Definite Matrix Classes
nlmeControl
Control Values for nlme Fit
nlsList
List of nls Objects with a Common Model
pairs.lmList
Pairs Plot of an lmList Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdDiag
Diagonal Positive-Definite Matrix
pairs.compareFits
Pairs Plot of compareFits Object
nlsList.selfStart
nlsList Fit from a selfStart Function
nlme.nlsList
NLME fit from nlsList Object
pdBlocked
Positive-Definite Block Diagonal Matrix
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdLogChol
General Positive-Definite Matrix
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdSymm
General Positive-Definite Matrix
plot.compareFits
Plot a compareFits Object
plot.ACF
Plot an ACF Object
plot.intervals.lmList
Plot lmList Confidence Intervals
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
phenoModel
Model function for the Phenobarb data
plot.augPred
Plot an augPred Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
plot.lmList
Plot an lmList Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
anova.gls
Compare Likelihoods of Fitted Objects
pdMat
Positive-Definite Matrix
plot.gls
Plot a gls Object
plot.Variogram
Plot a Variogram Object
getData.lme
Extract lme Object Data
getData
Extract Data from an Object
formula.pdMat
Extract pdMat Formula
getCovariate.data.frame
Extract Data Frame Covariate
formula.pdBlocked
Extract pdBlocked Formula
quinModel
Model function for the Quinidine data
getCovariate.varFunc
Extract varFunc Covariate
intervals.lmList
Confidence Intervals on lmList Coefficients
recalc.reStruct
Recalculate for an reStruct Object
residuals.gls
Extract gls Residuals
plot.lme
Plot an lme or nls object
recalc.corStruct
Recalculate for corStruct Object
print.summary.pdMat
Print a summary.pdMat Object
recalc
Recalculate Condensed Linear Model Object
predict.nlme
Predictions from an nlme Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
random.effects
Extract Random Effects
plot.ranef.lmList
Plot a ranef.lmList Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
residuals.lmeStruct
Calculate lmeStruct Residuals
getData.gls
Extract gls Object Data
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
plot.nffGroupedData
Plot an nffGroupedData Object
predict.gls
Predictions from a gls Object
recalc.modelStruct
Recalculate for a modelStruct Object
predict.gnls
Predictions from a gnls Object
predict.lmList
Predictions from an lmList Object
recalc.varFunc
Recalculate for varFunc Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
pooledSD
Extract Pooled Standard Deviation
residuals.nlmeStruct
Calculate nlmeStruct Residuals
reStruct
Random Effects Structure
getCovariate.corStruct
Extract corStruct Object Covariate
plot.nmGroupedData
Plot an nmGroupedData Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.ranef.lme
Plot a ranef.lme Object
fixef.lmList
Extract lmList Fixed Effects
print.varFunc
Print a varFunc Object
corSpatial
Spatial Correlation Structure
gsummary
Summarize by Groups
corGaus
Gaussian Correlation Structure
corSymm
General Correlation Structure
isBalanced
Check a Design for Balance
intervals.lme
Confidence Intervals on lme Parameters
getGroups.data.frame
Extract Groups from a Data Frame
residuals.lmList
Extract lmList Residuals
gnlsControl
Control Values for gnls Fit
glsControl
Control Values for gls Fit
residuals.lme
Extract lme Residuals
comparePred
Compare Predictions
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.lmeStruct
Calculate lmeStruct Fitted Values
residuals.glsStruct
Calculate glsStruct Residuals
isInitialized
Check if Object is Initialized
intervals.gls
Confidence Intervals on gls Parameters
gnlsObject
Fitted gnls Object
getCovariate
Extract Covariate from an Object
simulate.lme
Simulate Results from
lme
Models
getGroups.lme
Extract lme Object Groups
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
solve.reStruct
Apply Solve to an reStruct Object
summary.varFunc
Summarize varFunc Object
varFixed
Fixed Variance Function
varConstPower
Constant Plus Power Variance Function
update.varFunc
Update varFunc Object
Relaxin
Assay for Relaxin
summary.corStruct
Summarize a corStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
varIdent
Constant Variance Function
summary.nlsList
Summarize an nlsList Object
allCoef
Extract Coefficients from a Set of Objects
varComb
Combination of Variance Functions
ranef.lme
Extract lme Random Effects
varWeights.lmeStruct
Variance Weights for lmeStruct Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
varWeights
Extract Variance Function Weights
varExp
Exponential Variance Function
summary.lme
Summarize an lme Object
varPower
Power Variance Function
summary.lmList
Summarize an lmList Object
update.modelStruct
Update a modelStruct Object
summary.modelStruct
Summarize a modelStruct Object
varFunc
Variance Function Structure
Glucose
Glucose levels over time
ergoStool
Ergometrics experiment with stool types
summary.pdMat
Summarize a pdMat Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
intervals
Confidence Intervals on Coefficients
varClasses
Variance Function Classes
splitFormula
Split a Formula
ranef.lmList
Extract lmList Random Effects
coef.modelStruct
Extract modelStruct Object Coefficients
summary.gls
Summarize a gls Object
predict.lme
Predictions from an lme Object
Dim
Extract Dimensions from an Object