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nlme (version 3.1-119)
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
3.1-119
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
January 10th, 2015
Functions in nlme (3.1-119)
Search functions
pdNatural
General Positive-Definite Matrix in Natural Parametrization
recalc
Recalculate Condensed Linear Model Object
recalc.reStruct
Recalculate for an reStruct Object
splitFormula
Split a Formula
MathAchSchool
School demographic data for MathAchieve
LDEsysMat
Generate system matrix for LDEs
Fatigue
Cracks caused by metal fatigue
Oxide
Variability in Semiconductor Manufacturing
PBG
Effect of Phenylbiguanide on Blood Pressure
Names
Names Associated with an Object
Matrix.pdMat
Assign Matrix to a pdMat Object
Initialize.varFunc
Initialize varFunc Object
ergoStool
Ergometrics experiment with stool types
Tetracycline1
Pharmacokinetics of tetracycline
coef.reStruct
reStruct Object Coefficients
Names.formula
Extract Names from a formula
Covariate.varFunc
Assign varFunc Covariate
Spruce
Growth of Spruce Trees
Meat
Tenderness of meat
getData.lme
Extract lme Object Data
coef.lme
Extract lme Coefficients
balancedGrouped
Create a groupedData object from a matrix
pdMat
Positive-Definite Matrix
ACF.gls
Autocorrelation Function for gls Residuals
lmeObject
Fitted lme Object
ACF.lme
Autocorrelation Function for lme Residuals
corSpher
Spherical Correlation Structure
[.pdMat
Subscript a pdMat Object
Names.reStruct
Names of an reStruct Object
formula.pdBlocked
Extract pdBlocked Formula
Milk
Protein content of cows' milk
summary.pdMat
Summarize a pdMat Object
Coef
Assign Values to Coefficients
Matrix
Assign Matrix Values
logLik.lme
Log-Likelihood of an lme Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
coef.gnls
Extract gnls Coefficients
collapse
Collapse According to Groups
Initialize.glsStruct
Initialize a glsStruct Object
Wheat2
Wheat Yield Trials
Names.pdMat
Names of a pdMat Object
Orthodont
Growth curve data on an orthdontic measurement
ACF
Autocorrelation Function
Dim
Extract Dimensions from an Object
Initialize.reStruct
Initialize reStruct Object
Dialyzer
High-Flux Hemodialyzer
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
Matrix.reStruct
Assign reStruct Matrices
Relaxin
Assay for Relaxin
logLik.varFunc
Extract varFunc logLik
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
corLin
Linear Correlation Structure
Dim.corSpatial
Dimensions of a corSpatial Object
Muscle
Contraction of heart muscle sections
Initialize.corStruct
Initialize corStruct Object
plot.ranef.lme
Plot a ranef.lme Object
RatPupWeight
The weight of rat pups
VarCorr
Extract variance and correlation components
as.matrix.reStruct
Matrices of an reStruct Object
BodyWeight
Rat weight over time for different diets
corFactor
Factor of a Correlation Matrix
Ovary
Counts of Ovarian Follicles
corCompSymm
Compound Symmetry Correlation Structure
getResponse
Extract Response Variable from an Object
getCovariateFormula
Extract Covariates Formula
Dim.corStruct
Dimensions of a corStruct Object
glsObject
Fitted gls Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
getVarCov
Extract variance-covariance matrix
corAR1
AR(1) Correlation Structure
Quinidine
Quinidine Kinetics
Phenobarb
Phenobarbitol Kinetics
Initialize.lmeStruct
Initialize an lmeStruct Object
varWeights
Extract Variance Function Weights
Oats
Split-plot Experiment on Varieties of Oats
corCAR1
Continuous AR(1) Correlation Structure
bdf
Language scores
lme.lmList
LME fit from lmList Object
corSpatial
Spatial Correlation Structure
getCovariate.varFunc
Extract varFunc Covariate
logDet.reStruct
Extract reStruct Log-Determinants
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
fdHess
Finite difference Hessian
gnlsStruct
Generalized Nonlinear Least Squares Structure
Initialize
Initialize Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
random.effects
Extract Random Effects
as.matrix.corStruct
Matrix of a corStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Names.pdBlocked
Names of a pdBlocked Object
logLik.lmList
Log-Likelihood of an lmList Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
MathAchieve
Mathematics achievement scores
Tetracycline2
Pharmacokinetics of tetracycline
anova.lme
Compare Likelihoods of Fitted Objects
varWeights.lmeStruct
Variance Weights for lmeStruct Object
plot.lme
Plot an lme or nls object
gls
Fit Linear Model Using Generalized Least Squares
formula.reStruct
Extract reStruct Object Formula
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
lme
Linear Mixed-Effects Models
corARMA
ARMA(p,q) Correlation Structure
glsControl
Control Values for gls Fit
coef.lmList
Extract lmList Coefficients
gnlsControl
Control Values for gnls Fit
gnlsObject
Fitted gnls Object
getCovariate.corStruct
Extract corStruct Object Covariate
isBalanced
Check a Design for Balance
fitted.lme
Extract lme Fitted Values
asOneFormula
Combine Formulas of a Set of Objects
coef.pdMat
pdMat Object Coefficients
fixed.effects
Extract Fixed Effects
Soybean
Growth of soybean plants
glsStruct
Generalized Least Squares Structure
Nitrendipene
Assay of nitrendipene
getGroups.varFunc
Extract varFunc Groups
Dim.pdMat
Dimensions of a pdMat Object
Rail
Evaluation of Stress in Railway Rails
recalc.corStruct
Recalculate for corStruct Object
varConstPower
Constant Plus Power Variance Function
gnls
Fit Nonlinear Model Using Generalized Least Squares
predict.gls
Predictions from a gls Object
logLik.reStruct
Calculate reStruct Log-Likelihood
Glucose
Glucose levels over time
summary.corStruct
Summarize a corStruct Object
getGroups.lme
Extract lme Object Groups
nlme.nlsList
NLME fit from nlsList Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Variogram
Calculate Semi-variogram
coef.varFunc
varFunc Object Coefficients
nlsList.selfStart
nlsList Fit from a selfStart Function
Variogram.default
Calculate Semi-variogram
lmeControl
Control Values for lme Fit
corExp
Exponential Correlation Structure
Machines
Productivity Scores for Machines and Workers
getData
Extract Data from an Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
corFactor.corStruct
Factor of a corStruct Object Matrix
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
recalc.varFunc
Recalculate for varFunc Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
augPred
Augmented Predictions
varFunc
Variance Function Structure
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
fixef.lmList
Extract lmList Fixed Effects
nlmeObject
Fitted nlme Object
formula.pdMat
Extract pdMat Formula
getData.lmList
Extract lmList Object Data
pdBlocked
Positive-Definite Block Diagonal Matrix
print.varFunc
Print a varFunc Object
Pixel
X-ray pixel intensities over time
compareFits
Compare Fitted Objects
pdClasses
Positive-Definite Matrix Classes
plot.lmList
Plot an lmList Object
asTable
Convert groupedData to a matrix
corMatrix.corStruct
Matrix of a corStruct Object
pairs.compareFits
Pairs Plot of compareFits Object
phenoModel
Model function for the Phenobarb data
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
ranef.lme
Extract lme Random Effects
corRatio
Rational Quadratic Correlation Structure
predict.nlme
Predictions from an nlme Object
Wafer
Modeling of Analog MOS Circuits
getGroups.data.frame
Extract Groups from a Data Frame
getCovariate.data.frame
Extract Data Frame Covariate
Oxboys
Heights of Boys in Oxford
lmeStruct
Linear Mixed-Effects Structure
corSymm
General Correlation Structure
varIdent
Constant Variance Function
pdIdent
Multiple of the Identity Positive-Definite Matrix
Wheat
Yields by growing conditions
intervals.lmList
Confidence Intervals on lmList Coefficients
pairs.lme
Pairs Plot of an lme Object
lmList
List of lm Objects with a Common Model
gsummary
Summarize by Groups
IGF
Radioimmunoassay of IGF-I Protein
groupedData
Construct a groupedData Object
intervals
Confidence Intervals on Coefficients
getGroupsFormula
Extract Grouping Formula
plot.nfnGroupedData
Plot an nfnGroupedData Object
getData.gls
Extract gls Object Data
logDet.corStruct
Extract corStruct Log-Determinant
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
varExp
Exponential Variance Function
nlmeStruct
Nonlinear Mixed-Effects Structure
isInitialized
Check if Object is Initialized
predict.lme
Predictions from an lme Object
residuals.lmList
Extract lmList Residuals
logLik.corStruct
Extract corStruct Log-Likelihood
residuals.lme
Extract lme Residuals
varComb
Combination of Variance Functions
coef.corStruct
Coefficients of a corStruct Object
Remifentanil
Pharmacokinetics of remifentanil
pdConstruct.pdBlocked
Construct pdBlocked Objects
plot.ranef.lmList
Plot a ranef.lmList Object
corGaus
Gaussian Correlation Structure
getGroups.gls
Extract gls Object Groups
solve.reStruct
Apply Solve to an reStruct Object
logDet
Extract the Logarithm of the Determinant
getGroups.corStruct
Extract corStruct Groups
quinModel
Model function for the Quinidine data
residuals.glsStruct
Calculate glsStruct Residuals
lme.groupedData
LME fit from groupedData Object
fitted.glsStruct
Calculate glsStruct Fitted Values
update.modelStruct
Update a modelStruct Object
getResponseFormula
Extract Formula Specifying Response Variable
fitted.lmeStruct
Calculate lmeStruct Fitted Values
plot.Variogram
Plot a Variogram Object
summary.modelStruct
Summarize a modelStruct Object
update.varFunc
Update varFunc Object
plot.intervals.lmList
Plot lmList Confidence Intervals
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
pdLogChol
General Positive-Definite Matrix
Covariate
Assign Covariate Values
pdFactor
Square-Root Factor of a Positive-Definite Matrix
residuals.nlmeStruct
Calculate nlmeStruct Residuals
intervals.lme
Confidence Intervals on lme Parameters
recalc.modelStruct
Recalculate for a modelStruct Object
summary.lme
Summarize an lme Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
varWeights.glsStruct
Variance Weights for glsStruct Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
model.matrix.reStruct
reStruct Model Matrix
Assay
Bioassay on Cell Culture Plate
getGroups
Extract Grouping Factors from an Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
fitted.lmList
Extract lmList Fitted Values
Earthquake
Earthquake Intensity
plot.compareFits
Plot a compareFits Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
Cefamandole
Pharmacokinetics of Cefamandole
getCovariate
Extract Covariate from an Object
summary.lmList
Summarize an lmList Object
predict.lmList
Predictions from an lmList Object
getGroups.lmList
Extract lmList Object Groups
residuals.gnlsStruct
Calculate gnlsStruct Residuals
Glucose2
Glucose Levels Following Alcohol Ingestion
summary.nlsList
Summarize an nlsList Object
gls-internal
Auxiliary functions used by gls
Gun
Methods for firing naval guns
summary.gls
Summarize a gls Object
Gasoline
Refinery yield of gasoline
lmList.groupedData
lmList Fit from a groupedData Object
summary.varFunc
Summarize varFunc Object
nlmeControl
Control Values for nlme Fit
pdDiag
Diagonal Positive-Definite Matrix
allCoef
Extract Coefficients from a Set of Objects
plot.ACF
Plot an ACF Object
corMatrix
Extract Correlation Matrix
nlme
Nonlinear Mixed-Effects Models
corNatural
General correlation in natural parameterization
simulate.lme
Simulate Results from
lme
Models
intervals.gls
Confidence Intervals on gls Parameters
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
anova.gls
Compare Likelihoods of Fitted Objects
pairs.lmList
Pairs Plot of an lmList Object
coef.modelStruct
Extract modelStruct Object Coefficients
plot.gls
Plot a gls Object
needUpdate
Check if Update is Needed
as.matrix.pdMat
Matrix of a pdMat Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
collapse.groupedData
Collapse a groupedData Object
nlsList
List of nls Objects with a Common Model
pdSymm
General Positive-Definite Matrix
predict.gnls
Predictions from a gnls Object
comparePred
Compare Predictions
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pooledSD
Extract Pooled Standard Deviation
logLik.gnls
Log-Likelihood of a gnls Object
varClasses
Variance Function Classes
plot.augPred
Plot an augPred Object
plot.nmGroupedData
Plot an nmGroupedData Object
pdConstruct
Construct pdMat Objects
gapply
Apply a Function by Groups
plot.nffGroupedData
Plot an nffGroupedData Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
residuals.lmeStruct
Calculate lmeStruct Residuals
print.summary.pdMat
Print a summary.pdMat Object
varFixed
Fixed Variance Function
residuals.gls
Extract gls Residuals
varPower
Power Variance Function
corClasses
Correlation Structure Classes
ranef.lmList
Extract lmList Random Effects
reStruct
Random Effects Structure