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nlme (version 3.1-120)
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
3.1-120
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
February 20th, 2015
Functions in nlme (3.1-120)
Search functions
Earthquake
Earthquake Intensity
Variogram
Calculate Semi-variogram
Glucose2
Glucose Levels Following Alcohol Ingestion
corClasses
Correlation Structure Classes
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
getVarCov
Extract variance-covariance matrix
Rail
Evaluation of Stress in Railway Rails
pairs.lmList
Pairs Plot of an lmList Object
pdBlocked
Positive-Definite Block Diagonal Matrix
plot.lmList
Plot an lmList Object
Gasoline
Refinery yield of gasoline
IGF
Radioimmunoassay of IGF-I Protein
Matrix.reStruct
Assign reStruct Matrices
augPred
Augmented Predictions
predict.gls
Predictions from a gls Object
needUpdate
Check if Update is Needed
Orthodont
Growth curve data on an orthdontic measurement
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
ranef.lme
Extract lme Random Effects
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Wheat2
Wheat Yield Trials
collapse
Collapse According to Groups
nlmeControl
Control Values for nlme Fit
fitted.lme
Extract lme Fitted Values
plot.compareFits
Plot a compareFits Object
plot.intervals.lmList
Plot lmList Confidence Intervals
Dialyzer
High-Flux Hemodialyzer
Milk
Protein content of cows' milk
Names.pdBlocked
Names of a pdBlocked Object
Matrix.pdMat
Assign Matrix to a pdMat Object
as.matrix.reStruct
Matrices of an reStruct Object
Initialize.varFunc
Initialize varFunc Object
Oats
Split-plot Experiment on Varieties of Oats
Initialize.reStruct
Initialize reStruct Object
getResponseFormula
Extract Formula Specifying Response Variable
lmeControl
Control Values for lme Fit
Wafer
Modeling of Analog MOS Circuits
as.matrix.pdMat
Matrix of a pdMat Object
plot.ranef.lme
Plot a ranef.lme Object
solve.reStruct
Apply Solve to an reStruct Object
Soybean
Growth of soybean plants
Fatigue
Cracks caused by metal fatigue
BodyWeight
Rat weight over time for different diets
Variogram.default
Calculate Semi-variogram
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Wheat
Yields by growing conditions
getGroups.gls
Extract gls Object Groups
corCAR1
Continuous AR(1) Correlation Structure
logLik.corStruct
Extract corStruct Log-Likelihood
logLik.glsStruct
Log-Likelihood of a glsStruct Object
comparePred
Compare Predictions
corFactor.corStruct
Factor of a corStruct Object Matrix
varWeights
Extract Variance Function Weights
Dim
Extract Dimensions from an Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
Ovary
Counts of Ovarian Follicles
gnlsStruct
Generalized Nonlinear Least Squares Structure
fitted.lmList
Extract lmList Fitted Values
gnls
Fit Nonlinear Model Using Generalized Least Squares
getCovariate.corStruct
Extract corStruct Object Covariate
Names.formula
Extract Names from a formula
residuals.glsStruct
Calculate glsStruct Residuals
coef.lmList
Extract lmList Coefficients
intervals
Confidence Intervals on Coefficients
MathAchieve
Mathematics achievement scores
coef.gnls
Extract gnls Coefficients
Coef
Assign Values to Coefficients
residuals.gnlsStruct
Calculate gnlsStruct Residuals
recalc.varFunc
Recalculate for varFunc Object
compareFits
Compare Fitted Objects
corLin
Linear Correlation Structure
getGroups.varFunc
Extract varFunc Groups
lmeObject
Fitted lme Object
getGroups.corStruct
Extract corStruct Groups
lmList.groupedData
lmList Fit from a groupedData Object
coef.varFunc
varFunc Object Coefficients
pairs.compareFits
Pairs Plot of compareFits Object
pdMat
Positive-Definite Matrix
groupedData
Construct a groupedData Object
coef.modelStruct
Extract modelStruct Object Coefficients
Quinidine
Quinidine Kinetics
Matrix
Assign Matrix Values
varFixed
Fixed Variance Function
logDet.pdMat
Extract Log-Determinant from a pdMat Object
Cefamandole
Pharmacokinetics of Cefamandole
allCoef
Extract Coefficients from a Set of Objects
phenoModel
Model function for the Phenobarb data
corGaus
Gaussian Correlation Structure
logLik.reStruct
Calculate reStruct Log-Likelihood
ACF.gls
Autocorrelation Function for gls Residuals
RatPupWeight
The weight of rat pups
Names.pdMat
Names of a pdMat Object
Spruce
Growth of Spruce Trees
pooledSD
Extract Pooled Standard Deviation
Covariate.varFunc
Assign varFunc Covariate
isInitialized
Check if Object is Initialized
fitted.lmeStruct
Calculate lmeStruct Fitted Values
Names.reStruct
Names of an reStruct Object
getResponse
Extract Response Variable from an Object
Initialize.glsStruct
Initialize a glsStruct Object
Muscle
Contraction of heart muscle sections
formula.pdMat
Extract pdMat Formula
predict.nlme
Predictions from an nlme Object
nlsList.selfStart
nlsList Fit from a selfStart Function
ACF
Autocorrelation Function
plot.gls
Plot a gls Object
corRatio
Rational Quadratic Correlation Structure
lmeStruct
Linear Mixed-Effects Structure
plot.ACF
Plot an ACF Object
MathAchSchool
School demographic data for MathAchieve
nlmeStruct
Nonlinear Mixed-Effects Structure
bdf
Language scores
collapse.groupedData
Collapse a groupedData Object
Meat
Tenderness of meat
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
plot.lme
Plot an lme or nls object
quinModel
Model function for the Quinidine data
residuals.gls
Extract gls Residuals
balancedGrouped
Create a groupedData object from a matrix
residuals.lmList
Extract lmList Residuals
ranef.lmList
Extract lmList Random Effects
gnlsControl
Control Values for gnls Fit
corARMA
ARMA(p,q) Correlation Structure
corMatrix
Extract Correlation Matrix
coef.corStruct
Coefficients of a corStruct Object
Pixel
X-ray pixel intensities over time
reStruct
Random Effects Structure
Oxboys
Heights of Boys in Oxford
Initialize.lmeStruct
Initialize an lmeStruct Object
recalc.corStruct
Recalculate for corStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
coef.lme
Extract lme Coefficients
corMatrix.corStruct
Matrix of a corStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
glsObject
Fitted gls Object
plot.ranef.lmList
Plot a ranef.lmList Object
logLik.lme
Log-Likelihood of an lme Object
fixed.effects
Extract Fixed Effects
getData.lme
Extract lme Object Data
fixef.lmList
Extract lmList Fixed Effects
recalc.reStruct
Recalculate for an reStruct Object
gls-internal
Auxiliary functions used by gls
varComb
Combination of Variance Functions
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
summary.corStruct
Summarize a corStruct Object
print.summary.pdMat
Print a summary.pdMat Object
getData
Extract Data from an Object
gsummary
Summarize by Groups
glsStruct
Generalized Least Squares Structure
getGroupsFormula
Extract Grouping Formula
lme.groupedData
LME fit from groupedData Object
predict.lme
Predictions from an lme Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdClasses
Positive-Definite Matrix Classes
gls
Fit Linear Model Using Generalized Least Squares
asTable
Convert groupedData to a matrix
corSymm
General Correlation Structure
logDet
Extract the Logarithm of the Determinant
lme
Linear Mixed-Effects Models
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Glucose
Glucose levels over time
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdLogChol
General Positive-Definite Matrix
LDEsysMat
Generate system matrix for LDEs
Initialize
Initialize Object
Phenobarb
Phenobarbitol Kinetics
anova.gls
Compare Likelihoods of Fitted Objects
pdSymm
General Positive-Definite Matrix
Remifentanil
Pharmacokinetics of remifentanil
summary.gls
Summarize a gls Object
model.matrix.reStruct
reStruct Model Matrix
getCovariate.data.frame
Extract Data Frame Covariate
varPower
Power Variance Function
plot.augPred
Plot an augPred Object
varWeights.glsStruct
Variance Weights for glsStruct Object
nlmeObject
Fitted nlme Object
Oxide
Variability in Semiconductor Manufacturing
as.matrix.corStruct
Matrix of a corStruct Object
Dim.corStruct
Dimensions of a corStruct Object
recalc
Recalculate Condensed Linear Model Object
plot.nffGroupedData
Plot an nffGroupedData Object
random.effects
Extract Random Effects
logDet.corStruct
Extract corStruct Log-Determinant
varClasses
Variance Function Classes
lmList
List of lm Objects with a Common Model
summary.varFunc
Summarize varFunc Object
getCovariate
Extract Covariate from an Object
summary.pdMat
Summarize a pdMat Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
nlme.nlsList
NLME fit from nlsList Object
residuals.lme
Extract lme Residuals
varFunc
Variance Function Structure
varIdent
Constant Variance Function
Covariate
Assign Covariate Values
recalc.modelStruct
Recalculate for a modelStruct Object
isBalanced
Check a Design for Balance
pdConstruct.pdBlocked
Construct pdBlocked Objects
corSpatial
Spatial Correlation Structure
Relaxin
Assay for Relaxin
pdDiag
Diagonal Positive-Definite Matrix
summary.lme
Summarize an lme Object
Tetracycline2
Pharmacokinetics of tetracycline
simulate.lme
Simulate Results from
lme
Models
asOneFormula
Combine Formulas of a Set of Objects
lme.lmList
LME fit from lmList Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
varWeights.lmeStruct
Variance Weights for lmeStruct Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
ACF.lme
Autocorrelation Function for lme Residuals
summary.nlsList
Summarize an nlsList Object
VarCorr
Extract variance and correlation components
formula.pdBlocked
Extract pdBlocked Formula
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
Tetracycline1
Pharmacokinetics of tetracycline
predict.lmList
Predictions from an lmList Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
pdConstruct
Construct pdMat Objects
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
[.pdMat
Subscript a pdMat Object
Dim.pdMat
Dimensions of a pdMat Object
summary.modelStruct
Summarize a modelStruct Object
Gun
Methods for firing naval guns
fdHess
Finite difference Hessian
pairs.lme
Pairs Plot of an lme Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
corNatural
General correlation in natural parameterization
corAR1
AR(1) Correlation Structure
Dim.corSpatial
Dimensions of a corSpatial Object
corSpher
Spherical Correlation Structure
Initialize.corStruct
Initialize corStruct Object
logDet.reStruct
Extract reStruct Log-Determinants
getCovariateFormula
Extract Covariates Formula
corFactor
Factor of a Correlation Matrix
getCovariate.varFunc
Extract varFunc Covariate
glsControl
Control Values for gls Fit
nlme
Nonlinear Mixed-Effects Models
logLik.gnls
Log-Likelihood of a gnls Object
Machines
Productivity Scores for Machines and Workers
intervals.lme
Confidence Intervals on lme Parameters
nlsList
List of nls Objects with a Common Model
getGroups
Extract Grouping Factors from an Object
Nitrendipene
Assay of nitrendipene
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
update.varFunc
Update varFunc Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
predict.gnls
Predictions from a gnls Object
corCompSymm
Compound Symmetry Correlation Structure
summary.lmList
Summarize an lmList Object
varExp
Exponential Variance Function
corExp
Exponential Correlation Structure
splitFormula
Split a Formula
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getGroups.data.frame
Extract Groups from a Data Frame
getData.lmList
Extract lmList Object Data
gnlsObject
Fitted gnls Object
intervals.gls
Confidence Intervals on gls Parameters
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
residuals.lmeStruct
Calculate lmeStruct Residuals
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
update.modelStruct
Update a modelStruct Object
PBG
Effect of Phenylbiguanide on Blood Pressure
pdIdent
Multiple of the Identity Positive-Definite Matrix
Assay
Bioassay on Cell Culture Plate
Names
Names Associated with an Object
anova.lme
Compare Likelihoods of Fitted Objects
formula.reStruct
Extract reStruct Object Formula
getGroups.lme
Extract lme Object Groups
print.varFunc
Print a varFunc Object
varConstPower
Constant Plus Power Variance Function
coef.pdMat
pdMat Object Coefficients
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
ergoStool
Ergometrics experiment with stool types
fitted.glsStruct
Calculate glsStruct Fitted Values
coef.reStruct
reStruct Object Coefficients
gapply
Apply a Function by Groups
getGroups.lmList
Extract lmList Object Groups
getData.gls
Extract gls Object Data
intervals.lmList
Confidence Intervals on lmList Coefficients
logLik.varFunc
Extract varFunc logLik
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
plot.Variogram
Plot a Variogram Object
plot.nmGroupedData
Plot an nmGroupedData Object