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nlme (version 3.1-75)
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
117,966
Version
3.1-75
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
July 3rd, 2006
Functions in nlme (3.1-75)
Search functions
Initialize.reStruct
Initialize reStruct Object
Initialize.lmeStruct
Initialize an lmeStruct Object
Covariate.varFunc
Assign varFunc Covariate
Initialize.glsStruct
Initialize a glsStruct Object
LDEsysMat
Generate system matrix for LDEs
Dim.corStruct
Dimensions of a corStruct Object
Covariate
Assign Covariate Values
Names
Names Associated with an Object
Coef
Assign Values to Coefficients
augPred
Augmented Predictions
Dim.pdMat
Dimensions of a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
ACF.gls
Autocorrelation Function for gls Residuals
coef.varFunc
varFunc Object Coefficients
corNatural
General correlation in natural parameterization
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
asTable
Convert groupedData to a matrix
as.matrix.reStruct
Matrices of an reStruct Object
coef.reStruct
reStruct Object Coefficients
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
VarCorr
Extract variance and correlation components
Variogram.corExp
Calculate Semi-variogram for a corExp Object
getData
Extract Data from an Object
recalc.modelStruct
Recalculate for a modelStruct Object
recalc.varFunc
Recalculate for varFunc Object
varFunc
Variance Function Structure
Dim.corSpatial
Dimensions of a corSpatial Object
plot.ranef.lme
Plot a ranef.lme Object
ranef.lme
Extract lme Random Effects
Initialize.corStruct
Initialize corStruct Object
allCoef
Extract Coefficients from a Set of Objects
residuals.glsStruct
Calculate glsStruct Residuals
ACF
Autocorrelation Function
coef.gnls
Extract gnls Coefficients
[.pdMat
Subscript a pdMat Object
fitted.lmList
Extract lmList Fitted Values
update.varFunc
Update varFunc Object
varClasses
Variance Function Classes
fitted.lme
Extract lme Fitted Values
corMatrix.corStruct
Matrix of a corStruct Object
corFactor.corStruct
Factor of a corStruct Object Matrix
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.glsStruct
Calculate glsStruct Fitted Values
as.matrix.corStruct
Matrix of a corStruct Object
collapse
Collapse According to Groups
BIC.logLik
BIC of a logLik Object
corCompSymm
Compound Symmetry Correlation Structure
coef.modelStruct
Extract modelStruct Object Coefficients
Initialize
Initialize Object
summary.corStruct
Summarize a corStruct Object
Names.formula
Extract Names from a formula
comparePred
Compare Predictions
getGroupsFormula
Extract Grouping Formula
Names.pdMat
Names of a pdMat Object
corCAR1
Continuous AR(1) Correlation Structure
corFactor
Factor of a Correlation Matrix
random.effects
Extract Random Effects
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
fdHess
Finite difference Hessian
getCovariateFormula
Extract Covariates Formula
isInitialized
Check if Object is Initialized
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
formula.pdMat
Extract pdMat Formula
anova.lme
Compare Likelihoods of Fitted Objects
update.modelStruct
Update a modelStruct Object
getData.gls
Extract gls Object Data
collapse.groupedData
Collapse a groupedData Object
residuals.lme
Extract lme Residuals
predict.gls
Predictions from a gls Object
balancedGrouped
Create a groupedData object from a matrix
pairs.compareFits
Pairs Plot of compareFits Object
getGroups.gls
Extract gls Object Groups
ACF.lme
Autocorrelation Function for lme Residuals
plot.intervals.lmList
Plot lmList Confidence Intervals
getCovariate.data.frame
Extract Data Frame Covariate
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corSpher
Spherical Correlation Structure
quinModel
Model function for the Quinidine data
varConstPower
Constant Plus Power Variance Function
compareFits
Compare Fitted Objects
Variogram.corLin
Calculate Semi-variogram for a corLin Object
corGaus
Gaussian Correlation Structure
corARMA
ARMA(p,q) Correlation Structure
logLik.lme
Log-Likelihood of an lme Object
Initialize.varFunc
Initialize varFunc Object
corSpatial
Spatial Correlation Structure
varWeights
Extract Variance Function Weights
predict.lmList
Predictions from an lmList Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
recalc.corStruct
Recalculate for corStruct Object
solve.reStruct
Apply Solve to an reStruct Object
BIC
Bayesian Information Criterion
Dim
Extract Dimensions from an Object
Variogram
Calculate Semi-variogram
corMatrix
Extract Correlation Matrix
summary.varFunc
Summarize varFunc Object
asOneFormula
Combine Formulas of a Set of Objects
isBalanced
Check a Design for Balance
Variogram.default
Calculate Semi-variogram
formula.reStruct
Extract reStruct Object Formula
lmList
List of lm Objects with a Common Model
getCovariate.varFunc
Extract varFunc Covariate
intervals
Confidence Intervals on Coefficients
intervals.gls
Confidence Intervals on gls Parameters
residuals.lmList
Extract lmList Residuals
corSymm
General Correlation Structure
Matrix.pdMat
Assign Matrix to a pdMat Object
Names.reStruct
Names of an reStruct Object
splitFormula
Split a Formula
glsStruct
Generalized Least Squares Structure
plot.nmGroupedData
Plot an nmGroupedData Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
summary.nlsList
Summarize an nlsList Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
corRatio
Rational Quadratic Correlation Structure
lmList.groupedData
lmList Fit from a groupedData Object
varWeights.glsStruct
Variance Weights for glsStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
Matrix
Assign Matrix Values
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
reStruct
Random Effects Structure
residuals.lmeStruct
Calculate lmeStruct Residuals
simulate.lme
Simulate results from lme models
varPower
Power Variance Function
getResponse
Extract Response Variable from an Object
varFixed
Fixed Variance Function
gsummary
Summarize by Groups
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
summary.pdMat
Summarize a pdMat Object
logLik.varFunc
Extract varFunc logLik
residuals.gls
Extract gls Residuals
plot.lmList
Plot an lmList Object
fixed.effects
Extract Fixed Effects
pdNatural
General Positive-Definite Matrix in Natural Parametrization
summary.lmList
Summarize an lmList Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
gapply
Apply a Function by Groups
pooledSD
Extract Pooled Standard Deviation
as.matrix.pdMat
Matrix of a pdMat Object
varComb
Combination of Variance Functions
getCovariate.corStruct
Extract corStruct Object Covariate
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
lmeControl
Control Values for lme Fit
corExp
Exponential Correlation Structure
plot.Variogram
Plot a Variogram Object
coef.corStruct
Coefficients of a corStruct Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
formula.pdBlocked
Extract pdBlocked Formula
corClasses
Correlation Structure Classes
getGroups.lme
Extract lme Object Groups
lme.lmList
LME fit from lmList Object
summary.modelStruct
Summarize a modelStruct Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
varIdent
Constant Variance Function
gnlsControl
Control Values for gnls Fit
coef.lme
Extract lme Coefficients
ranef.lmList
Extract lmList Random Effects
corLin
Linear Correlation Structure
coef.pdMat
pdMat Object Coefficients
getGroups.varFunc
Extract varFunc Groups
logDet
Extract the Logarithm of the Determinant
getData.lme
Extract lme Object Data
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
plot.ACF
Plot an ACF Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
summary.gls
Summarize a gls Object
predict.lme
Predictions from an lme Object
needUpdate
Check if Update is Needed
getVarCov
Extract variance-covariance matrix
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.lmList
Log-Likelihood of an lmList Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
lmeScale
Scale for lme Optimization
getGroups
Extract Grouping Factors from an Object
nlmeStruct
Nonlinear Mixed-Effects Structure
pdClasses
Positive-Definite Matrix Classes
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
lme.groupedData
LME fit from groupedData Object
groupedData
Construct a groupedData Object
logLik.gnls
Log-Likelihood of a gnls Object
getCovariate
Extract Covariate from an Object
logDet.reStruct
Extract reStruct Log-Determinants
logLik.reStruct
Calculate reStruct Log-Likelihood
pdConstruct
Construct pdMat Objects
logLik.corStruct
Extract corStruct Log-Likelihood
recalc
Recalculate Condensed Linear Model Object
predict.nlme
Predictions from an nlme Object
getGroups.lmList
Extract lmList Object Groups
nlsList
List of nls Objects with a Common Model
nlmeControl
Control Values for nlme Fit
residuals.nlmeStruct
Calculate nlmeStruct Residuals
glsControl
Control Values for gls Fit
glsObject
Fitted gls Object
lme
Linear Mixed-Effects Models
intervals.lmList
Confidence Intervals on lmList Coefficients
lmeObject
Fitted lme Object
coef.lmList
Extract lmList Coefficients
corAR1
AR(1) Correlation Structure
Matrix.reStruct
Assign reStruct Matrices
lmeStruct
Linear Mixed-Effects Structure
recalc.reStruct
Recalculate for an reStruct Object
plot.gls
Plot a gls Object
nlme.nlsList
NLME fit from nlsList Object
print.varFunc
Print a varFunc Object
phenoModel
Model function for the Phenobarb data
getResponseFormula
Extract Formula Specifying Response Variable
summary.lme
Summarize an lme Object
gls
Fit Linear Model Using Generalized Least Squares
intervals.lme
Confidence Intervals on lme Parameters
anova.gls
Compare Likelihoods of Fitted Objects
plot.nffGroupedData
Plot an nffGroupedData Object
getGroups.corStruct
Extract corStruct Groups
pdSymm
General Positive-Definite Matrix
fixef.lmList
Extract lmList Fixed Effects
getData.lmList
Extract lmList Object Data
pdBlocked
Positive-Definite Block Diagonal Matrix
pdConstruct.pdBlocked
Construct pdBlocked Objects
plot.lme
Plot an lme or nls object
gnls
Fit Nonlinear Model Using Generalized Least Squares
print.summary.pdMat
Print a summary.pdMat Object
gnlsObject
Fitted gnls Object
predict.gnls
Predictions from a gnls Object
varExp
Exponential Variance Function
plot.augPred
Plot an augPred Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logDet.corStruct
Extract corStruct Log-Determinant
plot.ranef.lmList
Plot a ranef.lmList Object
nlme
Nonlinear Mixed-Effects Models
plot.compareFits
Plot a compareFits Object
nlsList.selfStart
nlsList Fit from a selfStart Function
pdMat
Positive-Definite Matrix
pdLogChol
General Positive-Definite Matrix
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdDiag
Diagonal Positive-Definite Matrix
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
model.matrix.reStruct
reStruct Model Matrix
nlmeObject
Fitted nlme Object
pairs.lmList
Pairs Plot of an lmList Object
pairs.lme
Pairs Plot of an lme Object
Assay
Bioassay on Cell Culture Plate
Glucose2
Glucose Levels Following Alcohol Ingestion
Earthquake
Earthquake Intensity
Gun
Methods for firing naval guns
Meat
Tenderness of meat
Wheat
Yields by growing conditions
Rail
Evaluation of Stress in Railway Rails
IGF
Radioimmunoassay of IGF-I Protein
Glucose
Glucose levels over time
Quinidine
Quinidine Kinetics
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
PBG
Effect of Phenylbiguanide on Blood Pressure
Nitrendipene
Assay of nitrendipene
Dialyzer
High-Flux Hemodialyzer
Milk
Protein content of cows' milk
Remifentanil
Pharmacokinetics of remifentanil
Phenobarb
Phenobarbitol Kinetics
Spruce
Growth of Spruce Trees
Wafer
Modeling of Analog MOS Circuits
Relaxin
Assay for Relaxin
Tetracycline1
Pharmacokinetics of tetracycline
RatPupWeight
The weight of rat pups
Wheat2
Wheat Yield Trials
Fatigue
Cracks caused by metal fatigue
Machines
Productivity Scores for Machines and Workers
Orthodont
Growth curve data on an orthdontic measurement
Ovary
Counts of Ovarian Follicles
Soybean
Growth of soybean plants
Oxide
Variability in Semiconductor Manufacturing
MathAchieve
Mathematics achievement scores
ergoStool
Ergometrics experiment with stool types
Muscle
Contraction of heart muscle sections
Oxboys
Heights of Boys in Oxford
Pixel
X-ray pixel intensities over time
Cefamandole
Pharmacokinetics of Cefamandole
Gasoline
Refinery yield of gasoline
BodyWeight
Rat weight over time for different diets
Oats
Split-plot Experiment on Varieties of Oats
MathAchSchool
School demographic data for MathAchieve
bdf
Language scores
Tetracycline2
Pharmacokinetics of tetracycline