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nlme (version 3.1-77)
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
3.1-77
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
September 28th, 2006
Functions in nlme (3.1-77)
Search functions
Dim.pdMat
Dimensions of a pdMat Object
Dim.corStruct
Dimensions of a corStruct Object
augPred
Augmented Predictions
recalc.varFunc
Recalculate for varFunc Object
Initialize.corStruct
Initialize corStruct Object
Covariate
Assign Covariate Values
Initialize.reStruct
Initialize reStruct Object
Initialize.varFunc
Initialize varFunc Object
gapply
Apply a Function by Groups
coef.varFunc
varFunc Object Coefficients
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Variogram
Calculate Semi-variogram
corLin
Linear Correlation Structure
formula.pdBlocked
Extract pdBlocked Formula
asTable
Convert groupedData to a matrix
glsControl
Control Values for gls Fit
corClasses
Correlation Structure Classes
corMatrix.corStruct
Matrix of a corStruct Object
corCAR1
Continuous AR(1) Correlation Structure
logLik.varFunc
Extract varFunc logLik
coef.modelStruct
Extract modelStruct Object Coefficients
LDEsysMat
Generate system matrix for LDEs
as.matrix.pdMat
Matrix of a pdMat Object
corFactor
Factor of a Correlation Matrix
getCovariate
Extract Covariate from an Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
formula.pdMat
Extract pdMat Formula
Initialize
Initialize Object
fdHess
Finite difference Hessian
getGroups
Extract Grouping Factors from an Object
[.pdMat
Subscript a pdMat Object
Covariate.varFunc
Assign varFunc Covariate
corMatrix
Extract Correlation Matrix
recalc
Recalculate Condensed Linear Model Object
formula.reStruct
Extract reStruct Object Formula
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
plot.nfnGroupedData
Plot an nfnGroupedData Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
gnls
Fit Nonlinear Model Using Generalized Least Squares
pairs.compareFits
Pairs Plot of compareFits Object
Names.reStruct
Names of an reStruct Object
predict.gls
Predictions from a gls Object
plot.compareFits
Plot a compareFits Object
lmeScale
Scale for lme Optimization
Initialize.lmeStruct
Initialize an lmeStruct Object
corNatural
General correlation in natural parameterization
Matrix.pdMat
Assign Matrix to a pdMat Object
asOneFormula
Combine Formulas of a Set of Objects
getCovariate.data.frame
Extract Data Frame Covariate
varFunc
Variance Function Structure
model.matrix.reStruct
reStruct Model Matrix
Dim
Extract Dimensions from an Object
coef.corStruct
Coefficients of a corStruct Object
splitFormula
Split a Formula
summary.pdMat
Summarize a pdMat Object
logLik.lmList
Log-Likelihood of an lmList Object
update.modelStruct
Update a modelStruct Object
isInitialized
Check if Object is Initialized
collapse
Collapse According to Groups
BIC.logLik
BIC of a logLik Object
print.summary.pdMat
Print a summary.pdMat Object
Coef
Assign Values to Coefficients
Names
Names Associated with an Object
fitted.lme
Extract lme Fitted Values
lme.groupedData
LME fit from groupedData Object
ACF
Autocorrelation Function
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
summary.lme
Summarize an lme Object
collapse.groupedData
Collapse a groupedData Object
coef.pdMat
pdMat Object Coefficients
getCovariateFormula
Extract Covariates Formula
as.matrix.corStruct
Matrix of a corStruct Object
coef.lmList
Extract lmList Coefficients
lmeControl
Control Values for lme Fit
allCoef
Extract Coefficients from a Set of Objects
Variogram.corExp
Calculate Semi-variogram for a corExp Object
getGroups.lmList
Extract lmList Object Groups
residuals.gls
Extract gls Residuals
varWeights.glsStruct
Variance Weights for glsStruct Object
getCovariate.corStruct
Extract corStruct Object Covariate
quinModel
Model function for the Quinidine data
balancedGrouped
Create a groupedData object from a matrix
residuals.gnlsStruct
Calculate gnlsStruct Residuals
ACF.lme
Autocorrelation Function for lme Residuals
getResponseFormula
Extract Formula Specifying Response Variable
summary.corStruct
Summarize a corStruct Object
varComb
Combination of Variance Functions
corGaus
Gaussian Correlation Structure
summary.gls
Summarize a gls Object
coef.reStruct
reStruct Object Coefficients
varWeights
Extract Variance Function Weights
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
pdClasses
Positive-Definite Matrix Classes
coef.gnls
Extract gnls Coefficients
pdSymm
General Positive-Definite Matrix
residuals.glsStruct
Calculate glsStruct Residuals
pdNatural
General Positive-Definite Matrix in Natural Parametrization
as.matrix.reStruct
Matrices of an reStruct Object
corAR1
AR(1) Correlation Structure
getGroups.lme
Extract lme Object Groups
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
corCompSymm
Compound Symmetry Correlation Structure
corExp
Exponential Correlation Structure
lmList.groupedData
lmList Fit from a groupedData Object
comparePred
Compare Predictions
Names.pdBlocked
Names of a pdBlocked Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
solve.reStruct
Apply Solve to an reStruct Object
lmList
List of lm Objects with a Common Model
phenoModel
Model function for the Phenobarb data
plot.ranef.lme
Plot a ranef.lme Object
print.varFunc
Print a varFunc Object
residuals.lme
Extract lme Residuals
pdLogChol
General Positive-Definite Matrix
pairs.lme
Pairs Plot of an lme Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
simulate.lme
Simulate results from lme models
predict.lmList
Predictions from an lmList Object
varClasses
Variance Function Classes
corARMA
ARMA(p,q) Correlation Structure
plot.ranef.lmList
Plot a ranef.lmList Object
varIdent
Constant Variance Function
getData.gls
Extract gls Object Data
Names.formula
Extract Names from a formula
pdMat
Positive-Definite Matrix
gnlsControl
Control Values for gnls Fit
summary.nlsList
Summarize an nlsList Object
plot.nmGroupedData
Plot an nmGroupedData Object
coef.lme
Extract lme Coefficients
plot.augPred
Plot an augPred Object
lme.lmList
LME fit from lmList Object
Variogram.default
Calculate Semi-variogram
plot.Variogram
Plot a Variogram Object
getCovariate.varFunc
Extract varFunc Covariate
getResponse
Extract Response Variable from an Object
Dim.corSpatial
Dimensions of a corSpatial Object
VarCorr
Extract variance and correlation components
corSpatial
Spatial Correlation Structure
anova.lme
Compare Likelihoods of Fitted Objects
gls
Fit Linear Model Using Generalized Least Squares
getGroupsFormula
Extract Grouping Formula
random.effects
Extract Random Effects
plot.lme
Plot an lme or nls object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
getData
Extract Data from an Object
corSpher
Spherical Correlation Structure
pdFactor
Square-Root Factor of a Positive-Definite Matrix
Names.pdMat
Names of a pdMat Object
fixed.effects
Extract Fixed Effects
recalc.reStruct
Recalculate for an reStruct Object
corSymm
General Correlation Structure
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
lmeStruct
Linear Mixed-Effects Structure
logDet.pdMat
Extract Log-Determinant from a pdMat Object
update.varFunc
Update varFunc Object
corFactor.corStruct
Factor of a corStruct Object Matrix
pdDiag
Diagonal Positive-Definite Matrix
BIC
Bayesian Information Criterion
predict.lme
Predictions from an lme Object
ranef.lme
Extract lme Random Effects
Matrix
Assign Matrix Values
summary.lmList
Summarize an lmList Object
fixef.lmList
Extract lmList Fixed Effects
nlmeObject
Fitted nlme Object
reStruct
Random Effects Structure
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
predict.nlme
Predictions from an nlme Object
getData.lmList
Extract lmList Object Data
varConstPower
Constant Plus Power Variance Function
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
nlmeControl
Control Values for nlme Fit
summary.modelStruct
Summarize a modelStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
pdIdent
Multiple of the Identity Positive-Definite Matrix
fitted.glsStruct
Calculate glsStruct Fitted Values
pdConstruct
Construct pdMat Objects
needUpdate
Check if Update is Needed
plot.nffGroupedData
Plot an nffGroupedData Object
summary.varFunc
Summarize varFunc Object
logLik.lme
Log-Likelihood of an lme Object
getVarCov
Extract variance-covariance matrix
ACF.gls
Autocorrelation Function for gls Residuals
gsummary
Summarize by Groups
glsObject
Fitted gls Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
compareFits
Compare Fitted Objects
nlsList.selfStart
nlsList Fit from a selfStart Function
getGroups.corStruct
Extract corStruct Groups
Matrix.reStruct
Assign reStruct Matrices
nlme.nlsList
NLME fit from nlsList Object
nlmeStruct
Nonlinear Mixed-Effects Structure
nlsList
List of nls Objects with a Common Model
getData.lme
Extract lme Object Data
residuals.nlmeStruct
Calculate nlmeStruct Residuals
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
plot.gls
Plot a gls Object
logDet
Extract the Logarithm of the Determinant
Initialize.glsStruct
Initialize a glsStruct Object
getGroups.varFunc
Extract varFunc Groups
lme
Linear Mixed-Effects Models
logDet.corStruct
Extract corStruct Log-Determinant
gnlsStruct
Generalized Nonlinear Least Squares Structure
isBalanced
Check a Design for Balance
varPower
Power Variance Function
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
pdBlocked
Positive-Definite Block Diagonal Matrix
gnlsObject
Fitted gnls Object
varFixed
Fixed Variance Function
qqnorm.gls
Normal Plot of Residuals from a gls Object
residuals.lmeStruct
Calculate lmeStruct Residuals
lmeObject
Fitted lme Object
ranef.lmList
Extract lmList Random Effects
logLik.glsStruct
Log-Likelihood of a glsStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
predict.gnls
Predictions from a gnls Object
varExp
Exponential Variance Function
recalc.corStruct
Recalculate for corStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
pooledSD
Extract Pooled Standard Deviation
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
residuals.lmList
Extract lmList Residuals
intervals.lme
Confidence Intervals on lme Parameters
plot.intervals.lmList
Plot lmList Confidence Intervals
anova.gls
Compare Likelihoods of Fitted Objects
plot.ACF
Plot an ACF Object
getGroups.gls
Extract gls Object Groups
groupedData
Construct a groupedData Object
plot.lmList
Plot an lmList Object
logLik.gnls
Log-Likelihood of a gnls Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
intervals.gls
Confidence Intervals on gls Parameters
pdConstruct.pdBlocked
Construct pdBlocked Objects
glsStruct
Generalized Least Squares Structure
intervals
Confidence Intervals on Coefficients
corRatio
Rational Quadratic Correlation Structure
pairs.lmList
Pairs Plot of an lmList Object
intervals.lmList
Confidence Intervals on lmList Coefficients
nlme
Nonlinear Mixed-Effects Models
logDet.reStruct
Extract reStruct Log-Determinants
fitted.lmList
Extract lmList Fitted Values
logLik.corStruct
Extract corStruct Log-Likelihood
Oxboys
Heights of Boys in Oxford
Tetracycline2
Pharmacokinetics of tetracycline
Gun
Methods for firing naval guns
Earthquake
Earthquake Intensity
Orthodont
Growth curve data on an orthdontic measurement
Cefamandole
Pharmacokinetics of Cefamandole
Phenobarb
Phenobarbitol Kinetics
ergoStool
Ergometrics experiment with stool types
Spruce
Growth of Spruce Trees
Assay
Bioassay on Cell Culture Plate
BodyWeight
Rat weight over time for different diets
Pixel
X-ray pixel intensities over time
RatPupWeight
The weight of rat pups
IGF
Radioimmunoassay of IGF-I Protein
Gasoline
Refinery yield of gasoline
MathAchSchool
School demographic data for MathAchieve
Milk
Protein content of cows' milk
Oats
Split-plot Experiment on Varieties of Oats
Oxide
Variability in Semiconductor Manufacturing
Quinidine
Quinidine Kinetics
Soybean
Growth of soybean plants
Wafer
Modeling of Analog MOS Circuits
Meat
Tenderness of meat
PBG
Effect of Phenylbiguanide on Blood Pressure
Remifentanil
Pharmacokinetics of remifentanil
Rail
Evaluation of Stress in Railway Rails
Fatigue
Cracks caused by metal fatigue
Nitrendipene
Assay of nitrendipene
Ovary
Counts of Ovarian Follicles
Glucose
Glucose levels over time
Glucose2
Glucose Levels Following Alcohol Ingestion
Wheat2
Wheat Yield Trials
bdf
Language scores
Machines
Productivity Scores for Machines and Workers
Tetracycline1
Pharmacokinetics of tetracycline
Dialyzer
High-Flux Hemodialyzer
Muscle
Contraction of heart muscle sections
Wheat
Yields by growing conditions
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Relaxin
Assay for Relaxin
MathAchieve
Mathematics achievement scores