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nlme (version 3.1-158)
Linear and Nonlinear Mixed Effects Models
Description
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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3.1-2 (1999/12/23)
3.1-1
Install
install.packages('nlme')
Monthly Downloads
147,192
Version
3.1-158
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
June 15th, 2022
Functions in nlme (3.1-158)
Search all functions
BodyWeight
Rat weight over time for different diets
Cefamandole
Pharmacokinetics of Cefamandole
Covariate.varFunc
Assign varFunc Covariate
ACF
Autocorrelation Function
Covariate
Assign Covariate Values
Assay
Bioassay on Cell Culture Plate
ACF.gls
Autocorrelation Function for gls Residuals
ACF.lme
Autocorrelation Function for lme Residuals
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Dialyzer
High-Flux Hemodialyzer
Coef
Assign Values to Coefficients
Initialize.lmeStruct
Initialize an lmeStruct Object
Initialize
Initialize Object
Fatigue
Cracks caused by metal fatigue
Gasoline
Refinery yield of gasoline
IGF
Radioimmunoassay of IGF-I Protein
Machines
Productivity Scores for Machines and Workers
[.pdMat
Subscript a pdMat Object
Initialize.varFunc
Initialize varFunc Object
Initialize.reStruct
Initialize reStruct Object
Glucose
Glucose levels over time
LDEsysMat
Generate system matrix for LDEs
Dim
Extract Dimensions from an Object
Oxide
Variability in Semiconductor Manufacturing
Names
Names Associated with an Object
Matrix
Assign Matrix Values
MathAchieve
Mathematics achievement scores
Oxboys
Heights of Boys in Oxford
Dim.pdMat
Dimensions of a pdMat Object
MathAchSchool
School demographic data for MathAchieve
Muscle
Contraction of heart muscle sections
Spruce
Growth of Spruce Trees
Soybean
Growth of soybean plants
Meat
Tenderness of meat
Dim.corSpatial
Dimensions of a corSpatial Object
Orthodont
Growth curve data on an orthdontic measurement
Ovary
Counts of Ovarian Follicles
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
fdHess
Finite difference Hessian
Variogram.corLin
Calculate Semi-variogram for a corLin Object
as.matrix.pdMat
Matrix of a pdMat Object
fitted.lmList
Extract lmList Fitted Values
ergoStool
Ergometrics experiment with stool types
Wheat2
Wheat Yield Trials
as.matrix.reStruct
Matrices of an reStruct Object
Wheat
Yields by growing conditions
Dim.corStruct
Dimensions of a corStruct Object
fitted.lme
Extract lme Fitted Values
Pixel
X-ray pixel intensities over time
Matrix.reStruct
Assign reStruct Matrices
Gun
Methods for firing naval guns
Names.pdBlocked
Names of a pdBlocked Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Initialize.glsStruct
Initialize a glsStruct Object
Earthquake
Earthquake Intensity
Names.formula
Extract Names from a formula
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Initialize.corStruct
Initialize corStruct Object
Nitrendipene
Assay of nitrendipene
Quinidine
Quinidine Kinetics
PBG
Effect of Phenylbiguanide on Blood Pressure
Phenobarb
Phenobarbitol Kinetics
Rail
Evaluation of Stress in Railway Rails
Oats
Split-plot Experiment on Varieties of Oats
RatPupWeight
The weight of rat pups
Tetracycline1
Pharmacokinetics of tetracycline
Relaxin
Assay for Relaxin
Tetracycline2
Pharmacokinetics of tetracycline
coef.pdMat
pdMat Object Coefficients
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Wafer
Modeling of Analog MOS Circuits
Milk
Protein content of cows' milk
Variogram.corExp
Calculate Semi-variogram for a corExp Object
coef.gnls
Extract gnls Coefficients
Variogram.default
Calculate Semi-variogram
as.matrix.corStruct
Matrix of a corStruct Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
augPred
Augmented Predictions
balancedGrouped
Create a groupedData object from a matrix
anova.lme
Compare Likelihoods of Fitted Objects
collapse.groupedData
Collapse a groupedData Object
Names.pdMat
Names of a pdMat Object
formula.reStruct
Extract reStruct Object Formula
getGroups.lmList
Extract lmList Object Groups
gapply
Apply a Function by Groups
corClasses
Correlation Structure Classes
coef.lme
Extract lme Coefficients
coef.modelStruct
Extract modelStruct Object Coefficients
coef.lmList
Extract lmList Coefficients
gls-internal
Auxiliary functions used by gls
getGroups.gls
Extract gls Object Groups
gls
Fit Linear Model Using Generalized Least Squares
compareFits
Compare Fitted Objects
Names.reStruct
Names of an reStruct Object
Remifentanil
Pharmacokinetics of Remifentanil
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
bdf
Language scores
comparePred
Compare Predictions
coef.corStruct
Coefficients of a corStruct Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
formula.pdBlocked
Extract pdBlocked Formula
corAR1
AR(1) Correlation Structure
corCompSymm
Compound Symmetry Correlation Structure
VarCorr
Extract variance and correlation components
corFactor.corStruct
Factor of a corStruct Object Matrix
corMatrix.corStruct
Matrix of a corStruct Object
getCovariate
Extract Covariate from an Object
fitted.glsStruct
Calculate glsStruct Fitted Values
corLin
Linear Correlation Structure
coef.reStruct
reStruct Object Coefficients
corGaus
Gaussian Correlation Structure
getCovariate.corStruct
Extract corStruct Object Covariate
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
formula.pdMat
Extract pdMat Formula
Variogram
Calculate Semi-variogram
corExp
Exponential Correlation Structure
allCoef
Extract Coefficients from a Set of Objects
asOneFormula
Combine Formulas of a Set of Objects
anova.gls
Compare Likelihoods of Fitted Objects
collapse
Collapse According to Groups
asTable
Convert groupedData to a matrix
coef.varFunc
varFunc Object Coefficients
lmList
List of lm Objects with a Common Model
isInitialized
Check if Object is Initialized
getGroups.lme
Extract lme Object Groups
corCAR1
Continuous AR(1) Correlation Structure
corARMA
ARMA(p,q) Correlation Structure
lmList.groupedData
lmList Fit from a groupedData Object
corMatrix
Extract Correlation Matrix
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
lme
Linear Mixed-Effects Models
corFactor
Factor of a Correlation Matrix
corSymm
General Correlation Structure
fixed.effects
Extract Fixed Effects
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
corSpher
Spherical Correlation Structure
logLik.lmList
Log-Likelihood of an lmList Object
getData.gls
Extract gls Object Data
getGroups.varFunc
Extract varFunc Groups
getData.lmList
Extract lmList Object Data
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getCovariateFormula
Extract Covariates Formula
corNatural
General correlation in natural parameterization
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getResponse
Extract Response Variable from an Object
getGroupsFormula
Extract Grouping Formula
getResponseFormula
Extract Formula Specifying Response Variable
corSpatial
Spatial Correlation Structure
getData.lme
Extract lme Object Data
corRatio
Rational Quadratic Correlation Structure
getGroups
Extract Grouping Factors from an Object
gnlsControl
Control Values for gnls Fit
gnlsObject
Fitted gnls Object
getData
Extract Data from an Object
getVarCov
Extract variance-covariance matrix
gsummary
Summarize by Groups
fixef.lmList
Extract lmList Fixed Effects
getCovariate.data.frame
Extract Data Frame Covariate
pairs.lme
Pairs Plot of an lme Object
getCovariate.varFunc
Extract varFunc Covariate
pdBlocked
Positive-Definite Block Diagonal Matrix
lme.groupedData
LME fit from groupedData Object
pdLogChol
General Positive-Definite Matrix
intervals
Confidence Intervals on Coefficients
pdMat
Positive-Definite Matrix
predict.lme
Predictions from an lme Object
getGroups.corStruct
Extract corStruct Groups
predict.nlme
Predictions from an nlme Object
lme.lmList
LME fit from lmList Object
logLik.lme
Log-Likelihood of an lme Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
glsControl
Control Values for gls Fit
residuals.gls
Extract gls Residuals
glsObject
Fitted gls Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
glsStruct
Generalized Least Squares Structure
intervals.lme
Confidence Intervals on lme Parameters
gnlsStruct
Generalized Nonlinear Least Squares Structure
logLik.reStruct
Calculate reStruct Log-Likelihood
logDet
Extract the Logarithm of the Determinant
lmeStruct
Linear Mixed-Effects Structure
residuals.glsStruct
Calculate glsStruct Residuals
varFixed
Fixed Variance Function
summary.corStruct
Summarize a corStruct Object
splitFormula
Split a Formula
logLik.varFunc
Extract varFunc logLik
varFunc
Variance Function Structure
nlme.nlsList
NLME fit from nlsList Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
logDet.corStruct
Extract corStruct Log-Determinant
groupedData
Construct a groupedData Object
intervals.gls
Confidence Intervals on gls Parameters
logDet.pdMat
Extract Log-Determinant from a pdMat Object
nlmeControl
Control Values for nlme Fit
intervals.lmList
Confidence Intervals on lmList Coefficients
lmeControl
Specifying Control Values for lme Fit
lmeObject
Fitted lme Object
isBalanced
Check a Design for Balance
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logLik.corStruct
Extract corStruct Log-Likelihood
logDet.reStruct
Extract reStruct Log-Determinants
nlsList.selfStart
nlsList Fit from a selfStart Function
logLik.gnls
Log-Likelihood of a gnls Object
nlsList
List of nls Objects with a Common Model
pdConstruct
Construct pdMat Objects
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdConstruct.pdBlocked
Construct pdBlocked Objects
nlmeStruct
Nonlinear Mixed-Effects Structure
pairs.compareFits
Pairs Plot of compareFits Object
pairs.lmList
Pairs Plot of an lmList Object
nlmeObject
Fitted nlme Object
plot.ACF
Plot an ACF Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
phenoModel
Model function for the Phenobarb data
nlme
Nonlinear Mixed-Effects Models
plot.nfnGroupedData
Plot an nfnGroupedData Object
predict.gnls
Predictions from a gnls Object
plot.nmGroupedData
Plot an nmGroupedData Object
model.matrix.reStruct
reStruct Model Matrix
pdClasses
Positive-Definite Matrix Classes
needUpdate
Check if Update is Needed
pdIdent
Multiple of the Identity Positive-Definite Matrix
plot.Variogram
Plot a Variogram Object
plot.augPred
Plot an augPred Object
plot.ranef.lmList
Plot a ranef.lmList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
plot.ranef.lme
Plot a ranef.lme Object
reStruct
Random Effects Structure
pdNatural
General Positive-Definite Matrix in Natural Parametrization
plot.lmList
Plot an lmList Object
plot.intervals.lmList
Plot lmList Confidence Intervals
pdSymm
General Positive-Definite Matrix
predict.lmList
Predictions from an lmList Object
plot.compareFits
Plot a compareFits Object
plot.gls
Plot a gls Object
pooledSD
Extract Pooled Standard Deviation
ranef.lmList
Extract lmList Random Effects
predict.gls
Predictions from a gls Object
ranef.lme
Extract lme Random Effects
recalc.corStruct
Recalculate for corStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
recalc
Recalculate Condensed Linear Model Object
residuals.lmeStruct
Calculate lmeStruct Residuals
residuals.lme
Extract lme Residuals
pdDiag
Diagonal Positive-Definite Matrix
update.modelStruct
Update a modelStruct Object
summary.varFunc
Summarize "varFunc" Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
residuals.lmList
Extract lmList Residuals
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
quinModel
Model function for the Quinidine data
random.effects
Extract Random Effects
update.varFunc
Update varFunc Object
recalc.reStruct
Recalculate for an reStruct Object
solve.reStruct
Apply Solve to an reStruct Object
varClasses
Variance Function Classes
summary.nlsList
Summarize an nlsList Object
summary.pdMat
Summarize a pdMat Object
recalc.varFunc
Recalculate for varFunc Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
varWeights.glsStruct
Variance Weights for glsStruct Object
varConstProp
Constant Plus Proportion Variance Function
summary.lmList
Summarize an lmList Object
varWeights
Extract Variance Function Weights
varExp
Exponential Variance Function
print.summary.pdMat
Print a summary.pdMat Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
print.varFunc
Print a varFunc Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.lme
Plot an lme or nls object
plot.nffGroupedData
Plot an nffGroupedData Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
simulate.lme
Simulate Results from
lme
Models
varComb
Combination of Variance Functions
summary.modelStruct
Summarize a modelStruct Object
summary.lme
Summarize an lme Object
varConstPower
Constant Plus Power Variance Function
varIdent
Constant Variance Function
varPower
Power Variance Function