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nlme (version 3.1-159)
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
149,202
Version
3.1-159
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
August 9th, 2022
Functions in nlme (3.1-159)
Search all functions
BodyWeight
Rat weight over time for different diets
ACF.lme
Autocorrelation Function for lme Residuals
ACF
Autocorrelation Function
ACF.gls
Autocorrelation Function for gls Residuals
Assay
Bioassay on Cell Culture Plate
Cefamandole
Pharmacokinetics of Cefamandole
Covariate.varFunc
Assign varFunc Covariate
Covariate
Assign Covariate Values
Coef
Assign Values to Coefficients
Dim.corSpatial
Dimensions of a corSpatial Object
Gasoline
Refinery yield of gasoline
Dim.pdMat
Dimensions of a pdMat Object
Initialize.reStruct
Initialize reStruct Object
Glucose
Glucose levels over time
Names.formula
Extract Names from a formula
Names.pdBlocked
Names of a pdBlocked Object
Initialize.lmeStruct
Initialize an lmeStruct Object
[.pdMat
Subscript a pdMat Object
Machines
Productivity Scores for Machines and Workers
Fatigue
Cracks caused by metal fatigue
MathAchSchool
School demographic data for MathAchieve
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Earthquake
Earthquake Intensity
Dim.corStruct
Dimensions of a corStruct Object
Meat
Tenderness of meat
Initialize.corStruct
Initialize corStruct Object
Initialize.varFunc
Initialize varFunc Object
Initialize.glsStruct
Initialize a glsStruct Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Initialize
Initialize Object
IGF
Radioimmunoassay of IGF-I Protein
Muscle
Contraction of heart muscle sections
LDEsysMat
Generate system matrix for LDEs
Dialyzer
High-Flux Hemodialyzer
MathAchieve
Mathematics achievement scores
Dim
Extract Dimensions from an Object
Matrix
Assign Matrix Values
Glucose2
Glucose Levels Following Alcohol Ingestion
Gun
Methods for firing naval guns
Names
Names Associated with an Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Ovary
Counts of Ovarian Follicles
Oxboys
Heights of Boys in Oxford
Oxide
Variability in Semiconductor Manufacturing
Pixel
X-ray pixel intensities over time
Orthodont
Growth curve data on an orthdontic measurement
Oats
Split-plot Experiment on Varieties of Oats
Nitrendipene
Assay of nitrendipene
RatPupWeight
The weight of rat pups
Rail
Evaluation of Stress in Railway Rails
Milk
Protein content of cows' milk
as.matrix.pdMat
Matrix of a pdMat Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Wheat
Yields by growing conditions
Names.pdMat
Names of a pdMat Object
PBG
Effect of Phenylbiguanide on Blood Pressure
Matrix.reStruct
Assign reStruct Matrices
VarCorr
Extract variance and correlation components
Variogram
Calculate Semi-variogram
Wheat2
Wheat Yield Trials
Quinidine
Quinidine Kinetics
Names.reStruct
Names of an reStruct Object
asOneFormula
Combine Formulas of a Set of Objects
Phenobarb
Phenobarbitol Kinetics
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Soybean
Growth of soybean plants
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Spruce
Growth of Spruce Trees
as.matrix.reStruct
Matrices of an reStruct Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
allCoef
Extract Coefficients from a Set of Objects
Wafer
Modeling of Analog MOS Circuits
asTable
Convert groupedData to a matrix
anova.lme
Compare Likelihoods of Fitted Objects
collapse.groupedData
Collapse a groupedData Object
as.matrix.corStruct
Matrix of a corStruct Object
Tetracycline2
Pharmacokinetics of tetracycline
Tetracycline1
Pharmacokinetics of tetracycline
coef.gnls
Extract gnls Coefficients
coef.lmList
Extract lmList Coefficients
coef.varFunc
varFunc Object Coefficients
augPred
Augmented Predictions
collapse
Collapse According to Groups
balancedGrouped
Create a groupedData object from a matrix
anova.gls
Compare Likelihoods of Fitted Objects
corClasses
Correlation Structure Classes
comparePred
Compare Predictions
corCompSymm
Compound Symmetry Correlation Structure
corAR1
AR(1) Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
corFactor
Factor of a Correlation Matrix
corExp
Exponential Correlation Structure
corSpher
Spherical Correlation Structure
Relaxin
Assay for Relaxin
fdHess
Finite difference Hessian
ergoStool
Ergometrics experiment with stool types
compareFits
Compare Fitted Objects
corMatrix
Extract Correlation Matrix
coef.lme
Extract lme Coefficients
corLin
Linear Correlation Structure
fixed.effects
Extract Fixed Effects
corGaus
Gaussian Correlation Structure
corARMA
ARMA(p,q) Correlation Structure
Remifentanil
Pharmacokinetics of Remifentanil
coef.modelStruct
Extract modelStruct Object Coefficients
Variogram.corExp
Calculate Semi-variogram for a corExp Object
corCAR1
Continuous AR(1) Correlation Structure
corSymm
General Correlation Structure
formula.reStruct
Extract reStruct Object Formula
getGroups.data.frame
Extract Groups from a Data Frame
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
gapply
Apply a Function by Groups
fitted.glsStruct
Calculate glsStruct Fitted Values
getGroups.corStruct
Extract corStruct Groups
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Variogram.default
Calculate Semi-variogram
fixef.lmList
Extract lmList Fixed Effects
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
bdf
Language scores
coef.pdMat
pdMat Object Coefficients
coef.corStruct
Coefficients of a corStruct Object
coef.reStruct
reStruct Object Coefficients
corSpatial
Spatial Correlation Structure
corRatio
Rational Quadratic Correlation Structure
fitted.lmList
Extract lmList Fitted Values
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
formula.pdMat
Extract pdMat Formula
formula.pdBlocked
Extract pdBlocked Formula
corNatural
General correlation in natural parameterization
corMatrix.corStruct
Matrix of a corStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getVarCov
Extract variance-covariance matrix
getResponseFormula
Extract Formula Specifying Response Variable
gsummary
Summarize by Groups
getCovariateFormula
Extract Covariates Formula
intervals
Confidence Intervals on Coefficients
gnlsControl
Control Values for gnls Fit
getData
Extract Data from an Object
intervals.gls
Confidence Intervals on gls Parameters
intervals.lmList
Confidence Intervals on lmList Coefficients
gnlsObject
Fitted gnls Object
lme.groupedData
LME fit from groupedData Object
plot.ACF
Plot an ACF Object
lmeControl
Specifying Control Values for lme Fit
plot.Variogram
Plot a Variogram Object
nlmeControl
Control Values for nlme Fit
lmeObject
Fitted lme Object
phenoModel
Model function for the Phenobarb data
getData.lmList
Extract lmList Object Data
nlme.nlsList
NLME fit from nlsList Object
getData.lme
Extract lme Object Data
getData.gls
Extract gls Object Data
fitted.lme
Extract lme Fitted Values
getCovariate
Extract Covariate from an Object
getCovariate.corStruct
Extract corStruct Object Covariate
getGroups.gls
Extract gls Object Groups
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getGroups.lmList
Extract lmList Object Groups
plot.augPred
Plot an augPred Object
glsControl
Control Values for gls Fit
gls
Fit Linear Model Using Generalized Least Squares
lme.lmList
LME fit from lmList Object
getGroups
Extract Grouping Factors from an Object
gls-internal
Auxiliary functions used by gls
isInitialized
Check if Object is Initialized
lmList
List of lm Objects with a Common Model
isBalanced
Check a Design for Balance
getGroups.lme
Extract lme Object Groups
intervals.lme
Confidence Intervals on lme Parameters
glsObject
Fitted gls Object
getGroups.varFunc
Extract varFunc Groups
logDet.reStruct
Extract reStruct Log-Determinants
lme
Linear Mixed-Effects Models
lmList.groupedData
lmList Fit from a groupedData Object
glsStruct
Generalized Least Squares Structure
gnls
Fit Nonlinear Model Using Generalized Least Squares
getCovariate.varFunc
Extract varFunc Covariate
nlmeObject
Fitted nlme Object
logLik.corStruct
Extract corStruct Log-Likelihood
getCovariate.data.frame
Extract Data Frame Covariate
nlmeStruct
Nonlinear Mixed-Effects Structure
logLik.reStruct
Calculate reStruct Log-Likelihood
logLik.varFunc
Extract varFunc logLik
nlsList.selfStart
nlsList Fit from a selfStart Function
nlsList
List of nls Objects with a Common Model
pdConstruct
Construct pdMat Objects
logDet.corStruct
Extract corStruct Log-Determinant
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.gnls
Log-Likelihood of a gnls Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
plot.ranef.lmList
Plot a ranef.lmList Object
getGroupsFormula
Extract Grouping Formula
groupedData
Construct a groupedData Object
getResponse
Extract Response Variable from an Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
lmeStruct
Linear Mixed-Effects Structure
pdConstruct.pdBlocked
Construct pdBlocked Objects
pooledSD
Extract Pooled Standard Deviation
plot.ranef.lme
Plot a ranef.lme Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
predict.gls
Predictions from a gls Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
model.matrix.reStruct
reStruct Model Matrix
needUpdate
Check if Update is Needed
logDet
Extract the Logarithm of the Determinant
recalc.modelStruct
Recalculate for a modelStruct Object
recalc.corStruct
Recalculate for corStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
reStruct
Random Effects Structure
recalc
Recalculate Condensed Linear Model Object
solve.reStruct
Apply Solve to an reStruct Object
pairs.compareFits
Pairs Plot of compareFits Object
summary.varFunc
Summarize "varFunc" Object
pairs.lme
Pairs Plot of an lme Object
pdBlocked
Positive-Definite Block Diagonal Matrix
update.modelStruct
Update a modelStruct Object
logLik.lme
Log-Likelihood of an lme Object
varWeights
Extract Variance Function Weights
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
ranef.lmList
Extract lmList Random Effects
plot.nfnGroupedData
Plot an nfnGroupedData Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
nlme
Nonlinear Mixed-Effects Models
plot.nmGroupedData
Plot an nmGroupedData Object
ranef.lme
Extract lme Random Effects
varWeights.glsStruct
Variance Weights for glsStruct Object
pdClasses
Positive-Definite Matrix Classes
residuals.gls
Extract gls Residuals
summary.corStruct
Summarize a corStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
residuals.gnlsStruct
Calculate gnlsStruct Residuals
splitFormula
Split a Formula
logLik.lmList
Log-Likelihood of an lmList Object
update.varFunc
Update varFunc Object
summary.modelStruct
Summarize a modelStruct Object
residuals.lmList
Extract lmList Residuals
varClasses
Variance Function Classes
summary.lme
Summarize an lme Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pairs.lmList
Pairs Plot of an lmList Object
plot.lme
Plot an lme or nls object
plot.nffGroupedData
Plot an nffGroupedData Object
pdDiag
Diagonal Positive-Definite Matrix
varConstPower
Constant Plus Power Variance Function
varComb
Combination of Variance Functions
plot.gls
Plot a gls Object
pdMat
Positive-Definite Matrix
pdLogChol
General Positive-Definite Matrix
quinModel
Model function for the Quinidine data
predict.gnls
Predictions from a gnls Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
print.varFunc
Print a varFunc Object
print.summary.pdMat
Print a summary.pdMat Object
plot.compareFits
Plot a compareFits Object
varIdent
Constant Variance Function
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdNatural
General Positive-Definite Matrix in Natural Parametrization
random.effects
Extract Random Effects
residuals.lme
Extract lme Residuals
residuals.lmeStruct
Calculate lmeStruct Residuals
varPower
Power Variance Function
predict.lmList
Predictions from an lmList Object
pdSymm
General Positive-Definite Matrix
qqnorm.gls
Normal Plot of Residuals from a gls Object
predict.lme
Predictions from an lme Object
plot.intervals.lmList
Plot lmList Confidence Intervals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
plot.lmList
Plot an lmList Object
predict.nlme
Predictions from an nlme Object
recalc.varFunc
Recalculate for varFunc Object
recalc.reStruct
Recalculate for an reStruct Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
summary.lmList
Summarize an lmList Object
summary.nlsList
Summarize an nlsList Object
simulate.lme
Simulate Results from
lme
Models
summary.pdMat
Summarize a pdMat Object
varFixed
Fixed Variance Function
varConstProp
Constant Plus Proportion Variance Function
varExp
Exponential Variance Function
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varFunc
Variance Function Structure