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nlme (version 3.1-164)
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
134,390
Version
3.1-164
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
November 27th, 2023
Functions in nlme (3.1-164)
Search all functions
[.pdMat
Subscript a pdMat Object
Machines
Productivity Scores for Machines and Workers
Relaxin
Assay for Relaxin
Milk
Protein content of cows' milk
Names.pdBlocked
Names of a pdBlocked Object
Dim
Extract Dimensions from an Object
Muscle
Contraction of heart muscle sections
Oats
Split-plot Experiment on Varieties of Oats
Meat
Tenderness of meat
Soybean
Growth of soybean plants
Initialize.lmeStruct
Initialize an lmeStruct Object
LDEsysMat
Generate system matrix for LDEs
Names.formula
Extract Names from a formula
Nitrendipene
Assay of nitrendipene
Names
Names Associated with an Object
Spruce
Growth of Spruce Trees
Initialize.reStruct
Initialize reStruct Object
Dim.corSpatial
Dimensions of a corSpatial Object
Remifentanil
Pharmacokinetics of Remifentanil
MathAchSchool
School demographic data for MathAchieve
Ovary
Counts of Ovarian Follicles
Dim.corStruct
Dimensions of a corStruct Object
Orthodont
Growth curve data on an orthdontic measurement
Initialize
Initialize Object
PBG
Effect of Phenylbiguanide on Blood Pressure
IGF
Radioimmunoassay of IGF-I Protein
Fatigue
Cracks caused by metal fatigue
Phenobarb
Phenobarbitol Kinetics
bdf
Language scores
coef.corStruct
Coefficients of a corStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Oxide
Variability in Semiconductor Manufacturing
Matrix.reStruct
Assign reStruct Matrices
Initialize.corStruct
Initialize corStruct Object
Oxboys
Heights of Boys in Oxford
Initialize.glsStruct
Initialize a glsStruct Object
Tetracycline1
Pharmacokinetics of tetracycline
Glucose2
Glucose Levels Following Alcohol Ingestion
MathAchieve
Mathematics achievement scores
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Gun
Methods for firing naval guns
Tetracycline2
Pharmacokinetics of tetracycline
asOneFormula
Combine Formulas of a Set of Objects
allCoef
Extract Coefficients from a Set of Objects
Rail
Evaluation of Stress in Railway Rails
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Variogram
Calculate Semi-variogram
Wafer
Modeling of Analog MOS Circuits
VarCorr
Extract variance and correlation components
augPred
Augmented Predictions
asTable
Convert groupedData to a matrix
balancedGrouped
Create a groupedData object from a matrix
collapse.groupedData
Collapse a groupedData Object
anova.gls
Compare Likelihoods of Fitted Objects
compareFits
Compare Fitted Objects
Quinidine
Quinidine Kinetics
Names.reStruct
Names of an reStruct Object
Matrix
Assign Matrix Values
Pixel
X-ray pixel intensities over time
Names.pdMat
Names of a pdMat Object
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
corCAR1
Continuous AR(1) Correlation Structure
corRatio
Rational Quadratic Correlation Structure
corARMA
ARMA(p,q) Correlation Structure
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
as.matrix.pdMat
Matrix of a pdMat Object
corSpatial
Spatial Correlation Structure
corNatural
General correlation in natural parameterization
coef.varFunc
varFunc Object Coefficients
corExp
Exponential Correlation Structure
corSymm
General Correlation Structure
corFactor
Factor of a Correlation Matrix
corSpher
Spherical Correlation Structure
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
as.matrix.reStruct
Matrices of an reStruct Object
getCovariate
Extract Covariate from an Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
Wheat
Yields by growing conditions
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
getCovariate.corStruct
Extract corStruct Object Covariate
fitted.glsStruct
Calculate glsStruct Fitted Values
collapse
Collapse According to Groups
Wheat2
Wheat Yield Trials
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
getGroups.gls
Extract gls Object Groups
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getGroupsFormula
Extract Grouping Formula
RatPupWeight
The weight of rat pups
getCovariateFormula
Extract Covariates Formula
coef.pdMat
pdMat Object Coefficients
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getGroups.lmList
Extract lmList Object Groups
Variogram.default
Calculate Semi-variogram
Variogram.corExp
Calculate Semi-variogram for a corExp Object
coef.reStruct
reStruct Object Coefficients
getResponse
Extract Response Variable from an Object
lmList
List of lm Objects with a Common Model
isInitialized
Check if Object is Initialized
corClasses
Correlation Structure Classes
coef.lme
Extract lme Coefficients
coef.modelStruct
Extract modelStruct Object Coefficients
corCompSymm
Compound Symmetry Correlation Structure
glsStruct
Generalized Least Squares Structure
corAR1
AR(1) Correlation Structure
intervals
Confidence Intervals on Coefficients
coef.gnls
Extract gnls Coefficients
comparePred
Compare Predictions
getData
Extract Data from an Object
gsummary
Summarize by Groups
coef.lmList
Extract lmList Coefficients
gnls
Fit Nonlinear Model Using Generalized Least Squares
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
lme.groupedData
LME fit from groupedData Object
corFactor.corStruct
Factor of a corStruct Object Matrix
corMatrix.corStruct
Matrix of a corStruct Object
corGaus
Gaussian Correlation Structure
corLin
Linear Correlation Structure
getResponseFormula
Extract Formula Specifying Response Variable
getVarCov
Extract variance-covariance matrix
ergoStool
Ergometrics experiment with stool types
fitted.lmList
Extract lmList Fitted Values
gnlsStruct
Generalized Nonlinear Least Squares Structure
fdHess
Finite difference Hessian
getGroups.lme
Extract lme Object Groups
gapply
Apply a Function by Groups
getCovariate.varFunc
Extract varFunc Covariate
corMatrix
Extract Correlation Matrix
fixed.effects
Extract Fixed Effects
getCovariate.data.frame
Extract Data Frame Covariate
fitted.lme
Extract lme Fitted Values
formula.reStruct
Extract reStruct Object Formula
fixef.lmList
Extract lmList Fixed Effects
getGroups.varFunc
Extract varFunc Groups
glsControl
Control Values for gls Fit
groupedData
Construct a groupedData Object
formula.pdBlocked
Extract pdBlocked Formula
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getGroups
Extract Grouping Factors from an Object
getData.lme
Extract lme Object Data
lme.lmList
LME fit from lmList Object
formula.pdMat
Extract pdMat Formula
getData.gls
Extract gls Object Data
lmList.groupedData
lmList Fit from a groupedData Object
nlmeControl
Control Values for nlme Fit
getData.lmList
Extract lmList Object Data
logDet.reStruct
Extract reStruct Log-Determinants
nlmeObject
Fitted nlme Object
logLik.corStruct
Extract corStruct Log-Likelihood
intervals.lmList
Confidence Intervals on lmList Coefficients
gls-internal
Auxiliary functions used by gls
gnlsObject
Fitted gnls Object
lmeStruct
Linear Mixed-Effects Structure
gnlsControl
Control Values for gnls Fit
lme
Linear Mixed-Effects Models
isBalanced
Check a Design for Balance
getGroups.data.frame
Extract Groups from a Data Frame
intervals.lme
Confidence Intervals on lme Parameters
getGroups.corStruct
Extract corStruct Groups
intervals.gls
Confidence Intervals on gls Parameters
gls
Fit Linear Model Using Generalized Least Squares
logDet.corStruct
Extract corStruct Log-Determinant
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
glsObject
Fitted gls Object
logLik.lme
Log-Likelihood of an lme Object
predict.lmList
Predictions from an lmList Object
plot.lmList
Plot an lmList Object
lmeObject
Fitted lme Object
logDet
Extract the Logarithm of the Determinant
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
lmeControl
Specifying Control Values for lme Fit
plot.lme
Plot an lme or nls object
pdSymm
General Positive-Definite Matrix
logLik.gnls
Log-Likelihood of a gnls Object
pairs.compareFits
Pairs Plot of compareFits Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
predict.lme
Predictions from an lme Object
nlsList.selfStart
nlsList Fit from a selfStart Function
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
nlsList
List of nls Objects with a Common Model
nlmeStruct
Nonlinear Mixed-Effects Structure
logLik.lmList
Log-Likelihood of an lmList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdConstruct
Construct pdMat Objects
qqnorm.gls
Normal Plot of Residuals from a gls Object
print.varFunc
Print a varFunc Object
nlme
Nonlinear Mixed-Effects Models
nlme.nlsList
NLME fit from nlsList Object
pdClasses
Positive-Definite Matrix Classes
pdBlocked
Positive-Definite Block Diagonal Matrix
logLik.varFunc
Extract varFunc logLik
plot.ACF
Plot an ACF Object
phenoModel
Model function for the Phenobarb data
plot.nfnGroupedData
Plot an nfnGroupedData Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdMat
Positive-Definite Matrix
plot.nffGroupedData
Plot an nffGroupedData Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
needUpdate
Check if Update is Needed
pdConstruct.pdBlocked
Construct pdBlocked Objects
plot.ranef.lme
Plot a ranef.lme Object
pdDiag
Diagonal Positive-Definite Matrix
model.matrix.reStruct
reStruct Model Matrix
plot.Variogram
Plot a Variogram Object
pooledSD
Extract Pooled Standard Deviation
predict.gls
Predictions from a gls Object
recalc.modelStruct
Recalculate for a modelStruct Object
ranef.lme
Extract lme Random Effects
reStruct
Random Effects Structure
nlme-deprecated
Deprecated Functions in Package
nlme
predict.gnls
Predictions from a gnls Object
quinModel
Model function for the Quinidine data
plot.intervals.lmList
Plot lmList Confidence Intervals
pdFactor
Square-Root Factor of a Positive-Definite Matrix
plot.gls
Plot a gls Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
random.effects
Extract Random Effects
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
recalc.reStruct
Recalculate for an reStruct Object
splitFormula
Split a Formula
solve.reStruct
Apply Solve to an reStruct Object
residuals.lmList
Extract lmList Residuals
summary.pdMat
Summarize a pdMat Object
plot.nmGroupedData
Plot an nmGroupedData Object
summary.varFunc
Summarize "varFunc" Object
residuals.gls
Extract gls Residuals
ranef.lmList
Extract lmList Random Effects
recalc.varFunc
Recalculate for varFunc Object
plot.ranef.lmList
Plot a ranef.lmList Object
pairs.lmList
Pairs Plot of an lmList Object
simulate.lme
Simulate Results from
lme
Models
varFunc
Variance Function Structure
update.modelStruct
Update a modelStruct Object
recalc.corStruct
Recalculate for corStruct Object
summary.nlsList
Summarize an nlsList Object
update.varFunc
Update varFunc Object
summary.modelStruct
Summarize a modelStruct Object
recalc
Recalculate Condensed Linear Model Object
residuals.lme
Extract lme Residuals
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
summary.lme
Summarize an lme Object
varClasses
Variance Function Classes
summary.lmList
Summarize an lmList Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdLogChol
General Positive-Definite Matrix
varIdent
Constant Variance Function
residuals.lmeStruct
Calculate lmeStruct Residuals
pairs.lme
Pairs Plot of an lme Object
varComb
Combination of Variance Functions
plot.augPred
Plot an augPred Object
plot.compareFits
Plot a compareFits Object
predict.nlme
Predictions from an nlme Object
print.summary.pdMat
Print a summary.pdMat Object
varExp
Exponential Variance Function
varFixed
Fixed Variance Function
varWeights.lmeStruct
Variance Weights for lmeStruct Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
varWeights.glsStruct
Variance Weights for glsStruct Object
varConstProp
Constant Plus Proportion Variance Function
summary.corStruct
Summarize a corStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.glsStruct
Calculate glsStruct Residuals
varConstPower
Constant Plus Power Variance Function
summary.gls
Summarize a Generalized Least Squares
gls
Object
varPower
Power Variance Function
varWeights
Extract Variance Function Weights
Assay
Bioassay on Cell Culture Plate
Dialyzer
High-Flux Hemodialyzer
Covariate
Assign Covariate Values
Coef
Assign Values to Coefficients
ACF.lme
Autocorrelation Function for lme Residuals
Cefamandole
Pharmacokinetics of Cefamandole
ACF
Autocorrelation Function
BodyWeight
Rat weight over time for different diets
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Gasoline
Refinery yield of gasoline
Dim.pdMat
Dimensions of a pdMat Object
Covariate.varFunc
Assign varFunc Covariate
Earthquake
Earthquake Intensity
ACF.gls
Autocorrelation Function for gls Residuals
Glucose
Glucose levels over time
Initialize.varFunc
Initialize varFunc Object