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nlme (version 3.1-160)
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
62,596
Version
3.1-160
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
October 10th, 2022
Functions in nlme (3.1-160)
Search all functions
Covariate.varFunc
Assign varFunc Covariate
Covariate
Assign Covariate Values
Cefamandole
Pharmacokinetics of Cefamandole
Coef
Assign Values to Coefficients
BodyWeight
Rat weight over time for different diets
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Assay
Bioassay on Cell Culture Plate
ACF.lme
Autocorrelation Function for lme Residuals
Dim
Extract Dimensions from an Object
Dim.pdMat
Dimensions of a pdMat Object
[.pdMat
Subscript a pdMat Object
ACF.gls
Autocorrelation Function for gls Residuals
Earthquake
Earthquake Intensity
Dim.corSpatial
Dimensions of a corSpatial Object
Fatigue
Cracks caused by metal fatigue
ACF
Autocorrelation Function
Dialyzer
High-Flux Hemodialyzer
Gasoline
Refinery yield of gasoline
Glucose
Glucose levels over time
Glucose2
Glucose Levels Following Alcohol Ingestion
Initialize.varFunc
Initialize varFunc Object
Dim.corStruct
Dimensions of a corStruct Object
Initialize.reStruct
Initialize reStruct Object
Initialize.lmeStruct
Initialize an lmeStruct Object
IGF
Radioimmunoassay of IGF-I Protein
Initialize
Initialize Object
LDEsysMat
Generate system matrix for LDEs
Names
Names Associated with an Object
Muscle
Contraction of heart muscle sections
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
MathAchSchool
School demographic data for MathAchieve
Machines
Productivity Scores for Machines and Workers
Gun
Methods for firing naval guns
Meat
Tenderness of meat
Nitrendipene
Assay of nitrendipene
Names.pdMat
Names of a pdMat Object
Names.reStruct
Names of an reStruct Object
Initialize.corStruct
Initialize corStruct Object
Initialize.glsStruct
Initialize a glsStruct Object
Names.pdBlocked
Names of a pdBlocked Object
MathAchieve
Mathematics achievement scores
Ovary
Counts of Ovarian Follicles
Milk
Protein content of cows' milk
Oats
Split-plot Experiment on Varieties of Oats
Matrix
Assign Matrix Values
Names.formula
Extract Names from a formula
Orthodont
Growth curve data on an orthdontic measurement
Rail
Evaluation of Stress in Railway Rails
Matrix.reStruct
Assign reStruct Matrices
Relaxin
Assay for Relaxin
Spruce
Growth of Spruce Trees
Soybean
Growth of soybean plants
Oxboys
Heights of Boys in Oxford
Remifentanil
Pharmacokinetics of Remifentanil
RatPupWeight
The weight of rat pups
PBG
Effect of Phenylbiguanide on Blood Pressure
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Oxide
Variability in Semiconductor Manufacturing
Quinidine
Quinidine Kinetics
Pixel
X-ray pixel intensities over time
VarCorr
Extract variance and correlation components
as.matrix.corStruct
Matrix of a corStruct Object
Phenobarb
Phenobarbitol Kinetics
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Tetracycline1
Pharmacokinetics of tetracycline
Wafer
Modeling of Analog MOS Circuits
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
anova.lme
Compare Likelihoods of Fitted Objects
Wheat
Yields by growing conditions
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
bdf
Language scores
Variogram
Calculate Semi-variogram
Wheat2
Wheat Yield Trials
asOneFormula
Combine Formulas of a Set of Objects
Tetracycline2
Pharmacokinetics of tetracycline
balancedGrouped
Create a groupedData object from a matrix
allCoef
Extract Coefficients from a Set of Objects
anova.gls
Compare Likelihoods of Fitted Objects
as.matrix.pdMat
Matrix of a pdMat Object
augPred
Augmented Predictions
comparePred
Compare Predictions
corAR1
AR(1) Correlation Structure
coef.corStruct
Coefficients of a corStruct Object
collapse
Collapse According to Groups
coef.varFunc
varFunc Object Coefficients
coef.modelStruct
Extract modelStruct Object Coefficients
as.matrix.reStruct
Matrices of an reStruct Object
coef.lme
Extract lme Coefficients
Variogram.default
Calculate Semi-variogram
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
corGaus
Gaussian Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
asTable
Convert groupedData to a matrix
coef.pdMat
pdMat Object Coefficients
coef.reStruct
reStruct Object Coefficients
corFactor
Factor of a Correlation Matrix
corExp
Exponential Correlation Structure
collapse.groupedData
Collapse a groupedData Object
corLin
Linear Correlation Structure
corSymm
General Correlation Structure
corClasses
Correlation Structure Classes
corCompSymm
Compound Symmetry Correlation Structure
corSpher
Spherical Correlation Structure
corARMA
ARMA(p,q) Correlation Structure
fixef.lmList
Extract lmList Fixed Effects
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corRatio
Rational Quadratic Correlation Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
compareFits
Compare Fitted Objects
fdHess
Finite difference Hessian
corCAR1
Continuous AR(1) Correlation Structure
ergoStool
Ergometrics experiment with stool types
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
corSpatial
Spatial Correlation Structure
fixed.effects
Extract Fixed Effects
fitted.lmList
Extract lmList Fitted Values
coef.gnls
Extract gnls Coefficients
coef.lmList
Extract lmList Coefficients
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
fitted.lme
Extract lme Fitted Values
corMatrix.corStruct
Matrix of a corStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corMatrix
Extract Correlation Matrix
getData
Extract Data from an Object
getCovariateFormula
Extract Covariates Formula
getCovariate.varFunc
Extract varFunc Covariate
getResponse
Extract Response Variable from an Object
getCovariate.corStruct
Extract corStruct Object Covariate
getGroupsFormula
Extract Grouping Formula
getCovariate
Extract Covariate from an Object
getGroups.data.frame
Extract Groups from a Data Frame
getCovariate.data.frame
Extract Data Frame Covariate
getGroups.corStruct
Extract corStruct Groups
gnls
Fit Nonlinear Model Using Generalized Least Squares
getGroups
Extract Grouping Factors from an Object
getData.lme
Extract lme Object Data
glsStruct
Generalized Least Squares Structure
gnlsObject
Fitted gnls Object
gnlsControl
Control Values for gnls Fit
formula.pdBlocked
Extract pdBlocked Formula
corNatural
General correlation in natural parameterization
getGroups.lme
Extract lme Object Groups
getGroups.varFunc
Extract varFunc Groups
formula.reStruct
Extract reStruct Object Formula
gapply
Apply a Function by Groups
formula.pdMat
Extract pdMat Formula
getGroups.lmList
Extract lmList Object Groups
getData.lmList
Extract lmList Object Data
getData.gls
Extract gls Object Data
getGroups.gls
Extract gls Object Groups
glsControl
Control Values for gls Fit
gsummary
Summarize by Groups
glsObject
Fitted gls Object
isInitialized
Check if Object is Initialized
logDet
Extract the Logarithm of the Determinant
lmList
List of lm Objects with a Common Model
lmeStruct
Linear Mixed-Effects Structure
intervals.lme
Confidence Intervals on lme Parameters
isBalanced
Check a Design for Balance
gnlsStruct
Generalized Nonlinear Least Squares Structure
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logDet.corStruct
Extract corStruct Log-Determinant
gls
Fit Linear Model Using Generalized Least Squares
lmList.groupedData
lmList Fit from a groupedData Object
logLik.reStruct
Calculate reStruct Log-Likelihood
logLik.lme
Log-Likelihood of an lme Object
gls-internal
Auxiliary functions used by gls
logLik.varFunc
Extract varFunc logLik
groupedData
Construct a groupedData Object
intervals
Confidence Intervals on Coefficients
logLik.glsStruct
Log-Likelihood of a glsStruct Object
lme.groupedData
LME fit from groupedData Object
logDet.reStruct
Extract reStruct Log-Determinants
lme.lmList
LME fit from lmList Object
lme
Linear Mixed-Effects Models
logLik.gnls
Log-Likelihood of a gnls Object
lmeControl
Specifying Control Values for lme Fit
lmeObject
Fitted lme Object
nlme.nlsList
NLME fit from nlsList Object
nlmeObject
Fitted nlme Object
nlmeControl
Control Values for nlme Fit
nlmeStruct
Nonlinear Mixed-Effects Structure
logLik.corStruct
Extract corStruct Log-Likelihood
nlsList.selfStart
nlsList Fit from a selfStart Function
nlsList
List of nls Objects with a Common Model
pairs.compareFits
Pairs Plot of compareFits Object
pairs.lme
Pairs Plot of an lme Object
pdBlocked
Positive-Definite Block Diagonal Matrix
pairs.lmList
Pairs Plot of an lmList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdClasses
Positive-Definite Matrix Classes
getVarCov
Extract variance-covariance matrix
intervals.gls
Confidence Intervals on gls Parameters
logLik.lmList
Log-Likelihood of an lmList Object
intervals.lmList
Confidence Intervals on lmList Coefficients
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
getResponseFormula
Extract Formula Specifying Response Variable
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdConstruct
Construct pdMat Objects
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
nlme
Nonlinear Mixed-Effects Models
pdFactor
Square-Root Factor of a Positive-Definite Matrix
plot.ACF
Plot an ACF Object
pdSymm
General Positive-Definite Matrix
phenoModel
Model function for the Phenobarb data
pdDiag
Diagonal Positive-Definite Matrix
pdNatural
General Positive-Definite Matrix in Natural Parametrization
model.matrix.reStruct
reStruct Model Matrix
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
needUpdate
Check if Update is Needed
pdLogChol
General Positive-Definite Matrix
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdMat
Positive-Definite Matrix
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
plot.compareFits
Plot a compareFits Object
plot.lme
Plot an lme or nls object
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.lmList
Plot an lmList Object
plot.nffGroupedData
Plot an nffGroupedData Object
plot.Variogram
Plot a Variogram Object
plot.augPred
Plot an augPred Object
plot.gls
Plot a gls Object
print.summary.pdMat
Print a summary.pdMat Object
predict.gnls
Predictions from a gnls Object
plot.ranef.lmList
Plot a ranef.lmList Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.ranef.lme
Plot a ranef.lme Object
predict.lmList
Predictions from an lmList Object
plot.nmGroupedData
Plot an nmGroupedData Object
print.varFunc
Print a varFunc Object
predict.nlme
Predictions from an nlme Object
predict.lme
Predictions from an lme Object
quinModel
Model function for the Quinidine data
random.effects
Extract Random Effects
ranef.lmList
Extract lmList Random Effects
recalc.corStruct
Recalculate for corStruct Object
recalc
Recalculate Condensed Linear Model Object
reStruct
Random Effects Structure
recalc.modelStruct
Recalculate for a modelStruct Object
ranef.lme
Extract lme Random Effects
pooledSD
Extract Pooled Standard Deviation
predict.gls
Predictions from a gls Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
residuals.lme
Extract lme Residuals
residuals.lmList
Extract lmList Residuals
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
simulate.lme
Simulate Results from
lme
Models
residuals.glsStruct
Calculate glsStruct Residuals
recalc.reStruct
Recalculate for an reStruct Object
residuals.gls
Extract gls Residuals
recalc.varFunc
Recalculate for varFunc Object
residuals.lmeStruct
Calculate lmeStruct Residuals
summary.gls
Summarize a Generalized Least Squares
gls
Object
summary.lmList
Summarize an lmList Object
solve.reStruct
Apply Solve to an reStruct Object
summary.corStruct
Summarize a corStruct Object
splitFormula
Split a Formula
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
summary.nlsList
Summarize an nlsList Object
summary.modelStruct
Summarize a modelStruct Object
summary.lme
Summarize an lme Object
summary.pdMat
Summarize a pdMat Object
varFunc
Variance Function Structure
varFixed
Fixed Variance Function
update.modelStruct
Update a modelStruct Object
varConstProp
Constant Plus Proportion Variance Function
update.varFunc
Update varFunc Object
varClasses
Variance Function Classes
varExp
Exponential Variance Function
varComb
Combination of Variance Functions
varConstPower
Constant Plus Power Variance Function
summary.varFunc
Summarize "varFunc" Object
varWeights
Extract Variance Function Weights
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
varPower
Power Variance Function
varIdent
Constant Variance Function