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nlme (version 3.1-152)

Linear and Nonlinear Mixed Effects Models

Description

Fit and compare Gaussian linear and nonlinear mixed-effects models.

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Version

Install

install.packages('nlme')

Monthly Downloads

149,202

Version

3.1-152

License

GPL (>= 2) | file LICENCE

Maintainer

R-core R-core@R-project.org

Last Published

February 4th, 2021

Functions in nlme (3.1-152)

Alfalfa

Split-Plot Experiment on Varieties of Alfalfa
BodyWeight

Rat weight over time for different diets
Coef

Assign Values to Coefficients
Covariate

Assign Covariate Values
ACF

Autocorrelation Function
ACF.lme

Autocorrelation Function for lme Residuals
Assay

Bioassay on Cell Culture Plate
Cefamandole

Pharmacokinetics of Cefamandole
Covariate.varFunc

Assign varFunc Covariate
ACF.gls

Autocorrelation Function for gls Residuals
[.pdMat

Subscript a pdMat Object
Dialyzer

High-Flux Hemodialyzer
Dim.corSpatial

Dimensions of a corSpatial Object
IGF

Radioimmunoassay of IGF-I Protein
Initialize.lmeStruct

Initialize an lmeStruct Object
Dim.corStruct

Dimensions of a corStruct Object
Initialize.reStruct

Initialize reStruct Object
Fatigue

Cracks caused by metal fatigue
Gasoline

Refinery yield of gasoline
Matrix.pdMat

Assign Matrix to a pdMat or pdBlocked Object
Dim

Extract Dimensions from an Object
Orthodont

Growth curve data on an orthdontic measurement
Initialize

Initialize Object
Glucose

Glucose levels over time
Gun

Methods for firing naval guns
Glucose2

Glucose Levels Following Alcohol Ingestion
Rail

Evaluation of Stress in Railway Rails
Dim.pdMat

Dimensions of a pdMat Object
Variogram.lme

Calculate Semi-variogram for Residuals from an lme Object
Matrix.reStruct

Assign reStruct Matrices
comparePred

Compare Predictions
Variogram.corExp

Calculate Semi-variogram for a corExp Object
MathAchieve

Mathematics achievement scores
Matrix

Assign Matrix Values
RatPupWeight

The weight of rat pups
corLin

Linear Correlation Structure
coef.pdMat

pdMat Object Coefficients
Initialize.varFunc

Initialize varFunc Object
allCoef

Extract Coefficients from a Set of Objects
Initialize.corStruct

Initialize corStruct Object
Earthquake

Earthquake Intensity
Variogram.corRatio

Calculate Semi-variogram for a corRatio Object
coef.lmList

Extract lmList Coefficients
Soybean

Growth of soybean plants
Muscle

Contraction of heart muscle sections
fixed.effects

Extract Fixed Effects
Meat

Tenderness of meat
LDEsysMat

Generate system matrix for LDEs
Names

Names Associated with an Object
Names.pdMat

Names of a pdMat Object
Wheat

Yields by growing conditions
Initialize.glsStruct

Initialize a glsStruct Object
anova.gls

Compare Likelihoods of Fitted Objects
Variogram.corSpatial

Calculate Semi-variogram for a corSpatial Object
Names.reStruct

Names of an reStruct Object
Names.formula

Extract Names from a formula
ergoStool

Ergometrics experiment with stool types
Pixel

X-ray pixel intensities over time
coef.varFunc

varFunc Object Coefficients
Wheat2

Wheat Yield Trials
Quinidine

Quinidine Kinetics
Machines

Productivity Scores for Machines and Workers
coef.gnls

Extract gnls Coefficients
Nitrendipene

Assay of nitrendipene
Oats

Split-plot Experiment on Varieties of Oats
Variogram.corLin

Calculate Semi-variogram for a corLin Object
MathAchSchool

School demographic data for MathAchieve
coef.lme

Extract lme Coefficients
corFactor.corStruct

Factor of a corStruct Object Matrix
Relaxin

Assay for Relaxin
Names.pdBlocked

Names of a pdBlocked Object
Remifentanil

Pharmacokinetics of Remifentanil
Milk

Protein content of cows' milk
Phenobarb

Phenobarbitol Kinetics
PBG

Effect of Phenylbiguanide on Blood Pressure
pdMatrix.reStruct

Extract Matrix or Square-Root Factor from Components of an reStruct Object
Tetracycline1

Pharmacokinetics of tetracycline
VarCorr

Extract variance and correlation components
getData.gls

Extract gls Object Data
bdf

Language scores
getCovariate.varFunc

Extract varFunc Covariate
isInitialized

Check if Object is Initialized
Ovary

Counts of Ovarian Follicles
lmeStruct

Linear Mixed-Effects Structure
Variogram.corGaus

Calculate Semi-variogram for a corGaus Object
getGroups.lme

Extract lme Object Groups
Oxboys

Heights of Boys in Oxford
asOneFormula

Combine Formulas of a Set of Objects
corClasses

Correlation Structure Classes
isBalanced

Check a Design for Balance
Oxide

Variability in Semiconductor Manufacturing
getCovariateFormula

Extract Covariates Formula
Tetracycline2

Pharmacokinetics of tetracycline
coef.modelStruct

Extract modelStruct Object Coefficients
groupedData

Construct a groupedData Object
Wafer

Modeling of Analog MOS Circuits
as.matrix.pdMat

Matrix of a pdMat Object
as.matrix.reStruct

Matrices of an reStruct Object
corCompSymm

Compound Symmetry Correlation Structure
asTable

Convert groupedData to a matrix
getCovariate.corStruct

Extract corStruct Object Covariate
Variogram.gls

Calculate Semi-variogram for Residuals from a gls Object
Variogram.default

Calculate Semi-variogram
augPred

Augmented Predictions
Variogram.corSpher

Calculate Semi-variogram for a corSpher Object
collapse

Collapse According to Groups
anova.lme

Compare Likelihoods of Fitted Objects
gnlsControl

Control Values for gnls Fit
corNatural

General correlation in natural parameterization
ranef.lme

Extract lme Random Effects
pooledSD

Extract Pooled Standard Deviation
coef.corStruct

Coefficients of a corStruct Object
corAR1

AR(1) Correlation Structure
getGroups.gls

Extract gls Object Groups
getData.lmList

Extract lmList Object Data
corMatrix

Extract Correlation Matrix
plot.nmGroupedData

Plot an nmGroupedData Object
fitted.glsStruct

Calculate glsStruct Fitted Values
fdHess

Finite difference Hessian
logLik.glsStruct

Log-Likelihood of a glsStruct Object
fitted.gnlsStruct

Calculate gnlsStruct Fitted Values
balancedGrouped

Create a groupedData object from a matrix
corMatrix.reStruct

Extract Correlation Matrix from Components of an reStruct Object
glsStruct

Generalized Least Squares Structure
getGroups.lmList

Extract lmList Object Groups
pdMatrix

Extract Matrix or Square-Root Factor from a pdMat Object
residuals.nlmeStruct

Calculate nlmeStruct Residuals
corGaus

Gaussian Correlation Structure
gnls

Fit Nonlinear Model Using Generalized Least Squares
logLik.corStruct

Extract corStruct Log-Likelihood
Spruce

Growth of Spruce Trees
intervals.gls

Confidence Intervals on gls Parameters
getData

Extract Data from an Object
getGroups

Extract Grouping Factors from an Object
gnlsStruct

Generalized Nonlinear Least Squares Structure
corMatrix.corStruct

Matrix of a corStruct Object
fixef.lmList

Extract lmList Fixed Effects
getCovariate

Extract Covariate from an Object
corRatio

Rational Quadratic Correlation Structure
fitted.lmeStruct

Calculate lmeStruct Fitted Values
corMatrix.pdMat

Extract Correlation Matrix from a pdMat Object
fitted.nlmeStruct

Calculate nlmeStruct Fitted Values
logLik.gnls

Log-Likelihood of a gnls Object
collapse.groupedData

Collapse a groupedData Object
getGroups.corStruct

Extract corStruct Groups
nlsList.selfStart

nlsList Fit from a selfStart Function
residuals.gls

Extract gls Residuals
formula.reStruct

Extract reStruct Object Formula
phenoModel

Model function for the Phenobarb data
compareFits

Compare Fitted Objects
gapply

Apply a Function by Groups
nlmeControl

Control Values for nlme Fit
getCovariate.data.frame

Extract Data Frame Covariate
getData.lme

Extract lme Object Data
lmList.groupedData

lmList Fit from a groupedData Object
gsummary

Summarize by Groups
coef.reStruct

reStruct Object Coefficients
pairs.lmList

Pairs Plot of an lmList Object
pairs.compareFits

Pairs Plot of compareFits Object
nlme.nlsList

NLME fit from nlsList Object
glsObject

Fitted gls Object
predict.gls

Predictions from a gls Object
plot.lmList

Plot an lmList Object
glsControl

Control Values for gls Fit
plot.intervals.lmList

Plot lmList Confidence Intervals
nlsList

List of nls Objects with a Common Model
solve.reStruct

Apply Solve to an reStruct Object
plot.ACF

Plot an ACF Object
intervals.lme

Confidence Intervals on lme Parameters
logLik.reStruct

Calculate reStruct Log-Likelihood
residuals.lmList

Extract lmList Residuals
Variogram

Calculate Semi-variogram
getResponse

Extract Response Variable from an Object
logLik.varFunc

Extract varFunc logLik
summary.varFunc

Summarize "varFunc" Object
recalc.corStruct

Recalculate for corStruct Object
corARMA

ARMA(p,q) Correlation Structure
logDet

Extract the Logarithm of the Determinant
as.matrix.corStruct

Matrix of a corStruct Object
print.varFunc

Print a varFunc Object
print.summary.pdMat

Print a summary.pdMat Object
corFactor

Factor of a Correlation Matrix
corSpatial

Spatial Correlation Structure
logLik.lme

Log-Likelihood of an lme Object
corExp

Exponential Correlation Structure
fitted.lme

Extract lme Fitted Values
reStruct

Random Effects Structure
fitted.lmList

Extract lmList Fitted Values
varFunc

Variance Function Structure
gls

Fit Linear Model Using Generalized Least Squares
gnlsObject

Fitted gnls Object
residuals.gnlsStruct

Calculate gnlsStruct Residuals
recalc.modelStruct

Recalculate for a modelStruct Object
logDet.reStruct

Extract reStruct Log-Determinants
getGroups.data.frame

Extract Groups from a Data Frame
logLik.lmeStruct

Log-Likelihood of an lmeStruct Object
splitFormula

Split a Formula
getGroups.varFunc

Extract varFunc Groups
solve.pdMat

Calculate Inverse of a Positive-Definite Matrix
lmList

List of lm Objects with a Common Model
logDet.corStruct

Extract corStruct Log-Determinant
intervals.lmList

Confidence Intervals on lmList Coefficients
formula.pdBlocked

Extract pdBlocked Formula
lme

Linear Mixed-Effects Models
summary.modelStruct

Summarize a modelStruct Object
gls-internal

Auxiliary functions used by gls
model.matrix.reStruct

reStruct Model Matrix
lmeObject

Fitted lme Object
recalc

Recalculate Condensed Linear Model Object
simulate.lme

Simulate Results from lme Models
plot.compareFits

Plot a compareFits Object
varConstProp

Constant Plus Proportion Variance Function
corCAR1

Continuous AR(1) Correlation Structure
summary.corStruct

Summarize a corStruct Object
needUpdate.modelStruct

Check if a modelStruct Object Needs Updating
varIdent

Constant Variance Function
corSymm

General Correlation Structure
update.modelStruct

Update a modelStruct Object
corSpher

Spherical Correlation Structure
getGroupsFormula

Extract Grouping Formula
logLik.lmList

Log-Likelihood of an lmList Object
pdCompSymm

Positive-Definite Matrix with Compound Symmetry Structure
formula.pdMat

Extract pdMat Formula
varWeights.lmeStruct

Variance Weights for lmeStruct Object
pdBlocked

Positive-Definite Block Diagonal Matrix
pairs.lme

Pairs Plot of an lme Object
nlme

Nonlinear Mixed-Effects Models
update.varFunc

Update varFunc Object
varClasses

Variance Function Classes
pdFactor

Square-Root Factor of a Positive-Definite Matrix
lmeControl

Specifying Control Values for lme Fit
lme.lmList

LME fit from lmList Object
varPower

Power Variance Function
logLik.gnlsStruct

Log-Likelihood of a gnlsStruct Object
lme.groupedData

LME fit from groupedData Object
plot.nfnGroupedData

Plot an nfnGroupedData Object
pdSymm

General Positive-Definite Matrix
needUpdate

Check if Update is Needed
ranef.lmList

Extract lmList Random Effects
pdConstruct

Construct pdMat Objects
recalc.reStruct

Recalculate for an reStruct Object
qqnorm.lme

Normal Plot of Residuals or Random Effects from an lme Object
logDet.pdMat

Extract Log-Determinant from a pdMat Object
predict.lmList

Predictions from an lmList Object
plot.lme

Plot an lme or nls object
pdLogChol

General Positive-Definite Matrix
getResponseFormula

Extract Formula Specifying Response Variable
pdDiag

Diagonal Positive-Definite Matrix
intervals

Confidence Intervals on Coefficients
plot.gls

Plot a gls Object
getVarCov

Extract variance-covariance matrix
varFixed

Fixed Variance Function
pdConstruct.pdBlocked

Construct pdBlocked Objects
recalc.varFunc

Recalculate for varFunc Object
pdMat

Positive-Definite Matrix
qqnorm.gls

Normal Plot of Residuals from a gls Object
summary.lme

Summarize an lme Object
nlmeObject

Fitted nlme Object
plot.ranef.lmList

Plot a ranef.lmList Object
predict.gnls

Predictions from a gnls Object
pdNatural

General Positive-Definite Matrix in Natural Parametrization
pdClasses

Positive-Definite Matrix Classes
plot.nffGroupedData

Plot an nffGroupedData Object
pdFactor.reStruct

Extract Square-Root Factor from Components of an reStruct Object
predict.lme

Predictions from an lme Object
pdIdent

Multiple of the Identity Positive-Definite Matrix
predict.nlme

Predictions from an nlme Object
nlmeStruct

Nonlinear Mixed-Effects Structure
varConstPower

Constant Plus Power Variance Function
plot.Variogram

Plot a Variogram Object
residuals.glsStruct

Calculate glsStruct Residuals
plot.augPred

Plot an augPred Object
varExp

Exponential Variance Function
residuals.lme

Extract lme Residuals
summary.nlsList

Summarize an nlsList Object
plot.ranef.lme

Plot a ranef.lme Object
varComb

Combination of Variance Functions
summary.pdMat

Summarize a pdMat Object
summary.gls

Summarize a Generalized Least Squares gls Object
quinModel

Model function for the Quinidine data
random.effects

Extract Random Effects
summary.lmList

Summarize an lmList Object
residuals.lmeStruct

Calculate lmeStruct Residuals
varWeights

Extract Variance Function Weights
varWeights.glsStruct

Variance Weights for glsStruct Object