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nlme (version 3.1-143)

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

3.1-143

License

GPL (>= 2) | file LICENCE

Maintainer

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

Last Published

December 10th, 2019

Functions in nlme (3.1-143)

[.pdMat

Subscript a pdMat Object
Initialize

Initialize Object
Dialyzer

High-Flux Hemodialyzer
Names

Names Associated with an Object
Dim

Extract Dimensions from an Object
Dim.pdMat

Dimensions of a pdMat Object
Muscle

Contraction of heart muscle sections
IGF

Radioimmunoassay of IGF-I Protein
Initialize.lmeStruct

Initialize an lmeStruct Object
Earthquake

Earthquake Intensity
Initialize.reStruct

Initialize reStruct Object
Glucose2

Glucose Levels Following Alcohol Ingestion
Nitrendipene

Assay of nitrendipene
Gun

Methods for firing naval guns
Fatigue

Cracks caused by metal fatigue
Gasoline

Refinery yield of gasoline
Ovary

Counts of Ovarian Follicles
MathAchSchool

School demographic data for MathAchieve
Orthodont

Growth curve data on an orthdontic measurement
Machines

Productivity Scores for Machines and Workers
Oats

Split-plot Experiment on Varieties of Oats
Covariate.varFunc

Assign varFunc Covariate
Dim.corSpatial

Dimensions of a corSpatial Object
Initialize.varFunc

Initialize varFunc Object
LDEsysMat

Generate system matrix for LDEs
Dim.corStruct

Dimensions of a corStruct Object
PBG

Effect of Phenylbiguanide on Blood Pressure
Initialize.corStruct

Initialize corStruct Object
Names.pdMat

Names of a pdMat Object
Glucose

Glucose levels over time
Matrix.pdMat

Assign Matrix to a pdMat or pdBlocked Object
Initialize.glsStruct

Initialize a glsStruct Object
Matrix.reStruct

Assign reStruct Matrices
Remifentanil

Pharmacokinetics of remifentanil
Relaxin

Assay for Relaxin
Tetracycline1

Pharmacokinetics of tetracycline
MathAchieve

Mathematics achievement scores
Matrix

Assign Matrix Values
as.matrix.pdMat

Matrix of a pdMat Object
Variogram.lme

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

Matrices of an reStruct Object
Wafer

Modeling of Analog MOS Circuits
Tetracycline2

Pharmacokinetics of tetracycline
coef.lme

Extract lme Coefficients
Names.formula

Extract Names from a formula
Soybean

Growth of soybean plants
Meat

Tenderness of meat
Names.reStruct

Names of an reStruct Object
Names.pdBlocked

Names of a pdBlocked Object
Spruce

Growth of Spruce Trees
Milk

Protein content of cows' milk
Phenobarb

Phenobarbitol Kinetics
Variogram.corLin

Calculate Semi-variogram for a corLin Object
Variogram.corRatio

Calculate Semi-variogram for a corRatio Object
Variogram.corSpatial

Calculate Semi-variogram for a corSpatial Object
Variogram.corSpher

Calculate Semi-variogram for a corSpher Object
Variogram.gls

Calculate Semi-variogram for Residuals from a gls Object
augPred

Augmented Predictions
Variogram.default

Calculate Semi-variogram
coef.modelStruct

Extract modelStruct Object Coefficients
anova.lme

Compare Likelihoods of Fitted Objects
corFactor.corStruct

Factor of a corStruct Object Matrix
Oxboys

Heights of Boys in Oxford
Oxide

Variability in Semiconductor Manufacturing
balancedGrouped

Create a groupedData object from a matrix
collapse.groupedData

Collapse a groupedData Object
as.matrix.corStruct

Matrix of a corStruct Object
Rail

Evaluation of Stress in Railway Rails
compareFits

Compare Fitted Objects
corLin

Linear Correlation Structure
Pixel

X-ray pixel intensities over time
asTable

Convert groupedData to a matrix
coef.pdMat

pdMat Object Coefficients
asOneFormula

Combine Formulas of a Set of Objects
corMatrix

Extract Correlation Matrix
Quinidine

Quinidine Kinetics
corSpher

Spherical Correlation Structure
corGaus

Gaussian Correlation Structure
fdHess

Finite difference Hessian
ergoStool

Ergometrics experiment with stool types
corSymm

General Correlation Structure
fitted.lmeStruct

Calculate lmeStruct Fitted Values
RatPupWeight

The weight of rat pups
fitted.glsStruct

Calculate glsStruct Fitted Values
coef.reStruct

reStruct Object Coefficients
Variogram

Calculate Semi-variogram
VarCorr

Extract variance and correlation components
fitted.nlmeStruct

Calculate nlmeStruct Fitted Values
getCovariate.data.frame

Extract Data Frame Covariate
Variogram.corExp

Calculate Semi-variogram for a corExp Object
getData.lmList

Extract lmList Object Data
getData.gls

Extract gls Object Data
getGroupsFormula

Extract Grouping Formula
fitted.gnlsStruct

Calculate gnlsStruct Fitted Values
getResponse

Extract Response Variable from an Object
Variogram.corGaus

Calculate Semi-variogram for a corGaus Object
allCoef

Extract Coefficients from a Set of Objects
bdf

Language scores
anova.gls

Compare Likelihoods of Fitted Objects
corClasses

Correlation Structure Classes
comparePred

Compare Predictions
coef.corStruct

Coefficients of a corStruct Object
corAR1

AR(1) Correlation Structure
corExp

Exponential Correlation Structure
corFactor

Factor of a Correlation Matrix
corMatrix.corStruct

Matrix of a corStruct Object
corMatrix.pdMat

Extract Correlation Matrix from a pdMat Object
fitted.lme

Extract lme Fitted Values
fitted.lmList

Extract lmList Fitted Values
getCovariate.varFunc

Extract varFunc Covariate
corCompSymm

Compound Symmetry Correlation Structure
corMatrix.reStruct

Extract Correlation Matrix from Components of an reStruct Object
getCovariate

Extract Covariate from an Object
getGroups.corStruct

Extract corStruct Groups
getResponseFormula

Extract Formula Specifying Response Variable
getData.lme

Extract lme Object Data
getGroups

Extract Grouping Factors from an Object
getCovariate.corStruct

Extract corStruct Object Covariate
lme.groupedData

LME fit from groupedData Object
glsObject

Fitted gls Object
glsControl

Control Values for gls Fit
intervals

Confidence Intervals on Coefficients
gsummary

Summarize by Groups
getVarCov

Extract variance-covariance matrix
getGroups.data.frame

Extract Groups from a Data Frame
Wheat

Yields by growing conditions
logDet.reStruct

Extract reStruct Log-Determinants
lme.lmList

LME fit from lmList Object
Wheat2

Wheat Yield Trials
collapse

Collapse According to Groups
coef.lmList

Extract lmList Coefficients
coef.gnls

Extract gnls Coefficients
coef.varFunc

varFunc Object Coefficients
corNatural

General correlation in natural parameterization
corARMA

ARMA(p,q) Correlation Structure
isInitialized

Check if Object is Initialized
logLik.corStruct

Extract corStruct Log-Likelihood
lmList

List of lm Objects with a Common Model
lmeControl

Specifying Control Values for lme Fit
fixed.effects

Extract Fixed Effects
needUpdate.modelStruct

Check if a modelStruct Object Needs Updating
plot.lme

Plot an lme or nls object
pdConstruct

Construct pdMat Objects
pdFactor.reStruct

Extract Square-Root Factor from Components of an reStruct Object
print.summary.pdMat

Print a summary.pdMat Object
nlme

Nonlinear Mixed-Effects Models
plot.nffGroupedData

Plot an nffGroupedData Object
pdConstruct.pdBlocked

Construct pdBlocked Objects
pdIdent

Multiple of the Identity Positive-Definite Matrix
glsStruct

Generalized Least Squares Structure
corCAR1

Continuous AR(1) Correlation Structure
gnls

Fit Nonlinear Model Using Generalized Least Squares
intervals.gls

Confidence Intervals on gls Parameters
corRatio

Rational Quadratic Correlation Structure
formula.pdBlocked

Extract pdBlocked Formula
corSpatial

Spatial Correlation Structure
formula.pdMat

Extract pdMat Formula
formula.reStruct

Extract reStruct Object Formula
gapply

Apply a Function by Groups
fixef.lmList

Extract lmList Fixed Effects
getGroups.gls

Extract gls Object Groups
lmeObject

Fitted lme Object
print.varFunc

Print a varFunc Object
logLik.reStruct

Calculate reStruct Log-Likelihood
recalc.corStruct

Recalculate for corStruct Object
recalc.reStruct

Recalculate for an reStruct Object
getCovariateFormula

Extract Covariates Formula
recalc.modelStruct

Recalculate for a modelStruct Object
getData

Extract Data from an Object
recalc.varFunc

Recalculate for varFunc Object
getGroups.lme

Extract lme Object Groups
intervals.lmList

Confidence Intervals on lmList Coefficients
solve.pdMat

Calculate Inverse of a Positive-Definite Matrix
getGroups.lmList

Extract lmList Object Groups
gnlsStruct

Generalized Nonlinear Least Squares Structure
gnlsControl

Control Values for gnls Fit
gnlsObject

Fitted gnls Object
getGroups.varFunc

Extract varFunc Groups
lmList.groupedData

lmList Fit from a groupedData Object
logLik.glsStruct

Log-Likelihood of a glsStruct Object
lme

Linear Mixed-Effects Models
logLik.gnls

Log-Likelihood of a gnls Object
groupedData

Construct a groupedData Object
solve.reStruct

Apply Solve to an reStruct Object
gls-internal

Auxiliary functions used by gls
logLik.varFunc

Extract varFunc logLik
lmeStruct

Linear Mixed-Effects Structure
isBalanced

Check a Design for Balance
gls

Fit Linear Model Using Generalized Least Squares
intervals.lme

Confidence Intervals on lme Parameters
logLik.lme

Log-Likelihood of an lme Object
logLik.lmeStruct

Log-Likelihood of an lmeStruct Object
logDet

Extract the Logarithm of the Determinant
model.matrix.reStruct

reStruct Model Matrix
logDet.corStruct

Extract corStruct Log-Determinant
nlsList

List of nls Objects with a Common Model
logDet.pdMat

Extract Log-Determinant from a pdMat Object
nlsList.selfStart

nlsList Fit from a selfStart Function
varIdent

Constant Variance Function
varFunc

Variance Function Structure
plot.ACF

Plot an ACF Object
pairs.lme

Pairs Plot of an lme Object
plot.compareFits

Plot a compareFits Object
phenoModel

Model function for the Phenobarb data
pdBlocked

Positive-Definite Block Diagonal Matrix
plot.gls

Plot a gls Object
plot.augPred

Plot an augPred Object
pdCompSymm

Positive-Definite Matrix with Compound Symmetry Structure
plot.Variogram

Plot a Variogram Object
nlmeObject

Fitted nlme Object
nlmeStruct

Nonlinear Mixed-Effects Structure
pdNatural

General Positive-Definite Matrix in Natural Parametrization
pdSymm

General Positive-Definite Matrix
pdClasses

Positive-Definite Matrix Classes
predict.lme

Predictions from an lme Object
pooledSD

Extract Pooled Standard Deviation
predict.nlme

Predictions from an nlme Object
predict.gls

Predictions from a gls Object
reStruct

Random Effects Structure
recalc

Recalculate Condensed Linear Model Object
quinModel

Model function for the Quinidine data
residuals.lme

Extract lme Residuals
residuals.lmeStruct

Calculate lmeStruct Residuals
summary.lmList

Summarize an lmList Object
update.varFunc

Update varFunc Object
summary.gls

Summarize a Generalized Least Squares gls Object
varClasses

Variance Function Classes
random.effects

Extract Random Effects
needUpdate

Check if Update is Needed
pairs.compareFits

Pairs Plot of compareFits Object
logLik.lmList

Log-Likelihood of an lmList Object
logLik.gnlsStruct

Log-Likelihood of a gnlsStruct Object
nlme.nlsList

NLME fit from nlsList Object
residuals.gnlsStruct

Calculate gnlsStruct Residuals
pdDiag

Diagonal Positive-Definite Matrix
nlmeControl

Control Values for nlme Fit
pdLogChol

General Positive-Definite Matrix
pdFactor

Square-Root Factor of a Positive-Definite Matrix
pairs.lmList

Pairs Plot of an lmList Object
pdMatrix.reStruct

Extract Matrix or Square-Root Factor from Components of an reStruct Object
predict.lmList

Predictions from an lmList Object
predict.gnls

Predictions from a gnls Object
plot.nfnGroupedData

Plot an nfnGroupedData Object
pdMatrix

Extract Matrix or Square-Root Factor from a pdMat Object
plot.nmGroupedData

Plot an nmGroupedData Object
ranef.lme

Extract lme Random Effects
residuals.gls

Extract gls Residuals
ranef.lmList

Extract lmList Random Effects
residuals.glsStruct

Calculate glsStruct Residuals
summary.lme

Summarize an lme Object
varComb

Combination of Variance Functions
summary.modelStruct

Summarize a modelStruct Object
varConstPower

Constant Plus Power Variance Function
varWeights.glsStruct

Variance Weights for glsStruct Object
varWeights.lmeStruct

Variance Weights for lmeStruct Object
residuals.lmList

Extract lmList Residuals
summary.corStruct

Summarize a corStruct Object
splitFormula

Split a Formula
varFixed

Fixed Variance Function
varExp

Exponential Variance Function
pdMat

Positive-Definite Matrix
plot.lmList

Plot an lmList Object
plot.ranef.lmList

Plot a ranef.lmList Object
plot.ranef.lme

Plot a ranef.lme Object
plot.intervals.lmList

Plot lmList Confidence Intervals
qqnorm.gls

Normal Plot of Residuals from a gls Object
simulate.lme

Simulate Results from lme Models
qqnorm.lme

Normal Plot of Residuals or Random Effects from an lme Object
residuals.nlmeStruct

Calculate nlmeStruct Residuals
summary.pdMat

Summarize a pdMat Object
summary.nlsList

Summarize an nlsList Object
summary.varFunc

Summarize varFunc Object
update.modelStruct

Update a modelStruct Object
varWeights

Extract Variance Function Weights
varPower

Power Variance Function
Cefamandole

Pharmacokinetics of Cefamandole
Alfalfa

Split-Plot Experiment on Varieties of Alfalfa
BodyWeight

Rat weight over time for different diets
ACF.gls

Autocorrelation Function for gls Residuals
Covariate

Assign Covariate Values
ACF

Autocorrelation Function
Assay

Bioassay on Cell Culture Plate
ACF.lme

Autocorrelation Function for lme Residuals
Coef

Assign Values to Coefficients