Learn R Programming

⚠️There's a newer version (3.1-168) of this package.Take me there.

nlme (version 3.1-148)

Linear and Nonlinear Mixed Effects Models

Description

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

Copy Link

Version

Install

install.packages('nlme')

Monthly Downloads

81,705

Version

3.1-148

License

GPL (>= 2) | file LICENCE

Maintainer

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

Last Published

May 24th, 2020

Functions in nlme (3.1-148)

Glucose

Glucose levels over time
Assay

Bioassay on Cell Culture Plate
BodyWeight

Rat weight over time for different diets
Gasoline

Refinery yield of gasoline
Initialize.varFunc

Initialize varFunc Object
Glucose2

Glucose Levels Following Alcohol Ingestion
Dim.pdMat

Dimensions of a pdMat Object
Coef

Assign Values to Coefficients
Earthquake

Earthquake Intensity
Gun

Methods for firing naval guns
Cefamandole

Pharmacokinetics of Cefamandole
Matrix.reStruct

Assign reStruct Matrices
Matrix.pdMat

Assign Matrix to a pdMat or pdBlocked Object
LDEsysMat

Generate system matrix for LDEs
PBG

Effect of Phenylbiguanide on Blood Pressure
Covariate

Assign Covariate Values
Initialize

Initialize Object
MathAchieve

Mathematics achievement scores
ACF.gls

Autocorrelation Function for gls Residuals
Matrix

Assign Matrix Values
Names.formula

Extract Names from a formula
Variogram.corSpatial

Calculate Semi-variogram for a corSpatial Object
Pixel

X-ray pixel intensities over time
Quinidine

Quinidine Kinetics
Variogram.corSpher

Calculate Semi-variogram for a corSpher Object
ACF

Autocorrelation Function
IGF

Radioimmunoassay of IGF-I Protein
Names.pdBlocked

Names of a pdBlocked Object
Covariate.varFunc

Assign varFunc Covariate
Phenobarb

Phenobarbitol Kinetics
Dim.corSpatial

Dimensions of a corSpatial Object
Wheat

Yields by growing conditions
Initialize.reStruct

Initialize reStruct Object
Wheat2

Wheat Yield Trials
Dim.corStruct

Dimensions of a corStruct Object
coef.gnls

Extract gnls Coefficients
coef.lmList

Extract lmList Coefficients
Initialize.lmeStruct

Initialize an lmeStruct Object
Variogram.corExp

Calculate Semi-variogram for a corExp Object
coef.pdMat

pdMat Object Coefficients
coef.reStruct

reStruct Object Coefficients
[.pdMat

Subscript a pdMat Object
Muscle

Contraction of heart muscle sections
Machines

Productivity Scores for Machines and Workers
Fatigue

Cracks caused by metal fatigue
augPred

Augmented Predictions
Variogram.corGaus

Calculate Semi-variogram for a corGaus Object
Oxboys

Heights of Boys in Oxford
Variogram.default

Calculate Semi-variogram
Variogram.gls

Calculate Semi-variogram for Residuals from a gls Object
MathAchSchool

School demographic data for MathAchieve
Initialize.corStruct

Initialize corStruct Object
Relaxin

Assay for Relaxin
balancedGrouped

Create a groupedData object from a matrix
Oxide

Variability in Semiconductor Manufacturing
coef.varFunc

varFunc Object Coefficients
Nitrendipene

Assay of nitrendipene
Initialize.glsStruct

Initialize a glsStruct Object
Soybean

Growth of soybean plants
Names

Names Associated with an Object
Oats

Split-plot Experiment on Varieties of Oats
Orthodont

Growth curve data on an orthdontic measurement
Remifentanil

Pharmacokinetics of Remifentanil
Ovary

Counts of Ovarian Follicles
RatPupWeight

The weight of rat pups
Rail

Evaluation of Stress in Railway Rails
Variogram.corLin

Calculate Semi-variogram for a corLin Object
collapse

Collapse According to Groups
fixed.effects

Extract Fixed Effects
corCAR1

Continuous AR(1) Correlation Structure
fixef.lmList

Extract lmList Fixed Effects
corGaus

Gaussian Correlation Structure
corFactor.corStruct

Factor of a corStruct Object Matrix
getCovariate

Extract Covariate from an Object
corARMA

ARMA(p,q) Correlation Structure
corRatio

Rational Quadratic Correlation Structure
Tetracycline1

Pharmacokinetics of tetracycline
Spruce

Growth of Spruce Trees
anova.lme

Compare Likelihoods of Fitted Objects
Tetracycline2

Pharmacokinetics of tetracycline
allCoef

Extract Coefficients from a Set of Objects
anova.gls

Compare Likelihoods of Fitted Objects
Variogram.corRatio

Calculate Semi-variogram for a corRatio Object
corLin

Linear Correlation Structure
corAR1

AR(1) Correlation Structure
comparePred

Compare Predictions
getCovariate.corStruct

Extract corStruct Object Covariate
as.matrix.corStruct

Matrix of a corStruct Object
corMatrix

Extract Correlation Matrix
corNatural

General correlation in natural parameterization
getGroups.corStruct

Extract corStruct Groups
corMatrix.reStruct

Extract Correlation Matrix from Components of an reStruct Object
bdf

Language scores
fitted.glsStruct

Calculate glsStruct Fitted Values
gnlsControl

Control Values for gnls Fit
gnlsObject

Fitted gnls Object
getGroups.data.frame

Extract Groups from a Data Frame
corSpatial

Spatial Correlation Structure
getData

Extract Data from an Object
getCovariateFormula

Extract Covariates Formula
coef.corStruct

Coefficients of a corStruct Object
collapse.groupedData

Collapse a groupedData Object
compareFits

Compare Fitted Objects
lmList

List of lm Objects with a Common Model
getGroups.gls

Extract gls Object Groups
isInitialized

Check if Object is Initialized
logDet.corStruct

Extract corStruct Log-Determinant
fitted.gnlsStruct

Calculate gnlsStruct Fitted Values
formula.pdMat

Extract pdMat Formula
formula.pdBlocked

Extract pdBlocked Formula
fdHess

Finite difference Hessian
ergoStool

Ergometrics experiment with stool types
logDet.pdMat

Extract Log-Determinant from a pdMat Object
getCovariate.data.frame

Extract Data Frame Covariate
VarCorr

Extract variance and correlation components
glsControl

Control Values for gls Fit
intervals

Confidence Intervals on Coefficients
glsObject

Fitted gls Object
gsummary

Summarize by Groups
getGroups.lmList

Extract lmList Object Groups
getCovariate.varFunc

Extract varFunc Covariate
formula.reStruct

Extract reStruct Object Formula
lmList.groupedData

lmList Fit from a groupedData Object
needUpdate

Check if Update is Needed
gapply

Apply a Function by Groups
model.matrix.reStruct

reStruct Model Matrix
Variogram

Calculate Semi-variogram
lme

Linear Mixed-Effects Models
nlmeStruct

Nonlinear Mixed-Effects Structure
gls-internal

Auxiliary functions used by gls
pdConstruct

Construct pdMat Objects
nlmeObject

Fitted nlme Object
pdClasses

Positive-Definite Matrix Classes
pdCompSymm

Positive-Definite Matrix with Compound Symmetry Structure
logLik.glsStruct

Log-Likelihood of a glsStruct Object
logLik.gnls

Log-Likelihood of a gnls Object
pdConstruct.pdBlocked

Construct pdBlocked Objects
pdNatural

General Positive-Definite Matrix in Natural Parametrization
pdSymm

General Positive-Definite Matrix
asOneFormula

Combine Formulas of a Set of Objects
plot.ACF

Plot an ACF Object
plot.nfnGroupedData

Plot an nfnGroupedData Object
plot.nffGroupedData

Plot an nffGroupedData Object
phenoModel

Model function for the Phenobarb data
quinModel

Model function for the Quinidine data
random.effects

Extract Random Effects
plot.lme

Plot an lme or nls object
getGroups.lme

Extract lme Object Groups
asTable

Convert groupedData to a matrix
ACF.lme

Autocorrelation Function for lme Residuals
residuals.lmList

Extract lmList Residuals
gls

Fit Linear Model Using Generalized Least Squares
getGroups.varFunc

Extract varFunc Groups
residuals.gnlsStruct

Calculate gnlsStruct Residuals
coef.lme

Extract lme Coefficients
Alfalfa

Split-Plot Experiment on Varieties of Alfalfa
getResponseFormula

Extract Formula Specifying Response Variable
plot.nmGroupedData

Plot an nmGroupedData Object
coef.modelStruct

Extract modelStruct Object Coefficients
summary.lme

Summarize an lme Object
corClasses

Correlation Structure Classes
corSymm

General Correlation Structure
logDet.reStruct

Extract reStruct Log-Determinants
corCompSymm

Compound Symmetry Correlation Structure
fitted.lmeStruct

Calculate lmeStruct Fitted Values
getVarCov

Extract variance-covariance matrix
logLik.corStruct

Extract corStruct Log-Likelihood
summary.modelStruct

Summarize a modelStruct Object
corSpher

Spherical Correlation Structure
plot.ranef.lme

Plot a ranef.lme Object
varComb

Combination of Variance Functions
plot.ranef.lmList

Plot a ranef.lmList Object
nlme.nlsList

NLME fit from nlsList Object
nlmeControl

Control Values for nlme Fit
plot.augPred

Plot an augPred Object
Dialyzer

High-Flux Hemodialyzer
plot.Variogram

Plot a Variogram Object
intervals.lmList

Confidence Intervals on lmList Coefficients
lmeControl

Specifying Control Values for lme Fit
fitted.nlmeStruct

Calculate nlmeStruct Fitted Values
getResponse

Extract Response Variable from an Object
pdBlocked

Positive-Definite Block Diagonal Matrix
intervals.gls

Confidence Intervals on gls Parameters
predict.lmList

Predictions from an lmList Object
predict.gnls

Predictions from a gnls Object
varConstPower

Constant Plus Power Variance Function
getGroupsFormula

Extract Grouping Formula
reStruct

Random Effects Structure
Dim

Extract Dimensions from an Object
lmeObject

Fitted lme Object
pairs.lme

Pairs Plot of an lme Object
recalc

Recalculate Condensed Linear Model Object
intervals.lme

Confidence Intervals on lme Parameters
logLik.varFunc

Extract varFunc logLik
ranef.lmList

Extract lmList Random Effects
isBalanced

Check a Design for Balance
ranef.lme

Extract lme Random Effects
logLik.reStruct

Calculate reStruct Log-Likelihood
residuals.nlmeStruct

Calculate nlmeStruct Residuals
residuals.gls

Extract gls Residuals
needUpdate.modelStruct

Check if a modelStruct Object Needs Updating
Meat

Tenderness of meat
nlme

Nonlinear Mixed-Effects Models
lme.groupedData

LME fit from groupedData Object
residuals.glsStruct

Calculate glsStruct Residuals
simulate.lme

Simulate Results from lme Models
pdMatrix.reStruct

Extract Matrix or Square-Root Factor from Components of an reStruct Object
pairs.compareFits

Pairs Plot of compareFits Object
pdMatrix

Extract Matrix or Square-Root Factor from a pdMat Object
print.summary.pdMat

Print a summary.pdMat Object
pairs.lmList

Pairs Plot of an lmList Object
Milk

Protein content of cows' milk
summary.gls

Summarize a Generalized Least Squares gls Object
Variogram.lme

Calculate Semi-variogram for Residuals from an lme Object
Names.pdMat

Names of a pdMat Object
splitFormula

Split a Formula
Wafer

Modeling of Analog MOS Circuits
lme.lmList

LME fit from lmList Object
Names.reStruct

Names of an reStruct Object
varWeights.glsStruct

Variance Weights for glsStruct Object
logLik.lme

Log-Likelihood of an lme Object
as.matrix.reStruct

Matrices of an reStruct Object
varWeights.lmeStruct

Variance Weights for lmeStruct Object
nlsList.selfStart

nlsList Fit from a selfStart Function
nlsList

List of nls Objects with a Common Model
pdIdent

Multiple of the Identity Positive-Definite Matrix
pdFactor.reStruct

Extract Square-Root Factor from Components of an reStruct Object
as.matrix.pdMat

Matrix of a pdMat Object
summary.corStruct

Summarize a corStruct Object
logLik.lmeStruct

Log-Likelihood of an lmeStruct Object
summary.lmList

Summarize an lmList Object
plot.compareFits

Plot a compareFits Object
print.varFunc

Print a varFunc Object
plot.gls

Plot a gls Object
pooledSD

Extract Pooled Standard Deviation
update.varFunc

Update varFunc Object
predict.gls

Predictions from a gls Object
corFactor

Factor of a Correlation Matrix
corMatrix.pdMat

Extract Correlation Matrix from a pdMat Object
corExp

Exponential Correlation Structure
fitted.lmList

Extract lmList Fitted Values
corMatrix.corStruct

Matrix of a corStruct Object
residuals.lme

Extract lme Residuals
recalc.corStruct

Recalculate for corStruct Object
recalc.modelStruct

Recalculate for a modelStruct Object
varClasses

Variance Function Classes
getData.gls

Extract gls Object Data
getData.lmList

Extract lmList Object Data
getGroups

Extract Grouping Factors from an Object
getData.lme

Extract lme Object Data
fitted.lme

Extract lme Fitted Values
glsStruct

Generalized Least Squares Structure
varPower

Power Variance Function
varFunc

Variance Function Structure
gnls

Fit Nonlinear Model Using Generalized Least Squares
varIdent

Constant Variance Function
gnlsStruct

Generalized Nonlinear Least Squares Structure
residuals.lmeStruct

Calculate lmeStruct Residuals
groupedData

Construct a groupedData Object
recalc.varFunc

Recalculate for varFunc Object
recalc.reStruct

Recalculate for an reStruct Object
lmeStruct

Linear Mixed-Effects Structure
varWeights

Extract Variance Function Weights
logLik.lmList

Log-Likelihood of an lmList Object
pdDiag

Diagonal Positive-Definite Matrix
logLik.gnlsStruct

Log-Likelihood of a gnlsStruct Object
logDet

Extract the Logarithm of the Determinant
update.modelStruct

Update a modelStruct Object
summary.varFunc

Summarize varFunc Object
solve.reStruct

Apply Solve to an reStruct Object
solve.pdMat

Calculate Inverse of a Positive-Definite Matrix
pdFactor

Square-Root Factor of a Positive-Definite Matrix
plot.intervals.lmList

Plot lmList Confidence Intervals
predict.lme

Predictions from an lme Object
pdMat

Positive-Definite Matrix
plot.lmList

Plot an lmList Object
pdLogChol

General Positive-Definite Matrix
predict.nlme

Predictions from an nlme Object
qqnorm.gls

Normal Plot of Residuals from a gls Object
summary.nlsList

Summarize an nlsList Object
summary.pdMat

Summarize a pdMat Object
qqnorm.lme

Normal Plot of Residuals or Random Effects from an lme Object
varExp

Exponential Variance Function
varFixed

Fixed Variance Function