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nlme (version 3.1-145)
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
81,705
Version
3.1-145
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
March 4th, 2020
Functions in nlme (3.1-145)
Search all functions
ACF
Autocorrelation Function
Dim
Extract Dimensions from an Object
Initialize
Initialize Object
Initialize.corStruct
Initialize corStruct Object
Names
Names Associated with an Object
Dim.corSpatial
Dimensions of a corSpatial Object
Initialize.glsStruct
Initialize a glsStruct Object
Remifentanil
Pharmacokinetics of remifentanil
Names.formula
Extract Names from a formula
Names.pdBlocked
Names of a pdBlocked Object
Soybean
Growth of soybean plants
Names.pdMat
Names of a pdMat Object
Relaxin
Assay for Relaxin
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Assay
Bioassay on Cell Culture Plate
Initialize.lmeStruct
Initialize an lmeStruct Object
BodyWeight
Rat weight over time for different diets
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
as.matrix.corStruct
Matrix of a corStruct Object
Cefamandole
Pharmacokinetics of Cefamandole
coef.lmList
Extract lmList Coefficients
coef.reStruct
reStruct Object Coefficients
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
coef.varFunc
varFunc Object Coefficients
[.pdMat
Subscript a pdMat Object
Fatigue
Cracks caused by metal fatigue
Initialize.reStruct
Initialize reStruct Object
MathAchSchool
School demographic data for MathAchieve
Initialize.varFunc
Initialize varFunc Object
Coef
Assign Values to Coefficients
Dim.corStruct
Dimensions of a corStruct Object
Glucose2
Glucose Levels Following Alcohol Ingestion
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
collapse
Collapse According to Groups
corMatrix
Extract Correlation Matrix
Dim.pdMat
Dimensions of a pdMat Object
Covariate
Assign Covariate Values
corMatrix.corStruct
Matrix of a corStruct Object
Gasoline
Refinery yield of gasoline
Machines
Productivity Scores for Machines and Workers
Earthquake
Earthquake Intensity
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
Gun
Methods for firing naval guns
LDEsysMat
Generate system matrix for LDEs
PBG
Effect of Phenylbiguanide on Blood Pressure
MathAchieve
Mathematics achievement scores
Oxide
Variability in Semiconductor Manufacturing
Phenobarb
Phenobarbitol Kinetics
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Muscle
Contraction of heart muscle sections
Pixel
X-ray pixel intensities over time
Matrix
Assign Matrix Values
IGF
Radioimmunoassay of IGF-I Protein
Meat
Tenderness of meat
Names.reStruct
Names of an reStruct Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Milk
Protein content of cows' milk
coef.corStruct
Coefficients of a corStruct Object
Matrix.reStruct
Assign reStruct Matrices
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
fixed.effects
Extract Fixed Effects
Variogram.default
Calculate Semi-variogram
getData.lmList
Extract lmList Object Data
bdf
Language scores
Orthodont
Growth curve data on an orthdontic measurement
Nitrendipene
Assay of nitrendipene
coef.gnls
Extract gnls Coefficients
Spruce
Growth of Spruce Trees
getGroups.data.frame
Extract Groups from a Data Frame
collapse.groupedData
Collapse a groupedData Object
fixef.lmList
Extract lmList Fixed Effects
comparePred
Compare Predictions
compareFits
Compare Fitted Objects
Oxboys
Heights of Boys in Oxford
corARMA
ARMA(p,q) Correlation Structure
corCAR1
Continuous AR(1) Correlation Structure
Oats
Split-plot Experiment on Varieties of Oats
formula.pdBlocked
Extract pdBlocked Formula
corClasses
Correlation Structure Classes
Ovary
Counts of Ovarian Follicles
getGroups.gls
Extract gls Object Groups
Tetracycline2
Pharmacokinetics of tetracycline
corSpher
Spherical Correlation Structure
Rail
Evaluation of Stress in Railway Rails
fitted.lme
Extract lme Fitted Values
getGroups.lmList
Extract lmList Object Groups
corSymm
General Correlation Structure
ergoStool
Ergometrics experiment with stool types
glsStruct
Generalized Least Squares Structure
Tetracycline1
Pharmacokinetics of tetracycline
Quinidine
Quinidine Kinetics
RatPupWeight
The weight of rat pups
VarCorr
Extract variance and correlation components
Variogram
Calculate Semi-variogram
gnls
Fit Nonlinear Model Using Generalized Least Squares
Variogram.corExp
Calculate Semi-variogram for a corExp Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getCovariate.corStruct
Extract corStruct Object Covariate
getData.lme
Extract lme Object Data
getGroups.corStruct
Extract corStruct Groups
gnlsObject
Fitted gnls Object
getGroups
Extract Grouping Factors from an Object
getCovariate.data.frame
Extract Data Frame Covariate
gnlsControl
Control Values for gnls Fit
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getCovariate.varFunc
Extract varFunc Covariate
anova.gls
Compare Likelihoods of Fitted Objects
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
intervals.lme
Confidence Intervals on lme Parameters
Wafer
Modeling of Analog MOS Circuits
lmList
List of lm Objects with a Common Model
allCoef
Extract Coefficients from a Set of Objects
logDet.corStruct
Extract corStruct Log-Determinant
asTable
Convert groupedData to a matrix
lmeStruct
Linear Mixed-Effects Structure
Wheat
Yields by growing conditions
logDet
Extract the Logarithm of the Determinant
lmList.groupedData
lmList Fit from a groupedData Object
isInitialized
Check if Object is Initialized
anova.lme
Compare Likelihoods of Fitted Objects
augPred
Augmented Predictions
logLik.corStruct
Extract corStruct Log-Likelihood
logLik.glsStruct
Log-Likelihood of a glsStruct Object
Wheat2
Wheat Yield Trials
logDet.reStruct
Extract reStruct Log-Determinants
as.matrix.reStruct
Matrices of an reStruct Object
isBalanced
Check a Design for Balance
lme
Linear Mixed-Effects Models
as.matrix.pdMat
Matrix of a pdMat Object
corCompSymm
Compound Symmetry Correlation Structure
logLik.varFunc
Extract varFunc logLik
nlsList.selfStart
nlsList Fit from a selfStart Function
corAR1
AR(1) Correlation Structure
lme.groupedData
LME fit from groupedData Object
asOneFormula
Combine Formulas of a Set of Objects
corExp
Exponential Correlation Structure
corFactor
Factor of a Correlation Matrix
nlsList
List of nls Objects with a Common Model
balancedGrouped
Create a groupedData object from a matrix
pdConstruct
Construct pdMat Objects
pairs.lme
Pairs Plot of an lme Object
nlmeObject
Fitted nlme Object
pairs.compareFits
Pairs Plot of compareFits Object
nlmeStruct
Nonlinear Mixed-Effects Structure
fdHess
Finite difference Hessian
pdConstruct.pdBlocked
Construct pdBlocked Objects
coef.modelStruct
Extract modelStruct Object Coefficients
plot.ACF
Plot an ACF Object
pairs.lmList
Pairs Plot of an lmList Object
formula.reStruct
Extract reStruct Object Formula
pdDiag
Diagonal Positive-Definite Matrix
formula.pdMat
Extract pdMat Formula
coef.lme
Extract lme Coefficients
plot.gls
Plot a gls Object
corGaus
Gaussian Correlation Structure
corLin
Linear Correlation Structure
plot.intervals.lmList
Plot lmList Confidence Intervals
phenoModel
Model function for the Phenobarb data
gapply
Apply a Function by Groups
pdNatural
General Positive-Definite Matrix in Natural Parametrization
coef.pdMat
pdMat Object Coefficients
corFactor.corStruct
Factor of a corStruct Object Matrix
pdSymm
General Positive-Definite Matrix
plot.nmGroupedData
Plot an nmGroupedData Object
corNatural
General correlation in natural parameterization
predict.gls
Predictions from a gls Object
plot.ranef.lmList
Plot a ranef.lmList Object
corRatio
Rational Quadratic Correlation Structure
corSpatial
Spatial Correlation Structure
plot.lmList
Plot an lmList Object
plot.ranef.lme
Plot a ranef.lme Object
pooledSD
Extract Pooled Standard Deviation
predict.gnls
Predictions from a gnls Object
fitted.lmList
Extract lmList Fitted Values
residuals.gnlsStruct
Calculate gnlsStruct Residuals
recalc.modelStruct
Recalculate for a modelStruct Object
getCovariate
Extract Covariate from an Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
residuals.glsStruct
Calculate glsStruct Residuals
residuals.lmList
Extract lmList Residuals
fitted.glsStruct
Calculate glsStruct Fitted Values
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
predict.lmList
Predictions from an lmList Object
random.effects
Extract Random Effects
varExp
Exponential Variance Function
ranef.lme
Extract lme Random Effects
getCovariateFormula
Extract Covariates Formula
getData
Extract Data from an Object
solve.reStruct
Apply Solve to an reStruct Object
getData.gls
Extract gls Object Data
splitFormula
Split a Formula
ranef.lmList
Extract lmList Random Effects
getGroups.lme
Extract lme Object Groups
getResponse
Extract Response Variable from an Object
varFixed
Fixed Variance Function
summary.corStruct
Summarize a corStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
getGroupsFormula
Extract Grouping Formula
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varFunc
Variance Function Structure
gls
Fit Linear Model Using Generalized Least Squares
recalc.reStruct
Recalculate for an reStruct Object
residuals.gls
Extract gls Residuals
getResponseFormula
Extract Formula Specifying Response Variable
glsObject
Fitted gls Object
glsControl
Control Values for gls Fit
getGroups.varFunc
Extract varFunc Groups
recalc.varFunc
Recalculate for varFunc Object
update.modelStruct
Update a modelStruct Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
groupedData
Construct a groupedData Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
gsummary
Summarize by Groups
getVarCov
Extract variance-covariance matrix
gls-internal
Auxiliary functions used by gls
summary.varFunc
Summarize varFunc Object
summary.lmList
Summarize an lmList Object
update.varFunc
Update varFunc Object
lme.lmList
LME fit from lmList Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
intervals
Confidence Intervals on Coefficients
intervals.lmList
Confidence Intervals on lmList Coefficients
lmeObject
Fitted lme Object
lmeControl
Specifying Control Values for lme Fit
intervals.gls
Confidence Intervals on gls Parameters
logLik.gnls
Log-Likelihood of a gnls Object
logLik.lmList
Log-Likelihood of an lmList Object
logLik.lme
Log-Likelihood of an lme Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
nlme
Nonlinear Mixed-Effects Models
nlme.nlsList
NLME fit from nlsList Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
logLik.reStruct
Calculate reStruct Log-Likelihood
model.matrix.reStruct
reStruct Model Matrix
nlmeControl
Control Values for nlme Fit
pdClasses
Positive-Definite Matrix Classes
pdMat
Positive-Definite Matrix
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
needUpdate
Check if Update is Needed
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdBlocked
Positive-Definite Block Diagonal Matrix
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdLogChol
General Positive-Definite Matrix
pdIdent
Multiple of the Identity Positive-Definite Matrix
plot.nffGroupedData
Plot an nffGroupedData Object
plot.Variogram
Plot a Variogram Object
plot.augPred
Plot an augPred Object
plot.lme
Plot an lme or nls object
varClasses
Variance Function Classes
plot.nfnGroupedData
Plot an nfnGroupedData Object
predict.lme
Predictions from an lme Object
plot.compareFits
Plot a compareFits Object
predict.nlme
Predictions from an nlme Object
print.varFunc
Print a varFunc Object
print.summary.pdMat
Print a summary.pdMat Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
quinModel
Model function for the Quinidine data
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
reStruct
Random Effects Structure
summary.nlsList
Summarize an nlsList Object
simulate.lme
Simulate Results from
lme
Models
summary.lme
Summarize an lme Object
summary.modelStruct
Summarize a modelStruct Object
varPower
Power Variance Function
recalc
Recalculate Condensed Linear Model Object
recalc.corStruct
Recalculate for corStruct Object
residuals.lme
Extract lme Residuals
varWeights
Extract Variance Function Weights
varComb
Combination of Variance Functions
summary.pdMat
Summarize a pdMat Object
residuals.lmeStruct
Calculate lmeStruct Residuals
residuals.nlmeStruct
Calculate nlmeStruct Residuals
varConstPower
Constant Plus Power Variance Function
varIdent
Constant Variance Function
Covariate.varFunc
Assign varFunc Covariate
Glucose
Glucose levels over time
ACF.gls
Autocorrelation Function for gls Residuals
ACF.lme
Autocorrelation Function for lme Residuals
Dialyzer
High-Flux Hemodialyzer