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nlme (version 3.1-147)
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
93,277
Version
3.1-147
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
April 13th, 2020
Functions in nlme (3.1-147)
Search all functions
ACF.lme
Autocorrelation Function for lme Residuals
Coef
Assign Values to Coefficients
ACF
Autocorrelation Function
[.pdMat
Subscript a pdMat Object
Dim
Extract Dimensions from an Object
Dialyzer
High-Flux Hemodialyzer
Cefamandole
Pharmacokinetics of Cefamandole
BodyWeight
Rat weight over time for different diets
Assay
Bioassay on Cell Culture Plate
ACF.gls
Autocorrelation Function for gls Residuals
Covariate.varFunc
Assign varFunc Covariate
Initialize.reStruct
Initialize reStruct Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Covariate
Assign Covariate Values
Initialize.lmeStruct
Initialize an lmeStruct Object
Gasoline
Refinery yield of gasoline
LDEsysMat
Generate system matrix for LDEs
Dim.pdMat
Dimensions of a pdMat Object
Earthquake
Earthquake Intensity
Initialize
Initialize Object
Machines
Productivity Scores for Machines and Workers
Glucose
Glucose levels over time
Matrix.reStruct
Assign reStruct Matrices
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
IGF
Radioimmunoassay of IGF-I Protein
Initialize.varFunc
Initialize varFunc Object
MathAchSchool
School demographic data for MathAchieve
Fatigue
Cracks caused by metal fatigue
MathAchieve
Mathematics achievement scores
Oxboys
Heights of Boys in Oxford
Dim.corSpatial
Dimensions of a corSpatial Object
Oxide
Variability in Semiconductor Manufacturing
Orthodont
Growth curve data on an orthdontic measurement
Rail
Evaluation of Stress in Railway Rails
Initialize.corStruct
Initialize corStruct Object
Matrix
Assign Matrix Values
Ovary
Counts of Ovarian Follicles
Pixel
X-ray pixel intensities over time
RatPupWeight
The weight of rat pups
Relaxin
Assay for Relaxin
Remifentanil
Pharmacokinetics of Remifentanil
Dim.corStruct
Dimensions of a corStruct Object
Names.pdMat
Names of a pdMat Object
Variogram
Calculate Semi-variogram
Initialize.glsStruct
Initialize a glsStruct Object
Tetracycline2
Pharmacokinetics of tetracycline
Names.reStruct
Names of an reStruct Object
Tetracycline1
Pharmacokinetics of tetracycline
allCoef
Extract Coefficients from a Set of Objects
augPred
Augmented Predictions
VarCorr
Extract variance and correlation components
Variogram.default
Calculate Semi-variogram
Glucose2
Glucose Levels Following Alcohol Ingestion
asOneFormula
Combine Formulas of a Set of Objects
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Quinidine
Quinidine Kinetics
Meat
Tenderness of meat
asTable
Convert groupedData to a matrix
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
balancedGrouped
Create a groupedData object from a matrix
Muscle
Contraction of heart muscle sections
Milk
Protein content of cows' milk
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Gun
Methods for firing naval guns
anova.gls
Compare Likelihoods of Fitted Objects
corFactor.corStruct
Factor of a corStruct Object Matrix
corAR1
AR(1) Correlation Structure
Wafer
Modeling of Analog MOS Circuits
comparePred
Compare Predictions
compareFits
Compare Fitted Objects
collapse.groupedData
Collapse a groupedData Object
Nitrendipene
Assay of nitrendipene
corExp
Exponential Correlation Structure
as.matrix.pdMat
Matrix of a pdMat Object
as.matrix.reStruct
Matrices of an reStruct Object
corSpatial
Spatial Correlation Structure
corRatio
Rational Quadratic Correlation Structure
Oats
Split-plot Experiment on Varieties of Oats
corFactor
Factor of a Correlation Matrix
Names
Names Associated with an Object
corGaus
Gaussian Correlation Structure
Names.formula
Extract Names from a formula
fitted.glsStruct
Calculate glsStruct Fitted Values
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
Names.pdBlocked
Names of a pdBlocked Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
PBG
Effect of Phenylbiguanide on Blood Pressure
coef.pdMat
pdMat Object Coefficients
corNatural
General correlation in natural parameterization
corClasses
Correlation Structure Classes
coef.reStruct
reStruct Object Coefficients
Spruce
Growth of Spruce Trees
Variogram.corExp
Calculate Semi-variogram for a corExp Object
corCompSymm
Compound Symmetry Correlation Structure
fitted.lmList
Extract lmList Fitted Values
corSymm
General Correlation Structure
formula.reStruct
Extract reStruct Object Formula
corSpher
Spherical Correlation Structure
fitted.lme
Extract lme Fitted Values
Phenobarb
Phenobarbitol Kinetics
Soybean
Growth of soybean plants
getCovariate.varFunc
Extract varFunc Covariate
getGroupsFormula
Extract Grouping Formula
getCovariate.data.frame
Extract Data Frame Covariate
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
gapply
Apply a Function by Groups
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getResponseFormula
Extract Formula Specifying Response Variable
getGroups.corStruct
Extract corStruct Groups
getData.lmList
Extract lmList Object Data
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
anova.lme
Compare Likelihoods of Fitted Objects
getData.gls
Extract gls Object Data
getResponse
Extract Response Variable from an Object
coef.corStruct
Coefficients of a corStruct Object
getGroups.gls
Extract gls Object Groups
Variogram.corLin
Calculate Semi-variogram for a corLin Object
bdf
Language scores
getGroups.data.frame
Extract Groups from a Data Frame
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
coef.lme
Extract lme Coefficients
as.matrix.corStruct
Matrix of a corStruct Object
coef.gnls
Extract gnls Coefficients
getGroups.lmList
Extract lmList Object Groups
Wheat
Yields by growing conditions
Wheat2
Wheat Yield Trials
coef.modelStruct
Extract modelStruct Object Coefficients
ergoStool
Ergometrics experiment with stool types
intervals.lme
Confidence Intervals on lme Parameters
glsObject
Fitted gls Object
glsControl
Control Values for gls Fit
getVarCov
Extract variance-covariance matrix
isBalanced
Check a Design for Balance
corLin
Linear Correlation Structure
corMatrix
Extract Correlation Matrix
logDet.corStruct
Extract corStruct Log-Determinant
lmeStruct
Linear Mixed-Effects Structure
isInitialized
Check if Object is Initialized
lmList
List of lm Objects with a Common Model
coef.lmList
Extract lmList Coefficients
logDet
Extract the Logarithm of the Determinant
fdHess
Finite difference Hessian
intervals
Confidence Intervals on Coefficients
gnlsObject
Fitted gnls Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
coef.varFunc
varFunc Object Coefficients
collapse
Collapse According to Groups
formula.pdBlocked
Extract pdBlocked Formula
gnlsControl
Control Values for gnls Fit
gsummary
Summarize by Groups
formula.pdMat
Extract pdMat Formula
corARMA
ARMA(p,q) Correlation Structure
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
corCAR1
Continuous AR(1) Correlation Structure
nlsList.selfStart
nlsList Fit from a selfStart Function
getCovariateFormula
Extract Covariates Formula
nlsList
List of nls Objects with a Common Model
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
lmList.groupedData
lmList Fit from a groupedData Object
pdDiag
Diagonal Positive-Definite Matrix
logLik.lme
Log-Likelihood of an lme Object
lme
Linear Mixed-Effects Models
corMatrix.corStruct
Matrix of a corStruct Object
getGroups.varFunc
Extract varFunc Groups
getData
Extract Data from an Object
logLik.reStruct
Calculate reStruct Log-Likelihood
fixed.effects
Extract Fixed Effects
logLik.gnls
Log-Likelihood of a gnls Object
getGroups.lme
Extract lme Object Groups
nlmeObject
Fitted nlme Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
fixef.lmList
Extract lmList Fixed Effects
glsStruct
Generalized Least Squares Structure
nlmeStruct
Nonlinear Mixed-Effects Structure
getCovariate
Extract Covariate from an Object
getCovariate.corStruct
Extract corStruct Object Covariate
pdLogChol
General Positive-Definite Matrix
pairs.lme
Pairs Plot of an lme Object
getData.lme
Extract lme Object Data
gnlsStruct
Generalized Nonlinear Least Squares Structure
nlme.nlsList
NLME fit from nlsList Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
pairs.compareFits
Pairs Plot of compareFits Object
getGroups
Extract Grouping Factors from an Object
groupedData
Construct a groupedData Object
pdMat
Positive-Definite Matrix
lmeControl
Specifying Control Values for lme Fit
lmeObject
Fitted lme Object
logLik.varFunc
Extract varFunc logLik
nlmeControl
Control Values for nlme Fit
pdBlocked
Positive-Definite Block Diagonal Matrix
gls
Fit Linear Model Using Generalized Least Squares
gls-internal
Auxiliary functions used by gls
intervals.lmList
Confidence Intervals on lmList Coefficients
plot.intervals.lmList
Plot lmList Confidence Intervals
intervals.gls
Confidence Intervals on gls Parameters
plot.compareFits
Plot a compareFits Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
predict.nlme
Predictions from an nlme Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
lme.groupedData
LME fit from groupedData Object
pdSymm
General Positive-Definite Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.gls
Plot a gls Object
lme.lmList
LME fit from lmList Object
predict.lme
Predictions from an lme Object
residuals.lme
Extract lme Residuals
logLik.lmList
Log-Likelihood of an lmList Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
pairs.lmList
Pairs Plot of an lmList Object
quinModel
Model function for the Quinidine data
random.effects
Extract Random Effects
model.matrix.reStruct
reStruct Model Matrix
print.summary.pdMat
Print a summary.pdMat Object
plot.lmList
Plot an lmList Object
plot.Variogram
Plot a Variogram Object
residuals.lmeStruct
Calculate lmeStruct Residuals
needUpdate
Check if Update is Needed
solve.reStruct
Apply Solve to an reStruct Object
recalc
Recalculate Condensed Linear Model Object
pdConstruct
Construct pdMat Objects
reStruct
Random Effects Structure
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
phenoModel
Model function for the Phenobarb data
pdConstruct.pdBlocked
Construct pdBlocked Objects
print.varFunc
Print a varFunc Object
varExp
Exponential Variance Function
residuals.nlmeStruct
Calculate nlmeStruct Residuals
plot.augPred
Plot an augPred Object
simulate.lme
Simulate Results from
lme
Models
nlme
Nonlinear Mixed-Effects Models
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
recalc.corStruct
Recalculate for corStruct Object
plot.ACF
Plot an ACF Object
logLik.corStruct
Extract corStruct Log-Likelihood
logDet.reStruct
Extract reStruct Log-Determinants
pooledSD
Extract Pooled Standard Deviation
varFixed
Fixed Variance Function
plot.ranef.lme
Plot a ranef.lme Object
predict.gls
Predictions from a gls Object
plot.lme
Plot an lme or nls object
plot.ranef.lmList
Plot a ranef.lmList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
summary.varFunc
Summarize varFunc Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdClasses
Positive-Definite Matrix Classes
recalc.modelStruct
Recalculate for a modelStruct Object
residuals.gls
Extract gls Residuals
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
summary.lmList
Summarize an lmList Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
residuals.lmList
Extract lmList Residuals
plot.nmGroupedData
Plot an nmGroupedData Object
plot.nffGroupedData
Plot an nffGroupedData Object
summary.lme
Summarize an lme Object
update.modelStruct
Update a modelStruct Object
summary.modelStruct
Summarize a modelStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
predict.gnls
Predictions from a gnls Object
predict.lmList
Predictions from an lmList Object
varFunc
Variance Function Structure
ranef.lmList
Extract lmList Random Effects
residuals.glsStruct
Calculate glsStruct Residuals
recalc.reStruct
Recalculate for an reStruct Object
ranef.lme
Extract lme Random Effects
varIdent
Constant Variance Function
recalc.varFunc
Recalculate for varFunc Object
splitFormula
Split a Formula
summary.corStruct
Summarize a corStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
update.varFunc
Update varFunc Object
summary.pdMat
Summarize a pdMat Object
summary.nlsList
Summarize an nlsList Object
varComb
Combination of Variance Functions
varConstPower
Constant Plus Power Variance Function
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varClasses
Variance Function Classes
varPower
Power Variance Function
varWeights
Extract Variance Function Weights