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nlme (version 3.1-149)
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
147,147
Version
3.1-149
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
August 23rd, 2020
Functions in nlme (3.1-149)
Search all functions
Dim.corSpatial
Dimensions of a corSpatial Object
Dim.corStruct
Dimensions of a corStruct Object
Initialize.reStruct
Initialize reStruct Object
Initialize.lmeStruct
Initialize an lmeStruct Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Matrix.reStruct
Assign reStruct Matrices
Nitrendipene
Assay of nitrendipene
Spruce
Growth of Spruce Trees
Oats
Split-plot Experiment on Varieties of Oats
Soybean
Growth of soybean plants
Tetracycline1
Pharmacokinetics of tetracycline
anova.gls
Compare Likelihoods of Fitted Objects
Tetracycline2
Pharmacokinetics of tetracycline
allCoef
Extract Coefficients from a Set of Objects
bdf
Language scores
coef.corStruct
Coefficients of a corStruct Object
ACF.lme
Autocorrelation Function for lme Residuals
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
corLin
Linear Correlation Structure
coef.pdMat
pdMat Object Coefficients
coef.reStruct
reStruct Object Coefficients
fitted.glsStruct
Calculate glsStruct Fitted Values
corMatrix
Extract Correlation Matrix
Dim.pdMat
Dimensions of a pdMat Object
Earthquake
Earthquake Intensity
Initialize.varFunc
Initialize varFunc Object
LDEsysMat
Generate system matrix for LDEs
Matrix
Assign Matrix Values
MathAchieve
Mathematics achievement scores
formula.reStruct
Extract reStruct Object Formula
Assay
Bioassay on Cell Culture Plate
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
gapply
Apply a Function by Groups
Names.pdMat
Names of a pdMat Object
getGroups.corStruct
Extract corStruct Groups
getGroups.data.frame
Extract Groups from a Data Frame
Names.reStruct
Names of an reStruct Object
gnlsObject
Fitted gnls Object
intervals.gls
Confidence Intervals on gls Parameters
intervals.lmList
Confidence Intervals on lmList Coefficients
gnlsControl
Control Values for gnls Fit
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
ACF.gls
Autocorrelation Function for gls Residuals
ACF
Autocorrelation Function
logLik.lmList
Log-Likelihood of an lmList Object
Wheat
Yields by growing conditions
Wheat2
Wheat Yield Trials
Glucose
Glucose levels over time
Gasoline
Refinery yield of gasoline
Cefamandole
Pharmacokinetics of Cefamandole
nlsList
List of nls Objects with a Common Model
nlsList.selfStart
nlsList Fit from a selfStart Function
pdLogChol
General Positive-Definite Matrix
Coef
Assign Values to Coefficients
BodyWeight
Rat weight over time for different diets
pdMat
Positive-Definite Matrix
Covariate
Assign Covariate Values
[.pdMat
Subscript a pdMat Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
coef.gnls
Extract gnls Coefficients
Fatigue
Cracks caused by metal fatigue
Initialize.corStruct
Initialize corStruct Object
Muscle
Contraction of heart muscle sections
Names
Names Associated with an Object
Initialize.glsStruct
Initialize a glsStruct Object
plot.nmGroupedData
Plot an nmGroupedData Object
Oxboys
Heights of Boys in Oxford
predict.nlme
Predictions from an nlme Object
predict.lme
Predictions from an lme Object
Rail
Evaluation of Stress in Railway Rails
Machines
Productivity Scores for Machines and Workers
Oxide
Variability in Semiconductor Manufacturing
Covariate.varFunc
Assign varFunc Covariate
coef.lmList
Extract lmList Coefficients
Gun
Methods for firing naval guns
collapse.groupedData
Collapse a groupedData Object
RatPupWeight
The weight of rat pups
Glucose2
Glucose Levels Following Alcohol Ingestion
compareFits
Compare Fitted Objects
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
anova.lme
Compare Likelihoods of Fitted Objects
MathAchSchool
School demographic data for MathAchieve
corFactor.corStruct
Factor of a corStruct Object Matrix
Orthodont
Growth curve data on an orthdontic measurement
Meat
Tenderness of meat
ergoStool
Ergometrics experiment with stool types
Dialyzer
High-Flux Hemodialyzer
corGaus
Gaussian Correlation Structure
Milk
Protein content of cows' milk
Ovary
Counts of Ovarian Follicles
reStruct
Random Effects Structure
Names.formula
Extract Names from a formula
recalc
Recalculate Condensed Linear Model Object
Names.pdBlocked
Names of a pdBlocked Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
varPower
Power Variance Function
simulate.lme
Simulate Results from
lme
Models
varClasses
Variance Function Classes
update.varFunc
Update varFunc Object
varWeights
Extract Variance Function Weights
PBG
Effect of Phenylbiguanide on Blood Pressure
Relaxin
Assay for Relaxin
Dim
Extract Dimensions from an Object
IGF
Radioimmunoassay of IGF-I Protein
Phenobarb
Phenobarbitol Kinetics
coef.lme
Extract lme Coefficients
as.matrix.corStruct
Matrix of a corStruct Object
asOneFormula
Combine Formulas of a Set of Objects
asTable
Convert groupedData to a matrix
coef.modelStruct
Extract modelStruct Object Coefficients
fdHess
Finite difference Hessian
Remifentanil
Pharmacokinetics of Remifentanil
Variogram.corExp
Calculate Semi-variogram for a corExp Object
fixed.effects
Extract Fixed Effects
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
VarCorr
Extract variance and correlation components
balancedGrouped
Create a groupedData object from a matrix
augPred
Augmented Predictions
coef.varFunc
varFunc Object Coefficients
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Quinidine
Quinidine Kinetics
Initialize
Initialize Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Pixel
X-ray pixel intensities over time
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
fixef.lmList
Extract lmList Fixed Effects
Variogram
Calculate Semi-variogram
getCovariate.data.frame
Extract Data Frame Covariate
getCovariate.varFunc
Extract varFunc Covariate
as.matrix.pdMat
Matrix of a pdMat Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
isInitialized
Check if Object is Initialized
Variogram.default
Calculate Semi-variogram
getGroups.gls
Extract gls Object Groups
getGroups.lmList
Extract lmList Object Groups
as.matrix.reStruct
Matrices of an reStruct Object
corSpher
Spherical Correlation Structure
pairs.lme
Pairs Plot of an lme Object
lmList.groupedData
lmList Fit from a groupedData Object
nlmeObject
Fitted nlme Object
lmList
List of lm Objects with a Common Model
lme
Linear Mixed-Effects Models
nlmeStruct
Nonlinear Mixed-Effects Structure
corSymm
General Correlation Structure
Wafer
Modeling of Analog MOS Circuits
formula.pdBlocked
Extract pdBlocked Formula
formula.pdMat
Extract pdMat Formula
getData.gls
Extract gls Object Data
collapse
Collapse According to Groups
comparePred
Compare Predictions
corFactor
Factor of a Correlation Matrix
corClasses
Correlation Structure Classes
corAR1
AR(1) Correlation Structure
corExp
Exponential Correlation Structure
corARMA
ARMA(p,q) Correlation Structure
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
corCAR1
Continuous AR(1) Correlation Structure
pdBlocked
Positive-Definite Block Diagonal Matrix
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corNatural
General correlation in natural parameterization
fitted.lme
Extract lme Fitted Values
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
fitted.lmList
Extract lmList Fitted Values
corMatrix.corStruct
Matrix of a corStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
print.varFunc
Print a varFunc Object
gls-internal
Auxiliary functions used by gls
getData
Extract Data from an Object
print.summary.pdMat
Print a summary.pdMat Object
getCovariateFormula
Extract Covariates Formula
isBalanced
Check a Design for Balance
getCovariate
Extract Covariate from an Object
intervals.lme
Confidence Intervals on lme Parameters
gls
Fit Linear Model Using Generalized Least Squares
quinModel
Model function for the Quinidine data
lmeStruct
Linear Mixed-Effects Structure
getGroups.lme
Extract lme Object Groups
getResponseFormula
Extract Formula Specifying Response Variable
random.effects
Extract Random Effects
getGroups.varFunc
Extract varFunc Groups
getData.lmList
Extract lmList Object Data
corSpatial
Spatial Correlation Structure
corRatio
Rational Quadratic Correlation Structure
corCompSymm
Compound Symmetry Correlation Structure
logDet
Extract the Logarithm of the Determinant
residuals.glsStruct
Calculate glsStruct Residuals
splitFormula
Split a Formula
residuals.gls
Extract gls Residuals
summary.corStruct
Summarize a corStruct Object
getCovariate.corStruct
Extract corStruct Object Covariate
logLik.lme
Log-Likelihood of an lme Object
varFunc
Variance Function Structure
varIdent
Constant Variance Function
getGroupsFormula
Extract Grouping Formula
getResponse
Extract Response Variable from an Object
glsStruct
Generalized Least Squares Structure
gnls
Fit Nonlinear Model Using Generalized Least Squares
gsummary
Summarize by Groups
intervals
Confidence Intervals on Coefficients
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
nlme
Nonlinear Mixed-Effects Models
logDet.corStruct
Extract corStruct Log-Determinant
logDet.reStruct
Extract reStruct Log-Determinants
logDet.pdMat
Extract Log-Determinant from a pdMat Object
getVarCov
Extract variance-covariance matrix
pdClasses
Positive-Definite Matrix Classes
logLik.corStruct
Extract corStruct Log-Likelihood
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
phenoModel
Model function for the Phenobarb data
lmeControl
Specifying Control Values for lme Fit
pdConstruct
Construct pdMat Objects
lmeObject
Fitted lme Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
plot.lme
Plot an lme or nls object
plot.nffGroupedData
Plot an nffGroupedData Object
logLik.reStruct
Calculate reStruct Log-Likelihood
model.matrix.reStruct
reStruct Model Matrix
logLik.varFunc
Extract varFunc logLik
predict.gnls
Predictions from a gnls Object
getGroups
Extract Grouping Factors from an Object
glsControl
Control Values for gls Fit
getData.lme
Extract lme Object Data
plot.ACF
Plot an ACF Object
plot.Variogram
Plot a Variogram Object
needUpdate
Check if Update is Needed
plot.augPred
Plot an augPred Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
glsObject
Fitted gls Object
groupedData
Construct a groupedData Object
ranef.lme
Extract lme Random Effects
pairs.compareFits
Pairs Plot of compareFits Object
ranef.lmList
Extract lmList Random Effects
predict.lmList
Predictions from an lmList Object
residuals.lme
Extract lme Residuals
lme.groupedData
LME fit from groupedData Object
pairs.lmList
Pairs Plot of an lmList Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
lme.lmList
LME fit from lmList Object
recalc.modelStruct
Recalculate for a modelStruct Object
recalc.corStruct
Recalculate for corStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.lmeStruct
Calculate lmeStruct Residuals
plot.compareFits
Plot a compareFits Object
plot.ranef.lmList
Plot a ranef.lmList Object
plot.gls
Plot a gls Object
plot.ranef.lme
Plot a ranef.lme Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
summary.lmList
Summarize an lmList Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
logLik.gnls
Log-Likelihood of a gnls Object
varFixed
Fixed Variance Function
varExp
Exponential Variance Function
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
summary.lme
Summarize an lme Object
nlmeControl
Control Values for nlme Fit
nlme.nlsList
NLME fit from nlsList Object
plot.intervals.lmList
Plot lmList Confidence Intervals
pdDiag
Diagonal Positive-Definite Matrix
plot.lmList
Plot an lmList Object
pdSymm
General Positive-Definite Matrix
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdNatural
General Positive-Definite Matrix in Natural Parametrization
residuals.lmList
Extract lmList Residuals
solve.reStruct
Apply Solve to an reStruct Object
pooledSD
Extract Pooled Standard Deviation
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
predict.gls
Predictions from a gls Object
recalc.varFunc
Recalculate for varFunc Object
summary.nlsList
Summarize an nlsList Object
recalc.reStruct
Recalculate for an reStruct Object
summary.pdMat
Summarize a pdMat Object
summary.varFunc
Summarize varFunc Object
summary.modelStruct
Summarize a modelStruct Object
update.modelStruct
Update a modelStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
varConstPower
Constant Plus Power Variance Function
varComb
Combination of Variance Functions