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nlme (version 3.1-139)
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
85,005
Version
3.1-139
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
April 9th, 2019
Functions in nlme (3.1-139)
Search all functions
Assay
Bioassay on Cell Culture Plate
Covariate
Assign Covariate Values
Nitrendipene
Assay of nitrendipene
Initialize.reStruct
Initialize reStruct Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Oats
Split-plot Experiment on Varieties of Oats
Pixel
X-ray pixel intensities over time
Matrix.reStruct
Assign reStruct Matrices
Quinidine
Quinidine Kinetics
Variogram.corExp
Calculate Semi-variogram for a corExp Object
BodyWeight
Rat weight over time for different diets
ACF.lme
Autocorrelation Function for lme Residuals
Glucose2
Glucose Levels Following Alcohol Ingestion
Names.pdMat
Names of a pdMat Object
Dim.corSpatial
Dimensions of a corSpatial Object
Soybean
Growth of soybean plants
Dim.corStruct
Dimensions of a corStruct Object
Names.reStruct
Names of an reStruct Object
Gun
Methods for firing naval guns
Coef
Assign Values to Coefficients
MathAchSchool
School demographic data for MathAchieve
Covariate.varFunc
Assign varFunc Covariate
Dim.pdMat
Dimensions of a pdMat Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
as.matrix.corStruct
Matrix of a corStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Tetracycline1
Pharmacokinetics of tetracycline
Spruce
Growth of Spruce Trees
Tetracycline2
Pharmacokinetics of tetracycline
Relaxin
Assay for Relaxin
Remifentanil
Pharmacokinetics of remifentanil
Initialize.corStruct
Initialize corStruct Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Wafer
Modeling of Analog MOS Circuits
Variogram.default
Calculate Semi-variogram
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
asOneFormula
Combine Formulas of a Set of Objects
Initialize.glsStruct
Initialize a glsStruct Object
asTable
Convert groupedData to a matrix
comparePred
Compare Predictions
Gasoline
Refinery yield of gasoline
Muscle
Contraction of heart muscle sections
corAR1
AR(1) Correlation Structure
Glucose
Glucose levels over time
collapse
Collapse According to Groups
coef.varFunc
varFunc Object Coefficients
Names.formula
Extract Names from a formula
Names
Names Associated with an Object
corRatio
Rational Quadratic Correlation Structure
corClasses
Correlation Structure Classes
corSpatial
Spatial Correlation Structure
Initialize.varFunc
Initialize varFunc Object
LDEsysMat
Generate system matrix for LDEs
as.matrix.pdMat
Matrix of a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
Earthquake
Earthquake Intensity
as.matrix.reStruct
Matrices of an reStruct Object
formula.pdMat
Extract pdMat Formula
formula.pdBlocked
Extract pdBlocked Formula
IGF
Radioimmunoassay of IGF-I Protein
Initialize
Initialize Object
coef.pdMat
pdMat Object Coefficients
Rail
Evaluation of Stress in Railway Rails
MathAchieve
Mathematics achievement scores
getCovariateFormula
Extract Covariates Formula
corCompSymm
Compound Symmetry Correlation Structure
Matrix
Assign Matrix Values
coef.reStruct
reStruct Object Coefficients
corLin
Linear Correlation Structure
corMatrix
Extract Correlation Matrix
Oxboys
Heights of Boys in Oxford
getData
Extract Data from an Object
gls-internal
Auxiliary functions used by gls
gls
Fit Linear Model Using Generalized Least Squares
Meat
Tenderness of meat
Oxide
Variability in Semiconductor Manufacturing
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corMatrix.corStruct
Matrix of a corStruct Object
corSpher
Spherical Correlation Structure
corSymm
General Correlation Structure
PBG
Effect of Phenylbiguanide on Blood Pressure
Milk
Protein content of cows' milk
RatPupWeight
The weight of rat pups
Phenobarb
Phenobarbitol Kinetics
VarCorr
Extract variance and correlation components
Variogram.corLin
Calculate Semi-variogram for a corLin Object
getCovariate.data.frame
Extract Data Frame Covariate
Variogram
Calculate Semi-variogram
Orthodont
Growth curve data on an orthdontic measurement
gnlsStruct
Generalized Nonlinear Least Squares Structure
bdf
Language scores
groupedData
Construct a groupedData Object
fixed.effects
Extract Fixed Effects
getCovariate.varFunc
Extract varFunc Covariate
fixef.lmList
Extract lmList Fixed Effects
getGroups.lme
Extract lme Object Groups
Ovary
Counts of Ovarian Follicles
getGroups.varFunc
Extract varFunc Groups
glsStruct
Generalized Least Squares Structure
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
formula.reStruct
Extract reStruct Object Formula
gapply
Apply a Function by Groups
coef.corStruct
Coefficients of a corStruct Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
coef.lme
Extract lme Coefficients
intervals.gls
Confidence Intervals on gls Parameters
lmList.groupedData
lmList Fit from a groupedData Object
coef.modelStruct
Extract modelStruct Object Coefficients
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
intervals.lmList
Confidence Intervals on lmList Coefficients
Wheat
Yields by growing conditions
lme
Linear Mixed-Effects Models
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
allCoef
Extract Coefficients from a Set of Objects
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
anova.gls
Compare Likelihoods of Fitted Objects
nlme
Nonlinear Mixed-Effects Models
pairs.compareFits
Pairs Plot of compareFits Object
corFactor.corStruct
Factor of a corStruct Object Matrix
corGaus
Gaussian Correlation Structure
pairs.lmList
Pairs Plot of an lmList Object
fitted.lmList
Extract lmList Fitted Values
Wheat2
Wheat Yield Trials
gsummary
Summarize by Groups
gnlsObject
Fitted gnls Object
getData.lme
Extract lme Object Data
gnlsControl
Control Values for gnls Fit
getGroups
Extract Grouping Factors from an Object
intervals
Confidence Intervals on Coefficients
augPred
Augmented Predictions
lme.groupedData
LME fit from groupedData Object
coef.gnls
Extract gnls Coefficients
plot.compareFits
Plot a compareFits Object
lme.lmList
LME fit from lmList Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
nlmeObject
Fitted nlme Object
logLik.lmList
Log-Likelihood of an lmList Object
coef.lmList
Extract lmList Coefficients
nlmeStruct
Nonlinear Mixed-Effects Structure
balancedGrouped
Create a groupedData object from a matrix
pdClasses
Positive-Definite Matrix Classes
plot.gls
Plot a gls Object
corExp
Exponential Correlation Structure
fitted.lme
Extract lme Fitted Values
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
getGroups.corStruct
Extract corStruct Groups
getCovariate.corStruct
Extract corStruct Object Covariate
getCovariate
Extract Covariate from an Object
corFactor
Factor of a Correlation Matrix
pooledSD
Extract Pooled Standard Deviation
collapse.groupedData
Collapse a groupedData Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
corNatural
General correlation in natural parameterization
compareFits
Compare Fitted Objects
logLik.lme
Log-Likelihood of an lme Object
pdSymm
General Positive-Definite Matrix
getGroups.data.frame
Extract Groups from a Data Frame
getResponseFormula
Extract Formula Specifying Response Variable
corARMA
ARMA(p,q) Correlation Structure
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
corCAR1
Continuous AR(1) Correlation Structure
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.nmGroupedData
Plot an nmGroupedData Object
ergoStool
Ergometrics experiment with stool types
fitted.glsStruct
Calculate glsStruct Fitted Values
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
recalc.corStruct
Recalculate for corStruct Object
residuals.gls
Extract gls Residuals
summary.modelStruct
Summarize a modelStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
summary.lme
Summarize an lme Object
predict.gls
Predictions from a gls Object
ranef.lmList
Extract lmList Random Effects
getVarCov
Extract variance-covariance matrix
getGroups.lmList
Extract lmList Object Groups
model.matrix.reStruct
reStruct Model Matrix
getGroups.gls
Extract gls Object Groups
needUpdate
Check if Update is Needed
isInitialized
Check if Object is Initialized
fdHess
Finite difference Hessian
lmList
List of lm Objects with a Common Model
lmeStruct
Linear Mixed-Effects Structure
pdDiag
Diagonal Positive-Definite Matrix
logDet
Extract the Logarithm of the Determinant
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdLogChol
General Positive-Definite Matrix
pdMat
Positive-Definite Matrix
print.varFunc
Print a varFunc Object
print.summary.pdMat
Print a summary.pdMat Object
logDet.corStruct
Extract corStruct Log-Determinant
fitted.lmeStruct
Calculate lmeStruct Fitted Values
ranef.lme
Extract lme Random Effects
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
quinModel
Model function for the Quinidine data
random.effects
Extract Random Effects
residuals.gnlsStruct
Calculate gnlsStruct Residuals
summary.gls
Summarize a Generalized Least Squares
gls
Object
residuals.lmList
Extract lmList Residuals
summary.lmList
Summarize an lmList Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
logDet.pdMat
Extract Log-Determinant from a pdMat Object
solve.reStruct
Apply Solve to an reStruct Object
varComb
Combination of Variance Functions
varIdent
Constant Variance Function
varFunc
Variance Function Structure
logDet.reStruct
Extract reStruct Log-Determinants
logLik.reStruct
Calculate reStruct Log-Likelihood
logLik.varFunc
Extract varFunc logLik
nlme.nlsList
NLME fit from nlsList Object
logLik.corStruct
Extract corStruct Log-Likelihood
pairs.lme
Pairs Plot of an lme Object
varConstPower
Constant Plus Power Variance Function
pdBlocked
Positive-Definite Block Diagonal Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
plot.lme
Plot an lme or nls object
plot.nffGroupedData
Plot an nffGroupedData Object
nlmeControl
Control Values for nlme Fit
getData.gls
Extract gls Object Data
plot.ranef.lmList
Plot a ranef.lmList Object
pdConstruct
Construct pdMat Objects
pdConstruct.pdBlocked
Construct pdBlocked Objects
getData.lmList
Extract lmList Object Data
plot.ranef.lme
Plot a ranef.lme Object
phenoModel
Model function for the Phenobarb data
plot.ACF
Plot an ACF Object
getGroupsFormula
Extract Grouping Formula
qqnorm.gls
Normal Plot of Residuals from a gls Object
getResponse
Extract Response Variable from an Object
glsControl
Control Values for gls Fit
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
plot.intervals.lmList
Plot lmList Confidence Intervals
glsObject
Fitted gls Object
residuals.lme
Extract lme Residuals
residuals.lmeStruct
Calculate lmeStruct Residuals
plot.lmList
Plot an lmList Object
intervals.lme
Confidence Intervals on lme Parameters
predict.gnls
Predictions from a gnls Object
update.varFunc
Update varFunc Object
varClasses
Variance Function Classes
predict.lmList
Predictions from an lmList Object
reStruct
Random Effects Structure
varWeights.glsStruct
Variance Weights for glsStruct Object
recalc
Recalculate Condensed Linear Model Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
simulate.lme
Simulate Results from
lme
Models
isBalanced
Check a Design for Balance
lmeControl
Specifying Control Values for lme Fit
summary.nlsList
Summarize an nlsList Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
summary.pdMat
Summarize a pdMat Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
lmeObject
Fitted lme Object
nlsList
List of nls Objects with a Common Model
logLik.gnls
Log-Likelihood of a gnls Object
varExp
Exponential Variance Function
varFixed
Fixed Variance Function
nlsList.selfStart
nlsList Fit from a selfStart Function
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
plot.Variogram
Plot a Variogram Object
plot.augPred
Plot an augPred Object
predict.lme
Predictions from an lme Object
predict.nlme
Predictions from an nlme Object
recalc.reStruct
Recalculate for an reStruct Object
recalc.varFunc
Recalculate for varFunc Object
splitFormula
Split a Formula
summary.corStruct
Summarize a corStruct Object
summary.varFunc
Summarize varFunc Object
update.modelStruct
Update a modelStruct Object
varPower
Power Variance Function
varWeights
Extract Variance Function Weights
Cefamandole
Pharmacokinetics of Cefamandole
ACF.gls
Autocorrelation Function for gls Residuals
Dim
Extract Dimensions from an Object
Dialyzer
High-Flux Hemodialyzer
[.pdMat
Subscript a pdMat Object
ACF
Autocorrelation Function
Initialize.lmeStruct
Initialize an lmeStruct Object
Fatigue
Cracks caused by metal fatigue
Machines
Productivity Scores for Machines and Workers