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nlme (version 3.1-152)
Linear and Nonlinear Mixed Effects Models
Description
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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Install
install.packages('nlme')
Monthly Downloads
132,908
Version
3.1-152
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
February 4th, 2021
Functions in nlme (3.1-152)
Search functions
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
BodyWeight
Rat weight over time for different diets
Coef
Assign Values to Coefficients
Covariate
Assign Covariate Values
ACF
Autocorrelation Function
ACF.lme
Autocorrelation Function for lme Residuals
Assay
Bioassay on Cell Culture Plate
Cefamandole
Pharmacokinetics of Cefamandole
Covariate.varFunc
Assign varFunc Covariate
ACF.gls
Autocorrelation Function for gls Residuals
[.pdMat
Subscript a pdMat Object
Dialyzer
High-Flux Hemodialyzer
Dim.corSpatial
Dimensions of a corSpatial Object
IGF
Radioimmunoassay of IGF-I Protein
Initialize.lmeStruct
Initialize an lmeStruct Object
Dim.corStruct
Dimensions of a corStruct Object
Initialize.reStruct
Initialize reStruct Object
Fatigue
Cracks caused by metal fatigue
Gasoline
Refinery yield of gasoline
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Dim
Extract Dimensions from an Object
Orthodont
Growth curve data on an orthdontic measurement
Initialize
Initialize Object
Glucose
Glucose levels over time
Gun
Methods for firing naval guns
Glucose2
Glucose Levels Following Alcohol Ingestion
Rail
Evaluation of Stress in Railway Rails
Dim.pdMat
Dimensions of a pdMat Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Matrix.reStruct
Assign reStruct Matrices
comparePred
Compare Predictions
Variogram.corExp
Calculate Semi-variogram for a corExp Object
MathAchieve
Mathematics achievement scores
Matrix
Assign Matrix Values
RatPupWeight
The weight of rat pups
corLin
Linear Correlation Structure
coef.pdMat
pdMat Object Coefficients
Initialize.varFunc
Initialize varFunc Object
allCoef
Extract Coefficients from a Set of Objects
Initialize.corStruct
Initialize corStruct Object
Earthquake
Earthquake Intensity
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
coef.lmList
Extract lmList Coefficients
Soybean
Growth of soybean plants
Muscle
Contraction of heart muscle sections
fixed.effects
Extract Fixed Effects
Meat
Tenderness of meat
LDEsysMat
Generate system matrix for LDEs
Names
Names Associated with an Object
Names.pdMat
Names of a pdMat Object
Wheat
Yields by growing conditions
Initialize.glsStruct
Initialize a glsStruct Object
anova.gls
Compare Likelihoods of Fitted Objects
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Names.reStruct
Names of an reStruct Object
Names.formula
Extract Names from a formula
ergoStool
Ergometrics experiment with stool types
Pixel
X-ray pixel intensities over time
coef.varFunc
varFunc Object Coefficients
Wheat2
Wheat Yield Trials
Quinidine
Quinidine Kinetics
Machines
Productivity Scores for Machines and Workers
coef.gnls
Extract gnls Coefficients
Nitrendipene
Assay of nitrendipene
Oats
Split-plot Experiment on Varieties of Oats
Variogram.corLin
Calculate Semi-variogram for a corLin Object
MathAchSchool
School demographic data for MathAchieve
coef.lme
Extract lme Coefficients
corFactor.corStruct
Factor of a corStruct Object Matrix
Relaxin
Assay for Relaxin
Names.pdBlocked
Names of a pdBlocked Object
Remifentanil
Pharmacokinetics of Remifentanil
Milk
Protein content of cows' milk
Phenobarb
Phenobarbitol Kinetics
PBG
Effect of Phenylbiguanide on Blood Pressure
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
Tetracycline1
Pharmacokinetics of tetracycline
VarCorr
Extract variance and correlation components
getData.gls
Extract gls Object Data
bdf
Language scores
getCovariate.varFunc
Extract varFunc Covariate
isInitialized
Check if Object is Initialized
Ovary
Counts of Ovarian Follicles
lmeStruct
Linear Mixed-Effects Structure
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
getGroups.lme
Extract lme Object Groups
Oxboys
Heights of Boys in Oxford
asOneFormula
Combine Formulas of a Set of Objects
corClasses
Correlation Structure Classes
isBalanced
Check a Design for Balance
Oxide
Variability in Semiconductor Manufacturing
getCovariateFormula
Extract Covariates Formula
Tetracycline2
Pharmacokinetics of tetracycline
coef.modelStruct
Extract modelStruct Object Coefficients
groupedData
Construct a groupedData Object
Wafer
Modeling of Analog MOS Circuits
as.matrix.pdMat
Matrix of a pdMat Object
as.matrix.reStruct
Matrices of an reStruct Object
corCompSymm
Compound Symmetry Correlation Structure
asTable
Convert groupedData to a matrix
getCovariate.corStruct
Extract corStruct Object Covariate
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Variogram.default
Calculate Semi-variogram
augPred
Augmented Predictions
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
collapse
Collapse According to Groups
anova.lme
Compare Likelihoods of Fitted Objects
gnlsControl
Control Values for gnls Fit
corNatural
General correlation in natural parameterization
ranef.lme
Extract lme Random Effects
pooledSD
Extract Pooled Standard Deviation
coef.corStruct
Coefficients of a corStruct Object
corAR1
AR(1) Correlation Structure
getGroups.gls
Extract gls Object Groups
getData.lmList
Extract lmList Object Data
corMatrix
Extract Correlation Matrix
plot.nmGroupedData
Plot an nmGroupedData Object
fitted.glsStruct
Calculate glsStruct Fitted Values
fdHess
Finite difference Hessian
logLik.glsStruct
Log-Likelihood of a glsStruct Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
balancedGrouped
Create a groupedData object from a matrix
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
glsStruct
Generalized Least Squares Structure
getGroups.lmList
Extract lmList Object Groups
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
corGaus
Gaussian Correlation Structure
gnls
Fit Nonlinear Model Using Generalized Least Squares
logLik.corStruct
Extract corStruct Log-Likelihood
Spruce
Growth of Spruce Trees
intervals.gls
Confidence Intervals on gls Parameters
getData
Extract Data from an Object
getGroups
Extract Grouping Factors from an Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
corMatrix.corStruct
Matrix of a corStruct Object
fixef.lmList
Extract lmList Fixed Effects
getCovariate
Extract Covariate from an Object
corRatio
Rational Quadratic Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
logLik.gnls
Log-Likelihood of a gnls Object
collapse.groupedData
Collapse a groupedData Object
getGroups.corStruct
Extract corStruct Groups
nlsList.selfStart
nlsList Fit from a selfStart Function
residuals.gls
Extract gls Residuals
formula.reStruct
Extract reStruct Object Formula
phenoModel
Model function for the Phenobarb data
compareFits
Compare Fitted Objects
gapply
Apply a Function by Groups
nlmeControl
Control Values for nlme Fit
getCovariate.data.frame
Extract Data Frame Covariate
getData.lme
Extract lme Object Data
lmList.groupedData
lmList Fit from a groupedData Object
gsummary
Summarize by Groups
coef.reStruct
reStruct Object Coefficients
pairs.lmList
Pairs Plot of an lmList Object
pairs.compareFits
Pairs Plot of compareFits Object
nlme.nlsList
NLME fit from nlsList Object
glsObject
Fitted gls Object
predict.gls
Predictions from a gls Object
plot.lmList
Plot an lmList Object
glsControl
Control Values for gls Fit
plot.intervals.lmList
Plot lmList Confidence Intervals
nlsList
List of nls Objects with a Common Model
solve.reStruct
Apply Solve to an reStruct Object
plot.ACF
Plot an ACF Object
intervals.lme
Confidence Intervals on lme Parameters
logLik.reStruct
Calculate reStruct Log-Likelihood
residuals.lmList
Extract lmList Residuals
Variogram
Calculate Semi-variogram
getResponse
Extract Response Variable from an Object
logLik.varFunc
Extract varFunc logLik
summary.varFunc
Summarize "varFunc" Object
recalc.corStruct
Recalculate for corStruct Object
corARMA
ARMA(p,q) Correlation Structure
logDet
Extract the Logarithm of the Determinant
as.matrix.corStruct
Matrix of a corStruct Object
print.varFunc
Print a varFunc Object
print.summary.pdMat
Print a summary.pdMat Object
corFactor
Factor of a Correlation Matrix
corSpatial
Spatial Correlation Structure
logLik.lme
Log-Likelihood of an lme Object
corExp
Exponential Correlation Structure
fitted.lme
Extract lme Fitted Values
reStruct
Random Effects Structure
fitted.lmList
Extract lmList Fitted Values
varFunc
Variance Function Structure
gls
Fit Linear Model Using Generalized Least Squares
gnlsObject
Fitted gnls Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
recalc.modelStruct
Recalculate for a modelStruct Object
logDet.reStruct
Extract reStruct Log-Determinants
getGroups.data.frame
Extract Groups from a Data Frame
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
splitFormula
Split a Formula
getGroups.varFunc
Extract varFunc Groups
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
lmList
List of lm Objects with a Common Model
logDet.corStruct
Extract corStruct Log-Determinant
intervals.lmList
Confidence Intervals on lmList Coefficients
formula.pdBlocked
Extract pdBlocked Formula
lme
Linear Mixed-Effects Models
summary.modelStruct
Summarize a modelStruct Object
gls-internal
Auxiliary functions used by gls
model.matrix.reStruct
reStruct Model Matrix
lmeObject
Fitted lme Object
recalc
Recalculate Condensed Linear Model Object
simulate.lme
Simulate Results from
lme
Models
plot.compareFits
Plot a compareFits Object
varConstProp
Constant Plus Proportion Variance Function
corCAR1
Continuous AR(1) Correlation Structure
summary.corStruct
Summarize a corStruct Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
varIdent
Constant Variance Function
corSymm
General Correlation Structure
update.modelStruct
Update a modelStruct Object
corSpher
Spherical Correlation Structure
getGroupsFormula
Extract Grouping Formula
logLik.lmList
Log-Likelihood of an lmList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
formula.pdMat
Extract pdMat Formula
varWeights.lmeStruct
Variance Weights for lmeStruct Object
pdBlocked
Positive-Definite Block Diagonal Matrix
pairs.lme
Pairs Plot of an lme Object
nlme
Nonlinear Mixed-Effects Models
update.varFunc
Update varFunc Object
varClasses
Variance Function Classes
pdFactor
Square-Root Factor of a Positive-Definite Matrix
lmeControl
Specifying Control Values for lme Fit
lme.lmList
LME fit from lmList Object
varPower
Power Variance Function
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
lme.groupedData
LME fit from groupedData Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
pdSymm
General Positive-Definite Matrix
needUpdate
Check if Update is Needed
ranef.lmList
Extract lmList Random Effects
pdConstruct
Construct pdMat Objects
recalc.reStruct
Recalculate for an reStruct Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
predict.lmList
Predictions from an lmList Object
plot.lme
Plot an lme or nls object
pdLogChol
General Positive-Definite Matrix
getResponseFormula
Extract Formula Specifying Response Variable
pdDiag
Diagonal Positive-Definite Matrix
intervals
Confidence Intervals on Coefficients
plot.gls
Plot a gls Object
getVarCov
Extract variance-covariance matrix
varFixed
Fixed Variance Function
pdConstruct.pdBlocked
Construct pdBlocked Objects
recalc.varFunc
Recalculate for varFunc Object
pdMat
Positive-Definite Matrix
qqnorm.gls
Normal Plot of Residuals from a gls Object
summary.lme
Summarize an lme Object
nlmeObject
Fitted nlme Object
plot.ranef.lmList
Plot a ranef.lmList Object
predict.gnls
Predictions from a gnls Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pdClasses
Positive-Definite Matrix Classes
plot.nffGroupedData
Plot an nffGroupedData Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
predict.lme
Predictions from an lme Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
predict.nlme
Predictions from an nlme Object
nlmeStruct
Nonlinear Mixed-Effects Structure
varConstPower
Constant Plus Power Variance Function
plot.Variogram
Plot a Variogram Object
residuals.glsStruct
Calculate glsStruct Residuals
plot.augPred
Plot an augPred Object
varExp
Exponential Variance Function
residuals.lme
Extract lme Residuals
summary.nlsList
Summarize an nlsList Object
plot.ranef.lme
Plot a ranef.lme Object
varComb
Combination of Variance Functions
summary.pdMat
Summarize a pdMat Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
quinModel
Model function for the Quinidine data
random.effects
Extract Random Effects
summary.lmList
Summarize an lmList Object
residuals.lmeStruct
Calculate lmeStruct Residuals
varWeights
Extract Variance Function Weights
varWeights.glsStruct
Variance Weights for glsStruct Object