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nlme (version 3.1-151)
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
3.1-151
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
December 10th, 2020
Functions in nlme (3.1-151)
Search all functions
Coef
Assign Values to Coefficients
ACF.gls
Autocorrelation Function for gls Residuals
ACF
Autocorrelation Function
Cefamandole
Pharmacokinetics of Cefamandole
Dialyzer
High-Flux Hemodialyzer
Covariate
Assign Covariate Values
Assay
Bioassay on Cell Culture Plate
Covariate.varFunc
Assign varFunc Covariate
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
ACF.lme
Autocorrelation Function for lme Residuals
BodyWeight
Rat weight over time for different diets
Dim
Extract Dimensions from an Object
LDEsysMat
Generate system matrix for LDEs
Initialize.varFunc
Initialize varFunc Object
Dim.pdMat
Dimensions of a pdMat Object
Gasoline
Refinery yield of gasoline
Glucose
Glucose levels over time
Oxide
Variability in Semiconductor Manufacturing
Remifentanil
Pharmacokinetics of Remifentanil
IGF
Radioimmunoassay of IGF-I Protein
Dim.corStruct
Dimensions of a corStruct Object
Relaxin
Assay for Relaxin
Dim.corSpatial
Dimensions of a corSpatial Object
Oxboys
Heights of Boys in Oxford
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Initialize.lmeStruct
Initialize an lmeStruct Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Initialize
Initialize Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Matrix.reStruct
Assign reStruct Matrices
Initialize.reStruct
Initialize reStruct Object
Milk
Protein content of cows' milk
Names.formula
Extract Names from a formula
Names.pdBlocked
Names of a pdBlocked Object
Meat
Tenderness of meat
Wheat
Yields by growing conditions
Earthquake
Earthquake Intensity
VarCorr
Extract variance and correlation components
RatPupWeight
The weight of rat pups
Rail
Evaluation of Stress in Railway Rails
balancedGrouped
Create a groupedData object from a matrix
PBG
Effect of Phenylbiguanide on Blood Pressure
Variogram
Calculate Semi-variogram
augPred
Augmented Predictions
Glucose2
Glucose Levels Following Alcohol Ingestion
Phenobarb
Phenobarbitol Kinetics
corARMA
ARMA(p,q) Correlation Structure
coef.gnls
Extract gnls Coefficients
corCAR1
Continuous AR(1) Correlation Structure
anova.lme
Compare Likelihoods of Fitted Objects
as.matrix.corStruct
Matrix of a corStruct Object
coef.lmList
Extract lmList Coefficients
Wheat2
Wheat Yield Trials
fitted.lmList
Extract lmList Fitted Values
MathAchSchool
School demographic data for MathAchieve
Initialize.corStruct
Initialize corStruct Object
fitted.lme
Extract lme Fitted Values
Fatigue
Cracks caused by metal fatigue
[.pdMat
Subscript a pdMat Object
Machines
Productivity Scores for Machines and Workers
Nitrendipene
Assay of nitrendipene
Initialize.glsStruct
Initialize a glsStruct Object
Gun
Methods for firing naval guns
logDet.corStruct
Extract corStruct Log-Determinant
compareFits
Compare Fitted Objects
collapse.groupedData
Collapse a groupedData Object
corLin
Linear Correlation Structure
Muscle
Contraction of heart muscle sections
corMatrix
Extract Correlation Matrix
Matrix
Assign Matrix Values
MathAchieve
Mathematics achievement scores
Orthodont
Growth curve data on an orthdontic measurement
Ovary
Counts of Ovarian Follicles
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
corNatural
General correlation in natural parameterization
fitted.glsStruct
Calculate glsStruct Fitted Values
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Oats
Split-plot Experiment on Varieties of Oats
allCoef
Extract Coefficients from a Set of Objects
Names.pdMat
Names of a pdMat Object
Names
Names Associated with an Object
Names.reStruct
Names of an reStruct Object
getCovariate.data.frame
Extract Data Frame Covariate
coef.varFunc
varFunc Object Coefficients
Soybean
Growth of soybean plants
logDet.pdMat
Extract Log-Determinant from a pdMat Object
corGaus
Gaussian Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
Spruce
Growth of Spruce Trees
collapse
Collapse According to Groups
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
nlme
Nonlinear Mixed-Effects Models
Pixel
X-ray pixel intensities over time
getGroups
Extract Grouping Factors from an Object
getCovariate.varFunc
Extract varFunc Covariate
pdConstruct
Construct pdMat Objects
getData.lme
Extract lme Object Data
bdf
Language scores
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
anova.gls
Compare Likelihoods of Fitted Objects
corRatio
Rational Quadratic Correlation Structure
Variogram.default
Calculate Semi-variogram
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
asOneFormula
Combine Formulas of a Set of Objects
comparePred
Compare Predictions
asTable
Convert groupedData to a matrix
corAR1
AR(1) Correlation Structure
coef.pdMat
pdMat Object Coefficients
corClasses
Correlation Structure Classes
Quinidine
Quinidine Kinetics
Tetracycline2
Pharmacokinetics of tetracycline
coef.corStruct
Coefficients of a corStruct Object
Tetracycline1
Pharmacokinetics of tetracycline
corSpatial
Spatial Correlation Structure
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
corCompSymm
Compound Symmetry Correlation Structure
pdConstruct.pdBlocked
Construct pdBlocked Objects
ergoStool
Ergometrics experiment with stool types
getResponseFormula
Extract Formula Specifying Response Variable
plot.Variogram
Plot a Variogram Object
pdSymm
General Positive-Definite Matrix
plot.augPred
Plot an augPred Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getVarCov
Extract variance-covariance matrix
Wafer
Modeling of Analog MOS Circuits
coef.reStruct
reStruct Object Coefficients
isBalanced
Check a Design for Balance
intervals.lme
Confidence Intervals on lme Parameters
corMatrix.corStruct
Matrix of a corStruct Object
getCovariateFormula
Extract Covariates Formula
fixed.effects
Extract Fixed Effects
fixef.lmList
Extract lmList Fixed Effects
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getData
Extract Data from an Object
getGroupsFormula
Extract Grouping Formula
getResponse
Extract Response Variable from an Object
gls
Fit Linear Model Using Generalized Least Squares
gls-internal
Auxiliary functions used by gls
as.matrix.pdMat
Matrix of a pdMat Object
intervals.gls
Confidence Intervals on gls Parameters
intervals.lmList
Confidence Intervals on lmList Coefficients
lme.groupedData
LME fit from groupedData Object
lme.lmList
LME fit from lmList Object
as.matrix.reStruct
Matrices of an reStruct Object
getGroups.gls
Extract gls Object Groups
getGroups.lmList
Extract lmList Object Groups
getCovariate.corStruct
Extract corStruct Object Covariate
getCovariate
Extract Covariate from an Object
ranef.lme
Extract lme Random Effects
ranef.lmList
Extract lmList Random Effects
fdHess
Finite difference Hessian
logLik.lme
Log-Likelihood of an lme Object
coef.modelStruct
Extract modelStruct Object Coefficients
coef.lme
Extract lme Coefficients
nlme.nlsList
NLME fit from nlsList Object
nlmeControl
Control Values for nlme Fit
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
corExp
Exponential Correlation Structure
pairs.lmList
Pairs Plot of an lmList Object
plot.ACF
Plot an ACF Object
pairs.compareFits
Pairs Plot of compareFits Object
phenoModel
Model function for the Phenobarb data
solve.reStruct
Apply Solve to an reStruct Object
lmeStruct
Linear Mixed-Effects Structure
varFixed
Fixed Variance Function
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
varFunc
Variance Function Structure
formula.reStruct
Extract reStruct Object Formula
plot.lme
Plot an lme or nls object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
gnlsControl
Control Values for gnls Fit
gnlsObject
Fitted gnls Object
pdMat
Positive-Definite Matrix
pdLogChol
General Positive-Definite Matrix
logDet
Extract the Logarithm of the Determinant
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
gnlsStruct
Generalized Nonlinear Least Squares Structure
pdClasses
Positive-Definite Matrix Classes
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.nmGroupedData
Plot an nmGroupedData Object
print.summary.pdMat
Print a summary.pdMat Object
gapply
Apply a Function by Groups
corSpher
Spherical Correlation Structure
formula.pdBlocked
Extract pdBlocked Formula
corSymm
General Correlation Structure
formula.pdMat
Extract pdMat Formula
corFactor
Factor of a Correlation Matrix
getData.gls
Extract gls Object Data
getGroups.lme
Extract lme Object Groups
getGroups.corStruct
Extract corStruct Groups
getData.lmList
Extract lmList Object Data
print.varFunc
Print a varFunc Object
groupedData
Construct a groupedData Object
lmList.groupedData
lmList Fit from a groupedData Object
plot.nffGroupedData
Plot an nffGroupedData Object
recalc
Recalculate Condensed Linear Model Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
lme
Linear Mixed-Effects Models
reStruct
Random Effects Structure
predict.gls
Predictions from a gls Object
glsStruct
Generalized Least Squares Structure
pooledSD
Extract Pooled Standard Deviation
residuals.nlmeStruct
Calculate nlmeStruct Residuals
getGroups.varFunc
Extract varFunc Groups
gsummary
Summarize by Groups
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
nlsList
List of nls Objects with a Common Model
logLik.lmList
Log-Likelihood of an lmList Object
residuals.lmList
Extract lmList Residuals
summary.lmList
Summarize an lmList Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
summary.gls
Summarize a Generalized Least Squares
gls
Object
varComb
Combination of Variance Functions
varConstPower
Constant Plus Power Variance Function
splitFormula
Split a Formula
simulate.lme
Simulate Results from
lme
Models
intervals
Confidence Intervals on Coefficients
summary.corStruct
Summarize a corStruct Object
lmeControl
Specifying Control Values for lme Fit
varPower
Power Variance Function
varIdent
Constant Variance Function
lmList
List of lm Objects with a Common Model
glsControl
Control Values for gls Fit
isInitialized
Check if Object is Initialized
glsObject
Fitted gls Object
getGroups.data.frame
Extract Groups from a Data Frame
nlsList.selfStart
nlsList Fit from a selfStart Function
lmeObject
Fitted lme Object
pairs.lme
Pairs Plot of an lme Object
logDet.reStruct
Extract reStruct Log-Determinants
nlmeObject
Fitted nlme Object
logLik.corStruct
Extract corStruct Log-Likelihood
pdBlocked
Positive-Definite Block Diagonal Matrix
nlmeStruct
Nonlinear Mixed-Effects Structure
needUpdate
Check if Update is Needed
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
model.matrix.reStruct
reStruct Model Matrix
logLik.varFunc
Extract varFunc logLik
logLik.reStruct
Calculate reStruct Log-Likelihood
plot.ranef.lmList
Plot a ranef.lmList Object
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.lmList
Plot an lmList Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
plot.ranef.lme
Plot a ranef.lme Object
pdDiag
Diagonal Positive-Definite Matrix
residuals.glsStruct
Calculate glsStruct Residuals
residuals.gls
Extract gls Residuals
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.gls
Plot a gls Object
predict.lme
Predictions from an lme Object
plot.compareFits
Plot a compareFits Object
predict.nlme
Predictions from an nlme Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
summary.modelStruct
Summarize a modelStruct Object
summary.lme
Summarize an lme Object
varExp
Exponential Variance Function
varConstProp
Constant Plus Proportion Variance Function
quinModel
Model function for the Quinidine data
random.effects
Extract Random Effects
residuals.lme
Extract lme Residuals
recalc.reStruct
Recalculate for an reStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
recalc.corStruct
Recalculate for corStruct Object
summary.pdMat
Summarize a pdMat Object
predict.lmList
Predictions from an lmList Object
summary.nlsList
Summarize an nlsList Object
predict.gnls
Predictions from a gnls Object
recalc.varFunc
Recalculate for varFunc Object
residuals.lmeStruct
Calculate lmeStruct Residuals
summary.varFunc
Summarize "varFunc" Object
update.modelStruct
Update a modelStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
varWeights
Extract Variance Function Weights
update.varFunc
Update varFunc Object
varClasses
Variance Function Classes