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nlme (version 3.1-153)
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
134,390
Version
3.1-153
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
September 7th, 2021
Functions in nlme (3.1-153)
Search all functions
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Cefamandole
Pharmacokinetics of Cefamandole
ACF.gls
Autocorrelation Function for gls Residuals
Assay
Bioassay on Cell Culture Plate
ACF
Autocorrelation Function
Coef
Assign Values to Coefficients
Covariate
Assign Covariate Values
Covariate.varFunc
Assign varFunc Covariate
ACF.lme
Autocorrelation Function for lme Residuals
BodyWeight
Rat weight over time for different diets
[.pdMat
Subscript a pdMat Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Initialize.lmeStruct
Initialize an lmeStruct Object
Initialize.corStruct
Initialize corStruct Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Initialize.reStruct
Initialize reStruct Object
Fatigue
Cracks caused by metal fatigue
Gasoline
Refinery yield of gasoline
Milk
Protein content of cows' milk
Gun
Methods for firing naval guns
Meat
Tenderness of meat
Glucose
Glucose levels over time
Matrix.reStruct
Assign reStruct Matrices
Initialize.glsStruct
Initialize a glsStruct Object
Oxide
Variability in Semiconductor Manufacturing
Oxboys
Heights of Boys in Oxford
Nitrendipene
Assay of nitrendipene
Dim
Extract Dimensions from an Object
Dialyzer
High-Flux Hemodialyzer
MathAchieve
Mathematics achievement scores
Rail
Evaluation of Stress in Railway Rails
Dim.pdMat
Dimensions of a pdMat Object
Oats
Split-plot Experiment on Varieties of Oats
Matrix
Assign Matrix Values
PBG
Effect of Phenylbiguanide on Blood Pressure
Phenobarb
Phenobarbitol Kinetics
Relaxin
Assay for Relaxin
Dim.corSpatial
Dimensions of a corSpatial Object
Names
Names Associated with an Object
Names.formula
Extract Names from a formula
Muscle
Contraction of heart muscle sections
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Quinidine
Quinidine Kinetics
Names.pdBlocked
Names of a pdBlocked Object
Pixel
X-ray pixel intensities over time
LDEsysMat
Generate system matrix for LDEs
Orthodont
Growth curve data on an orthdontic measurement
Initialize.varFunc
Initialize varFunc Object
Earthquake
Earthquake Intensity
Ovary
Counts of Ovarian Follicles
Dim.corStruct
Dimensions of a corStruct Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Spruce
Growth of Spruce Trees
Soybean
Growth of soybean plants
anova.lme
Compare Likelihoods of Fitted Objects
Wheat2
Wheat Yield Trials
Wheat
Yields by growing conditions
IGF
Radioimmunoassay of IGF-I Protein
RatPupWeight
The weight of rat pups
Initialize
Initialize Object
as.matrix.pdMat
Matrix of a pdMat Object
compareFits
Compare Fitted Objects
corLin
Linear Correlation Structure
as.matrix.reStruct
Matrices of an reStruct Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
collapse.groupedData
Collapse a groupedData Object
Remifentanil
Pharmacokinetics of Remifentanil
as.matrix.corStruct
Matrix of a corStruct Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Names.reStruct
Names of an reStruct Object
MathAchSchool
School demographic data for MathAchieve
asOneFormula
Combine Formulas of a Set of Objects
Machines
Productivity Scores for Machines and Workers
asTable
Convert groupedData to a matrix
Names.pdMat
Names of a pdMat Object
Tetracycline2
Pharmacokinetics of tetracycline
Tetracycline1
Pharmacokinetics of tetracycline
corMatrix
Extract Correlation Matrix
fdHess
Finite difference Hessian
ergoStool
Ergometrics experiment with stool types
Wafer
Modeling of Analog MOS Circuits
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
allCoef
Extract Coefficients from a Set of Objects
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Variogram
Calculate Semi-variogram
VarCorr
Extract variance and correlation components
anova.gls
Compare Likelihoods of Fitted Objects
balancedGrouped
Create a groupedData object from a matrix
augPred
Augmented Predictions
corGaus
Gaussian Correlation Structure
formula.reStruct
Extract reStruct Object Formula
fixed.effects
Extract Fixed Effects
fixef.lmList
Extract lmList Fixed Effects
corFactor.corStruct
Factor of a corStruct Object Matrix
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Variogram.default
Calculate Semi-variogram
gapply
Apply a Function by Groups
getGroups.lme
Extract lme Object Groups
coef.lme
Extract lme Coefficients
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
collapse
Collapse According to Groups
coef.varFunc
varFunc Object Coefficients
getGroups.varFunc
Extract varFunc Groups
coef.lmList
Extract lmList Coefficients
coef.pdMat
pdMat Object Coefficients
coef.gnls
Extract gnls Coefficients
corNatural
General correlation in natural parameterization
coef.modelStruct
Extract modelStruct Object Coefficients
corARMA
ARMA(p,q) Correlation Structure
coef.reStruct
reStruct Object Coefficients
bdf
Language scores
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getCovariateFormula
Extract Covariates Formula
fitted.glsStruct
Calculate glsStruct Fitted Values
corSpher
Spherical Correlation Structure
corCAR1
Continuous AR(1) Correlation Structure
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
corSymm
General Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getData.lmList
Extract lmList Object Data
getData.gls
Extract gls Object Data
corExp
Exponential Correlation Structure
glsStruct
Generalized Least Squares Structure
getGroups.data.frame
Extract Groups from a Data Frame
gnls
Fit Nonlinear Model Using Generalized Least Squares
getData
Extract Data from an Object
coef.corStruct
Coefficients of a corStruct Object
getGroups.corStruct
Extract corStruct Groups
gnlsStruct
Generalized Nonlinear Least Squares Structure
lme.lmList
LME fit from lmList Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
lme.groupedData
LME fit from groupedData Object
corClasses
Correlation Structure Classes
comparePred
Compare Predictions
logLik.gnls
Log-Likelihood of a gnls Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corMatrix.corStruct
Matrix of a corStruct Object
corAR1
AR(1) Correlation Structure
formula.pdMat
Extract pdMat Formula
getCovariate
Extract Covariate from an Object
formula.pdBlocked
Extract pdBlocked Formula
getCovariate.corStruct
Extract corStruct Object Covariate
corFactor
Factor of a Correlation Matrix
nlmeControl
Control Values for nlme Fit
nlme.nlsList
NLME fit from nlsList Object
pdClasses
Positive-Definite Matrix Classes
lmeStruct
Linear Mixed-Effects Structure
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.lme
Log-Likelihood of an lme Object
groupedData
Construct a groupedData Object
logDet
Extract the Logarithm of the Determinant
gnlsControl
Control Values for gnls Fit
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
gnlsObject
Fitted gnls Object
pairs.lmList
Pairs Plot of an lmList Object
pairs.compareFits
Pairs Plot of compareFits Object
getGroups.gls
Extract gls Object Groups
getGroups.lmList
Extract lmList Object Groups
plot.lmList
Plot an lmList Object
predict.lmList
Predictions from an lmList Object
plot.intervals.lmList
Plot lmList Confidence Intervals
predict.gnls
Predictions from a gnls Object
corCompSymm
Compound Symmetry Correlation Structure
getGroups
Extract Grouping Factors from an Object
getData.lme
Extract lme Object Data
pdLogChol
General Positive-Definite Matrix
corSpatial
Spatial Correlation Structure
corRatio
Rational Quadratic Correlation Structure
recalc
Recalculate Condensed Linear Model Object
reStruct
Random Effects Structure
fitted.lmList
Extract lmList Fitted Values
glsControl
Control Values for gls Fit
lmeControl
Specifying Control Values for lme Fit
intervals.lme
Confidence Intervals on lme Parameters
isBalanced
Check a Design for Balance
lmeObject
Fitted lme Object
logDet.reStruct
Extract reStruct Log-Determinants
logLik.corStruct
Extract corStruct Log-Likelihood
getResponseFormula
Extract Formula Specifying Response Variable
glsObject
Fitted gls Object
getCovariate.data.frame
Extract Data Frame Covariate
fitted.lme
Extract lme Fitted Values
plot.lme
Plot an lme or nls object
pdMat
Positive-Definite Matrix
plot.nffGroupedData
Plot an nffGroupedData Object
predict.lme
Predictions from an lme Object
intervals.gls
Confidence Intervals on gls Parameters
getVarCov
Extract variance-covariance matrix
predict.nlme
Predictions from an nlme Object
isInitialized
Check if Object is Initialized
getCovariate.varFunc
Extract varFunc Covariate
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
residuals.lme
Extract lme Residuals
qqnorm.gls
Normal Plot of Residuals from a gls Object
residuals.lmeStruct
Calculate lmeStruct Residuals
splitFormula
Split a Formula
getGroupsFormula
Extract Grouping Formula
intervals.lmList
Confidence Intervals on lmList Coefficients
summary.corStruct
Summarize a corStruct Object
lmList.groupedData
lmList Fit from a groupedData Object
lme
Linear Mixed-Effects Models
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.lmList
Log-Likelihood of an lmList Object
lmList
List of lm Objects with a Common Model
getResponse
Extract Response Variable from an Object
gls-internal
Auxiliary functions used by gls
update.varFunc
Update varFunc Object
logLik.varFunc
Extract varFunc logLik
logLik.reStruct
Calculate reStruct Log-Likelihood
recalc.reStruct
Recalculate for an reStruct Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
nlme
Nonlinear Mixed-Effects Models
gls
Fit Linear Model Using Generalized Least Squares
varIdent
Constant Variance Function
varClasses
Variance Function Classes
recalc.varFunc
Recalculate for varFunc Object
nlsList.selfStart
nlsList Fit from a selfStart Function
nlsList
List of nls Objects with a Common Model
pdConstruct
Construct pdMat Objects
varPower
Power Variance Function
model.matrix.reStruct
reStruct Model Matrix
needUpdate
Check if Update is Needed
pdDiag
Diagonal Positive-Definite Matrix
summary.pdMat
Summarize a pdMat Object
varComb
Combination of Variance Functions
summary.nlsList
Summarize an nlsList Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
intervals
Confidence Intervals on Coefficients
pdConstruct.pdBlocked
Construct pdBlocked Objects
gsummary
Summarize by Groups
phenoModel
Model function for the Phenobarb data
logDet.corStruct
Extract corStruct Log-Determinant
pdFactor
Square-Root Factor of a Positive-Definite Matrix
nlmeObject
Fitted nlme Object
ranef.lme
Extract lme Random Effects
ranef.lmList
Extract lmList Random Effects
pairs.lme
Pairs Plot of an lme Object
pdBlocked
Positive-Definite Block Diagonal Matrix
plot.ACF
Plot an ACF Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
varConstPower
Constant Plus Power Variance Function
plot.compareFits
Plot a compareFits Object
nlmeStruct
Nonlinear Mixed-Effects Structure
pdNatural
General Positive-Definite Matrix in Natural Parametrization
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.lmList
Extract lmList Residuals
pdSymm
General Positive-Definite Matrix
plot.Variogram
Plot a Variogram Object
summary.modelStruct
Summarize a modelStruct Object
summary.lme
Summarize an lme Object
plot.nmGroupedData
Plot an nmGroupedData Object
plot.ranef.lmList
Plot a ranef.lmList Object
quinModel
Model function for the Quinidine data
plot.ranef.lme
Plot a ranef.lme Object
plot.augPred
Plot an augPred Object
pooledSD
Extract Pooled Standard Deviation
predict.gls
Predictions from a gls Object
recalc.corStruct
Recalculate for corStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
random.effects
Extract Random Effects
residuals.gls
Extract gls Residuals
simulate.lme
Simulate Results from
lme
Models
varFunc
Variance Function Structure
summary.lmList
Summarize an lmList Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
varConstProp
Constant Plus Proportion Variance Function
summary.gls
Summarize a Generalized Least Squares
gls
Object
varFixed
Fixed Variance Function
residuals.glsStruct
Calculate glsStruct Residuals
varExp
Exponential Variance Function
varWeights.glsStruct
Variance Weights for glsStruct Object
varWeights
Extract Variance Function Weights
plot.gls
Plot a gls Object
print.summary.pdMat
Print a summary.pdMat Object
print.varFunc
Print a varFunc Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
solve.reStruct
Apply Solve to an reStruct Object
summary.varFunc
Summarize "varFunc" Object
update.modelStruct
Update a modelStruct Object