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nlme (version 3.1-68.1)
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
139,641
Version
3.1-68.1
License
GPL version 2 or later
Maintainer
R-core R-core@R-project.org
Last Published
August 16th, 2024
Functions in nlme (3.1-68.1)
Search all functions
ACF.lme
Autocorrelation Function for lme Residuals
LDEsysMat
Generate system matrix for LDEs
Names.pdMat
Names of a pdMat Object
Names.pdBlocked
Names of a pdBlocked Object
ACF
Autocorrelation Function
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
corCompSymm
Compound Symmetry Correlation Structure
BIC
Bayesian Information Criterion
corFactor.corStruct
Factor of a corStruct Object Matrix
formula.reStruct
Extract reStruct Object Formula
corNatural
General correlation in natural parameterization
fdHess
Finite difference Hessian
getCovariate.data.frame
Extract Data Frame Covariate
Initialize.lmeStruct
Initialize an lmeStruct Object
Coef
Assign Values to Coefficients
fixed.effects
Extract Fixed Effects
Variogram
Calculate Semi-variogram
Variogram.default
Calculate Semi-variogram
gapply
Apply a Function by Groups
Initialize.corStruct
Initialize corStruct Object
coef.reStruct
reStruct Object Coefficients
getVarCov
Extract variance-covariance matrix
BIC.logLik
BIC of a logLik Object
getData
Extract Data from an Object
gnlsObject
Fitted gnls Object
corFactor
Factor of a Correlation Matrix
Matrix.pdMat
Assign Matrix to a pdMat Object
gnlsControl
Control Values for gnls Fit
gnls
Fit Nonlinear Model Using Generalized Least Squares
intervals.lmList
Confidence Intervals on lmList Coefficients
pdLogChol
General Positive-Definite Matrix
Matrix.reStruct
Assign reStruct Matrices
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
coef.varFunc
varFunc Object Coefficients
isInitialized
Check if Object is Initialized
getData.lmList
Extract lmList Object Data
getData.gls
Extract gls Object Data
corAR1
AR(1) Correlation Structure
corClasses
Correlation Structure Classes
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
lme.lmList
LME fit from lmList Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
Dim.corSpatial
Dimensions of a corSpatial Object
getGroups
Extract Grouping Factors from an Object
corMatrix.corStruct
Matrix of a corStruct Object
getGroups.lme
Extract lme Object Groups
pooledSD
Extract Pooled Standard Deviation
logLik.glsStruct
Log-Likelihood of a glsStruct Object
Initialize.varFunc
Initialize varFunc Object
predict.nlme
Predictions from an nlme Object
allCoef
Extract Coefficients from a Set of Objects
logLik.gnls
Log-Likelihood of a gnls Object
solve.reStruct
Apply Solve to an reStruct Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
as.matrix.reStruct
Matrices of an reStruct Object
augPred
Augmented Predictions
Names.formula
Extract Names from a formula
fitted.lme
Extract lme Fitted Values
varConstPower
Constant Plus Power Variance Function
glsStruct
Generalized Least Squares Structure
logLik.reStruct
Calculate reStruct Log-Likelihood
Dim.corStruct
Dimensions of a corStruct Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
Covariate
Assign Covariate Values
lmeObject
Fitted lme Object
getCovariate.corStruct
Extract corStruct Object Covariate
getData.lme
Extract lme Object Data
glsObject
Fitted gls Object
Dim
Extract Dimensions from an Object
update.modelStruct
Update a modelStruct Object
Initialize.glsStruct
Initialize a glsStruct Object
Matrix
Assign Matrix Values
glsControl
Control Values for gls Fit
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
Dim.pdMat
Dimensions of a pdMat Object
as.matrix.pdMat
Matrix of a pdMat Object
pdMat
Positive-Definite Matrix
gsummary
Summarize by Groups
pdSymm
General Positive-Definite Matrix
Initialize.reStruct
Initialize reStruct Object
logLik.corStruct
Extract corStruct Log-Likelihood
coef.lme
Extract lme Coefficients
Initialize
Initialize Object
balancedGrouped
Create a groupedData object from a matrix
plot.lme
Plot an lme or nls object
asOneFormula
Combine Formulas of a Set of Objects
compareFits
Compare Fitted Objects
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
corSpatial
Spatial Correlation Structure
Names.reStruct
Names of an reStruct Object
comparePred
Compare Predictions
lmList.groupedData
lmList Fit from a groupedData Object
formula.pdMat
Extract pdMat Formula
plot.ranef.lme
Plot a ranef.lme Object
nlmeStruct
Nonlinear Mixed-Effects Structure
coef.gnls
Extract gnls Coefficients
lme
Linear Mixed-Effects Models
pdClasses
Positive-Definite Matrix Classes
nlme.nlsList
NLME fit from nlsList Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
needUpdate
Check if Update is Needed
corGaus
Gaussian Correlation Structure
getGroups.corStruct
Extract corStruct Groups
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
anova.lme
Compare Likelihoods of Fitted Objects
predict.lmList
Predictions from an lmList Object
lmeScale
Scale for lme Optimization
corMatrix
Extract Correlation Matrix
random.effects
Extract Random Effects
corExp
Exponential Correlation Structure
coef.corStruct
Coefficients of a corStruct Object
Names
Names Associated with an Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
predict.gls
Predictions from a gls Object
corSymm
General Correlation Structure
plot.augPred
Plot an augPred Object
varFunc
Variance Function Structure
pairs.lme
Pairs Plot of an lme Object
fitted.lmList
Extract lmList Fitted Values
recalc.reStruct
Recalculate for an reStruct Object
coef.lmList
Extract lmList Coefficients
fitted.glsStruct
Calculate glsStruct Fitted Values
as.matrix.corStruct
Matrix of a corStruct Object
getCovariateFormula
Extract Covariates Formula
collapse.groupedData
Collapse a groupedData Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
getGroups.data.frame
Extract Groups from a Data Frame
coef.pdMat
pdMat Object Coefficients
coef.modelStruct
Extract modelStruct Object Coefficients
predict.lme
Predictions from an lme Object
fixef.lmList
Extract lmList Fixed Effects
reStruct
Random Effects Structure
pdConstruct
Construct pdMat Objects
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
quinModel
Model function for the Quinidine data
fitted.lmeStruct
Calculate lmeStruct Fitted Values
collapse
Collapse According to Groups
corCAR1
Continuous AR(1) Correlation Structure
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
VarCorr
Extract variance and correlation components
ranef.lmList
Extract lmList Random Effects
getGroups.gls
Extract gls Object Groups
getCovariate
Extract Covariate from an Object
recalc.varFunc
Recalculate for varFunc Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
summary.varFunc
Summarize varFunc Object
formula.pdBlocked
Extract pdBlocked Formula
summary.corStruct
Summarize a corStruct Object
intervals.gls
Confidence Intervals on gls Parameters
corARMA
ARMA(p,q) Correlation Structure
lme.groupedData
LME fit from groupedData Object
simulate.lme
Simulate results from lme models
corRatio
Rational Quadratic Correlation Structure
pdDiag
Diagonal Positive-Definite Matrix
getCovariate.varFunc
Extract varFunc Covariate
summary.gls
Summarize a gls Object
summary.nlsList
Summarize an nlsList Object
getGroups.varFunc
Extract varFunc Groups
pairs.lmList
Pairs Plot of an lmList Object
splitFormula
Split a Formula
varWeights
Extract Variance Function Weights
corSpher
Spherical Correlation Structure
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
intervals.lme
Confidence Intervals on lme Parameters
varComb
Combination of Variance Functions
logDet.pdMat
Extract Log-Determinant from a pdMat Object
summary.lme
Summarize an lme Object
summary.pdMat
Summarize a pdMat Object
groupedData
Construct a groupedData Object
update.varFunc
Update varFunc Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
isBalanced
Check a Design for Balance
intervals
Confidence Intervals on Coefficients
lmList
List of lm Objects with a Common Model
logDet.reStruct
Extract reStruct Log-Determinants
ACF.gls
Autocorrelation Function for gls Residuals
nlmeObject
Fitted nlme Object
plot.lmList
Plot an lmList Object
Covariate.varFunc
Assign varFunc Covariate
lmeControl
Control Values for lme Fit
lmeStruct
Linear Mixed-Effects Structure
logDet.corStruct
Extract corStruct Log-Determinant
[.pdMat
Subscript a pdMat Object
plot.ranef.lmList
Plot a ranef.lmList Object
varExp
Exponential Variance Function
logLik.lme
Log-Likelihood of an lme Object
logLik.lmList
Log-Likelihood of an lmList Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
nlsList.selfStart
nlsList Fit from a selfStart Function
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.varFunc
Extract varFunc logLik
nlmeControl
Control Values for nlme Fit
plot.Variogram
Plot a Variogram Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
plot.ACF
Plot an ACF Object
phenoModel
Model function for the Phenobarb data
varIdent
Constant Variance Function
model.matrix.reStruct
reStruct Model Matrix
Variogram.corExp
Calculate Semi-variogram for a corExp Object
predict.gnls
Predictions from a gnls Object
print.varFunc
Print a varFunc Object
nlsList
List of nls Objects with a Common Model
asTable
Convert groupedData to a matrix
residuals.glsStruct
Calculate glsStruct Residuals
anova.gls
Compare Likelihoods of Fitted Objects
recalc
Recalculate Condensed Linear Model Object
corLin
Linear Correlation Structure
pairs.compareFits
Pairs Plot of compareFits Object
varClasses
Variance Function Classes
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.gls
Plot a gls Object
summary.lmList
Summarize an lmList Object
varFixed
Fixed Variance Function
plot.nmGroupedData
Plot an nmGroupedData Object
recalc.modelStruct
Recalculate for a modelStruct Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
print.summary.pdMat
Print a summary.pdMat Object
getGroups.lmList
Extract lmList Object Groups
getResponse
Extract Response Variable from an Object
residuals.lme
Extract lme Residuals
gls
Fit Linear Model Using Generalized Least Squares
summary.modelStruct
Summarize a modelStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
getResponseFormula
Extract Formula Specifying Response Variable
logDet
Extract the Logarithm of the Determinant
getGroupsFormula
Extract Grouping Formula
varPower
Power Variance Function
nlme
Nonlinear Mixed-Effects Models
pdBlocked
Positive-Definite Block Diagonal Matrix
pdFactor
Square-Root Factor of a Positive-Definite Matrix
plot.compareFits
Plot a compareFits Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
residuals.gls
Extract gls Residuals
ranef.lme
Extract lme Random Effects
residuals.lmList
Extract lmList Residuals
residuals.gnlsStruct
Calculate gnlsStruct Residuals
residuals.lmeStruct
Calculate lmeStruct Residuals
recalc.corStruct
Recalculate for corStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
Remifentanil
Pharmacokinetics of remifentanil
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
BodyWeight
Rat weight over time for different diets
Gasoline
Refinery yield of gasoline
Fatigue
Cracks caused by metal fatigue
Glucose
Glucose levels over time
Orthodont
Growth curve data on an orthdontic measurement
Earthquake
Earthquake Intensity
Oats
Split-plot Experiment on Varieties of Oats
Cefamandole
Pharmacokinetics of Cefamandole
Soybean
Growth of soybean plants
Dialyzer
High-Flux Hemodialyzer
Tetracycline1
Pharmacokinetics of tetracycline
ergoStool
Ergometrics experiment with stool types
Wheat2
Wheat Yield Trials
Assay
Bioassay on Cell Culture Plate
Glucose2
Glucose Levels Following Alcohol Ingestion
Pixel
X-ray pixel intensities over time
Relaxin
Assay for Relaxin
Meat
Tenderness of meat
Rail
Evaluation of Stress in Railway Rails
Nitrendipene
Assay of nitrendipene
Phenobarb
Phenobarbitol Kinetics
Quinidine
Quinidine Kinetics
Wheat
Yields by growing conditions
Oxide
Variability in Semiconductor Manufacturing
Spruce
Growth of Spruce Trees
RatPupWeight
The weight of rat pups
Milk
Protein content of cows' milk
MathAchieve
Mathematics achievement scores
Machines
Productivity Scores for Machines and Workers
PBG
Effect of Phenylbiguanide on Blood Pressure
Oxboys
Heights of Boys in Oxford
MathAchSchool
School demographic data for MathAchieve
Muscle
Contraction of heart muscle sections
Wafer
Modeling of Analog MOS Circuits
IGF
Radioimmunoassay of IGF-I Protein
Ovary
Counts of Ovarian Follicles
Gun
Methods for firing naval guns
Tetracycline2
Pharmacokinetics of tetracycline
bdf
Language scores