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nlme (version 3.1-144)
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
3.1-144
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
February 6th, 2020
Functions in nlme (3.1-144)
Search all functions
Assay
Bioassay on Cell Culture Plate
ACF
Autocorrelation Function
ACF.lme
Autocorrelation Function for lme Residuals
ACF.gls
Autocorrelation Function for gls Residuals
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Cefamandole
Pharmacokinetics of Cefamandole
BodyWeight
Rat weight over time for different diets
Covariate
Assign Covariate Values
Covariate.varFunc
Assign varFunc Covariate
Dim.pdMat
Dimensions of a pdMat Object
Dim.corSpatial
Dimensions of a corSpatial Object
Earthquake
Earthquake Intensity
Dialyzer
High-Flux Hemodialyzer
Coef
Assign Values to Coefficients
IGF
Radioimmunoassay of IGF-I Protein
Initialize
Initialize Object
Glucose
Glucose levels over time
Dim
Extract Dimensions from an Object
Dim.corStruct
Dimensions of a corStruct Object
[.pdMat
Subscript a pdMat Object
Initialize.corStruct
Initialize corStruct Object
Gasoline
Refinery yield of gasoline
Names.pdMat
Names of a pdMat Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Fatigue
Cracks caused by metal fatigue
Initialize.glsStruct
Initialize a glsStruct Object
Gun
Methods for firing naval guns
Initialize.varFunc
Initialize varFunc Object
Muscle
Contraction of heart muscle sections
LDEsysMat
Generate system matrix for LDEs
Machines
Productivity Scores for Machines and Workers
Relaxin
Assay for Relaxin
Names
Names Associated with an Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Remifentanil
Pharmacokinetics of remifentanil
Matrix.reStruct
Assign reStruct Matrices
MathAchSchool
School demographic data for MathAchieve
Initialize.lmeStruct
Initialize an lmeStruct Object
Names.reStruct
Names of an reStruct Object
Initialize.reStruct
Initialize reStruct Object
Nitrendipene
Assay of nitrendipene
Meat
Tenderness of meat
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Names.formula
Extract Names from a formula
Milk
Protein content of cows' milk
Oxide
Variability in Semiconductor Manufacturing
Oats
Split-plot Experiment on Varieties of Oats
Oxboys
Heights of Boys in Oxford
Soybean
Growth of soybean plants
Names.pdBlocked
Names of a pdBlocked Object
Ovary
Counts of Ovarian Follicles
Spruce
Growth of Spruce Trees
Quinidine
Quinidine Kinetics
Matrix
Assign Matrix Values
MathAchieve
Mathematics achievement scores
Pixel
X-ray pixel intensities over time
Rail
Evaluation of Stress in Railway Rails
Wafer
Modeling of Analog MOS Circuits
bdf
Language scores
Tetracycline1
Pharmacokinetics of tetracycline
coef.corStruct
Coefficients of a corStruct Object
PBG
Effect of Phenylbiguanide on Blood Pressure
anova.lme
Compare Likelihoods of Fitted Objects
coef.varFunc
varFunc Object Coefficients
RatPupWeight
The weight of rat pups
as.matrix.corStruct
Matrix of a corStruct Object
Orthodont
Growth curve data on an orthdontic measurement
corLin
Linear Correlation Structure
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Tetracycline2
Pharmacokinetics of tetracycline
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
collapse
Collapse According to Groups
asOneFormula
Combine Formulas of a Set of Objects
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Phenobarb
Phenobarbitol Kinetics
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
VarCorr
Extract variance and correlation components
fitted.glsStruct
Calculate glsStruct Fitted Values
Wheat2
Wheat Yield Trials
getData.gls
Extract gls Object Data
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
asTable
Convert groupedData to a matrix
getData.lmList
Extract lmList Object Data
Wheat
Yields by growing conditions
Variogram.default
Calculate Semi-variogram
corRatio
Rational Quadratic Correlation Structure
corMatrix
Extract Correlation Matrix
corSpatial
Spatial Correlation Structure
Variogram
Calculate Semi-variogram
as.matrix.pdMat
Matrix of a pdMat Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
allCoef
Extract Coefficients from a Set of Objects
as.matrix.reStruct
Matrices of an reStruct Object
anova.gls
Compare Likelihoods of Fitted Objects
coef.pdMat
pdMat Object Coefficients
augPred
Augmented Predictions
balancedGrouped
Create a groupedData object from a matrix
comparePred
Compare Predictions
corARMA
ARMA(p,q) Correlation Structure
collapse.groupedData
Collapse a groupedData Object
getGroups.varFunc
Extract varFunc Groups
getVarCov
Extract variance-covariance matrix
getGroups.lme
Extract lme Object Groups
corCAR1
Continuous AR(1) Correlation Structure
corAR1
AR(1) Correlation Structure
coef.gnls
Extract gnls Coefficients
getResponseFormula
Extract Formula Specifying Response Variable
coef.reStruct
reStruct Object Coefficients
fdHess
Finite difference Hessian
ergoStool
Ergometrics experiment with stool types
coef.lme
Extract lme Coefficients
coef.lmList
Extract lmList Coefficients
isInitialized
Check if Object is Initialized
compareFits
Compare Fitted Objects
corClasses
Correlation Structure Classes
corExp
Exponential Correlation Structure
coef.modelStruct
Extract modelStruct Object Coefficients
corCompSymm
Compound Symmetry Correlation Structure
corMatrix.corStruct
Matrix of a corStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
lmeObject
Fitted lme Object
corSpher
Spherical Correlation Structure
lmList
List of lm Objects with a Common Model
corFactor
Factor of a Correlation Matrix
fitted.lmList
Extract lmList Fitted Values
corSymm
General Correlation Structure
lmeControl
Specifying Control Values for lme Fit
corFactor.corStruct
Factor of a corStruct Object Matrix
getData
Extract Data from an Object
logLik.lme
Log-Likelihood of an lme Object
corGaus
Gaussian Correlation Structure
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
fitted.lmeStruct
Calculate lmeStruct Fitted Values
fitted.lme
Extract lme Fitted Values
getCovariateFormula
Extract Covariates Formula
getData.lme
Extract lme Object Data
corNatural
General correlation in natural parameterization
formula.pdBlocked
Extract pdBlocked Formula
glsStruct
Generalized Least Squares Structure
isBalanced
Check a Design for Balance
lmeStruct
Linear Mixed-Effects Structure
getGroups
Extract Grouping Factors from an Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
logDet
Extract the Logarithm of the Determinant
intervals.lme
Confidence Intervals on lme Parameters
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
getCovariate.data.frame
Extract Data Frame Covariate
getCovariate
Extract Covariate from an Object
getGroups.corStruct
Extract corStruct Groups
fixed.effects
Extract Fixed Effects
gapply
Apply a Function by Groups
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
fixef.lmList
Extract lmList Fixed Effects
getCovariate.varFunc
Extract varFunc Covariate
logLik.lmList
Log-Likelihood of an lmList Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
getGroups.data.frame
Extract Groups from a Data Frame
model.matrix.reStruct
reStruct Model Matrix
getGroupsFormula
Extract Grouping Formula
getCovariate.corStruct
Extract corStruct Object Covariate
needUpdate
Check if Update is Needed
formula.pdMat
Extract pdMat Formula
pdDiag
Diagonal Positive-Definite Matrix
gnlsStruct
Generalized Nonlinear Least Squares Structure
formula.reStruct
Extract reStruct Object Formula
gnlsObject
Fitted gnls Object
getGroups.gls
Extract gls Object Groups
getGroups.lmList
Extract lmList Object Groups
gnlsControl
Control Values for gnls Fit
getResponse
Extract Response Variable from an Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
gls-internal
Auxiliary functions used by gls
nlsList
List of nls Objects with a Common Model
gls
Fit Linear Model Using Generalized Least Squares
glsObject
Fitted gls Object
glsControl
Control Values for gls Fit
groupedData
Construct a groupedData Object
gsummary
Summarize by Groups
lmList.groupedData
lmList Fit from a groupedData Object
plot.augPred
Plot an augPred Object
lme
Linear Mixed-Effects Models
phenoModel
Model function for the Phenobarb data
logLik.glsStruct
Log-Likelihood of a glsStruct Object
plot.ACF
Plot an ACF Object
intervals.gls
Confidence Intervals on gls Parameters
plot.Variogram
Plot a Variogram Object
nlsList.selfStart
nlsList Fit from a selfStart Function
intervals.lmList
Confidence Intervals on lmList Coefficients
predict.gnls
Predictions from a gnls Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pairs.compareFits
Pairs Plot of compareFits Object
logLik.gnls
Log-Likelihood of a gnls Object
lme.groupedData
LME fit from groupedData Object
intervals
Confidence Intervals on Coefficients
lme.lmList
LME fit from lmList Object
pdClasses
Positive-Definite Matrix Classes
predict.lmList
Predictions from an lmList Object
logLik.reStruct
Calculate reStruct Log-Likelihood
nlme
Nonlinear Mixed-Effects Models
logDet.reStruct
Extract reStruct Log-Determinants
quinModel
Model function for the Quinidine data
random.effects
Extract Random Effects
residuals.gls
Extract gls Residuals
logDet.corStruct
Extract corStruct Log-Determinant
logDet.pdMat
Extract Log-Determinant from a pdMat Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
residuals.gnlsStruct
Calculate gnlsStruct Residuals
plot.ranef.lmList
Plot a ranef.lmList Object
ranef.lme
Extract lme Random Effects
plot.lmList
Plot an lmList Object
residuals.lmList
Extract lmList Residuals
plot.intervals.lmList
Plot lmList Confidence Intervals
ranef.lmList
Extract lmList Random Effects
residuals.glsStruct
Calculate glsStruct Residuals
plot.ranef.lme
Plot a ranef.lme Object
summary.nlsList
Summarize an nlsList Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
nlme.nlsList
NLME fit from nlsList Object
nlmeControl
Control Values for nlme Fit
logLik.corStruct
Extract corStruct Log-Likelihood
pdBlocked
Positive-Definite Block Diagonal Matrix
plot.lme
Plot an lme or nls object
pairs.lme
Pairs Plot of an lme Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
logLik.varFunc
Extract varFunc logLik
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.nffGroupedData
Plot an nffGroupedData Object
pairs.lmList
Pairs Plot of an lmList Object
splitFormula
Split a Formula
predict.nlme
Predictions from an nlme Object
predict.lme
Predictions from an lme Object
pdSymm
General Positive-Definite Matrix
summary.pdMat
Summarize a pdMat Object
varConstPower
Constant Plus Power Variance Function
varPower
Power Variance Function
summary.corStruct
Summarize a corStruct Object
varComb
Combination of Variance Functions
update.varFunc
Update varFunc Object
varWeights
Extract Variance Function Weights
nlmeStruct
Nonlinear Mixed-Effects Structure
nlmeObject
Fitted nlme Object
pdConstruct
Construct pdMat Objects
plot.compareFits
Plot a compareFits Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
pdLogChol
General Positive-Definite Matrix
plot.nmGroupedData
Plot an nmGroupedData Object
pooledSD
Extract Pooled Standard Deviation
pdConstruct.pdBlocked
Construct pdBlocked Objects
recalc.modelStruct
Recalculate for a modelStruct Object
varClasses
Variance Function Classes
recalc.corStruct
Recalculate for corStruct Object
residuals.lmeStruct
Calculate lmeStruct Residuals
plot.gls
Plot a gls Object
residuals.lme
Extract lme Residuals
print.varFunc
Print a varFunc Object
recalc
Recalculate Condensed Linear Model Object
reStruct
Random Effects Structure
pdMat
Positive-Definite Matrix
residuals.nlmeStruct
Calculate nlmeStruct Residuals
qqnorm.gls
Normal Plot of Residuals from a gls Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
predict.gls
Predictions from a gls Object
recalc.reStruct
Recalculate for an reStruct Object
solve.reStruct
Apply Solve to an reStruct Object
print.summary.pdMat
Print a summary.pdMat Object
summary.varFunc
Summarize varFunc Object
update.modelStruct
Update a modelStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
simulate.lme
Simulate Results from
lme
Models
summary.gls
Summarize a Generalized Least Squares
gls
Object
varWeights.glsStruct
Variance Weights for glsStruct Object
summary.modelStruct
Summarize a modelStruct Object
varExp
Exponential Variance Function
varFixed
Fixed Variance Function
varFunc
Variance Function Structure
varWeights.lmeStruct
Variance Weights for lmeStruct Object
recalc.varFunc
Recalculate for varFunc Object
summary.lmList
Summarize an lmList Object
summary.lme
Summarize an lme Object
varIdent
Constant Variance Function