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nlme (version 3.1-137)
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
3.1-137
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
April 7th, 2018
Functions in nlme (3.1-137)
Search all functions
Cefamandole
Pharmacokinetics of Cefamandole
Dim.corSpatial
Dimensions of a corSpatial Object
Earthquake
Earthquake Intensity
Dim.pdMat
Dimensions of a pdMat Object
ACF
Autocorrelation Function
Dim.corStruct
Dimensions of a corStruct Object
Initialize.corStruct
Initialize corStruct Object
ACF.gls
Autocorrelation Function for gls Residuals
Glucose2
Glucose Levels Following Alcohol Ingestion
Assay
Bioassay on Cell Culture Plate
Gun
Methods for firing naval guns
Initialize.glsStruct
Initialize a glsStruct Object
BodyWeight
Rat weight over time for different diets
Gasoline
Refinery yield of gasoline
Glucose
Glucose levels over time
ACF.lme
Autocorrelation Function for lme Residuals
Initialize
Initialize Object
Dim
Extract Dimensions from an Object
IGF
Radioimmunoassay of IGF-I Protein
Dialyzer
High-Flux Hemodialyzer
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Initialize.varFunc
Initialize varFunc Object
Machines
Productivity Scores for Machines and Workers
LDEsysMat
Generate system matrix for LDEs
Muscle
Contraction of heart muscle sections
Names
Names Associated with an Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
[.pdMat
Subscript a pdMat Object
Fatigue
Cracks caused by metal fatigue
MathAchSchool
School demographic data for MathAchieve
Names.reStruct
Names of an reStruct Object
Names.pdMat
Names of a pdMat Object
Matrix.reStruct
Assign reStruct Matrices
Nitrendipene
Assay of nitrendipene
Initialize.lmeStruct
Initialize an lmeStruct Object
MathAchieve
Mathematics achievement scores
Matrix
Assign Matrix Values
Oats
Split-plot Experiment on Varieties of Oats
Rail
Evaluation of Stress in Railway Rails
Initialize.reStruct
Initialize reStruct Object
Ovary
Counts of Ovarian Follicles
Orthodont
Growth curve data on an orthdontic measurement
RatPupWeight
The weight of rat pups
Relaxin
Assay for Relaxin
Names.formula
Extract Names from a formula
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Names.pdBlocked
Names of a pdBlocked Object
Meat
Tenderness of meat
Remifentanil
Pharmacokinetics of remifentanil
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Milk
Protein content of cows' milk
Pixel
X-ray pixel intensities over time
Quinidine
Quinidine Kinetics
Phenobarb
Phenobarbitol Kinetics
PBG
Effect of Phenylbiguanide on Blood Pressure
Tetracycline2
Pharmacokinetics of tetracycline
Tetracycline1
Pharmacokinetics of tetracycline
Variogram.corExp
Calculate Semi-variogram for a corExp Object
anova.lme
Compare Likelihoods of Fitted Objects
as.matrix.corStruct
Matrix of a corStruct Object
allCoef
Extract Coefficients from a Set of Objects
anova.gls
Compare Likelihoods of Fitted Objects
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
as.matrix.pdMat
Matrix of a pdMat Object
as.matrix.reStruct
Matrices of an reStruct Object
Oxboys
Heights of Boys in Oxford
Oxide
Variability in Semiconductor Manufacturing
augPred
Augmented Predictions
Wheat
Yields by growing conditions
coef.varFunc
varFunc Object Coefficients
balancedGrouped
Create a groupedData object from a matrix
collapse
Collapse According to Groups
Wheat2
Wheat Yield Trials
corExp
Exponential Correlation Structure
Variogram.default
Calculate Semi-variogram
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Soybean
Growth of soybean plants
bdf
Language scores
corAR1
AR(1) Correlation Structure
coef.gnls
Extract gnls Coefficients
comparePred
Compare Predictions
coef.corStruct
Coefficients of a corStruct Object
corFactor
Factor of a Correlation Matrix
coef.lmList
Extract lmList Coefficients
VarCorr
Extract variance and correlation components
coef.pdMat
pdMat Object Coefficients
Variogram
Calculate Semi-variogram
Spruce
Growth of Spruce Trees
coef.reStruct
reStruct Object Coefficients
collapse.groupedData
Collapse a groupedData Object
corClasses
Correlation Structure Classes
ergoStool
Ergometrics experiment with stool types
corARMA
ARMA(p,q) Correlation Structure
fdHess
Finite difference Hessian
corCompSymm
Compound Symmetry Correlation Structure
compareFits
Compare Fitted Objects
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
corMatrix.corStruct
Matrix of a corStruct Object
corCAR1
Continuous AR(1) Correlation Structure
Wafer
Modeling of Analog MOS Circuits
corSpher
Spherical Correlation Structure
corSymm
General Correlation Structure
formula.pdBlocked
Extract pdBlocked Formula
asOneFormula
Combine Formulas of a Set of Objects
fitted.lmList
Extract lmList Fitted Values
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
asTable
Convert groupedData to a matrix
formula.pdMat
Extract pdMat Formula
fitted.lme
Extract lme Fitted Values
fitted.lmeStruct
Calculate lmeStruct Fitted Values
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
formula.reStruct
Extract reStruct Object Formula
corFactor.corStruct
Factor of a corStruct Object Matrix
coef.lme
Extract lme Coefficients
getCovariate.data.frame
Extract Data Frame Covariate
gapply
Apply a Function by Groups
corGaus
Gaussian Correlation Structure
getGroups.gls
Extract gls Object Groups
getCovariate.varFunc
Extract varFunc Covariate
getGroups.lmList
Extract lmList Object Groups
coef.modelStruct
Extract modelStruct Object Coefficients
getResponseFormula
Extract Formula Specifying Response Variable
getVarCov
Extract variance-covariance matrix
corSpatial
Spatial Correlation Structure
corRatio
Rational Quadratic Correlation Structure
corLin
Linear Correlation Structure
fitted.glsStruct
Calculate glsStruct Fitted Values
corMatrix
Extract Correlation Matrix
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getCovariateFormula
Extract Covariates Formula
getCovariate
Extract Covariate from an Object
getGroupsFormula
Extract Grouping Formula
getData
Extract Data from an Object
getCovariate.corStruct
Extract corStruct Object Covariate
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
getResponse
Extract Response Variable from an Object
corNatural
General correlation in natural parameterization
getGroups.lme
Extract lme Object Groups
getGroups.varFunc
Extract varFunc Groups
glsStruct
Generalized Least Squares Structure
getGroups.corStruct
Extract corStruct Groups
gnls
Fit Nonlinear Model Using Generalized Least Squares
gls-internal
Auxiliary functions used by gls
getGroups.data.frame
Extract Groups from a Data Frame
gls
Fit Linear Model Using Generalized Least Squares
gsummary
Summarize by Groups
fixed.effects
Extract Fixed Effects
gnlsStruct
Generalized Nonlinear Least Squares Structure
fixef.lmList
Extract lmList Fixed Effects
intervals
Confidence Intervals on Coefficients
getData.gls
Extract gls Object Data
getData.lmList
Extract lmList Object Data
groupedData
Construct a groupedData Object
lme.groupedData
LME fit from groupedData Object
gnlsControl
Control Values for gnls Fit
lmList.groupedData
lmList Fit from a groupedData Object
gnlsObject
Fitted gnls Object
lme
Linear Mixed-Effects Models
lme.lmList
LME fit from lmList Object
intervals.gls
Confidence Intervals on gls Parameters
intervals.lme
Confidence Intervals on lme Parameters
getData.lme
Extract lme Object Data
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logLik.reStruct
Calculate reStruct Log-Likelihood
getGroups
Extract Grouping Factors from an Object
isBalanced
Check a Design for Balance
logLik.varFunc
Extract varFunc logLik
glsControl
Control Values for gls Fit
logLik.lmList
Log-Likelihood of an lmList Object
glsObject
Fitted gls Object
logDet.corStruct
Extract corStruct Log-Determinant
logDet.pdMat
Extract Log-Determinant from a pdMat Object
intervals.lmList
Confidence Intervals on lmList Coefficients
pairs.lme
Pairs Plot of an lme Object
pdClasses
Positive-Definite Matrix Classes
pdBlocked
Positive-Definite Block Diagonal Matrix
nlmeControl
Control Values for nlme Fit
model.matrix.reStruct
reStruct Model Matrix
nlme.nlsList
NLME fit from nlsList Object
logDet.reStruct
Extract reStruct Log-Determinants
lmeStruct
Linear Mixed-Effects Structure
pdConstruct
Construct pdMat Objects
needUpdate
Check if Update is Needed
isInitialized
Check if Object is Initialized
logDet
Extract the Logarithm of the Determinant
lmList
List of lm Objects with a Common Model
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
logLik.corStruct
Extract corStruct Log-Likelihood
nlmeStruct
Nonlinear Mixed-Effects Structure
phenoModel
Model function for the Phenobarb data
nlmeObject
Fitted nlme Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
update.varFunc
Update varFunc Object
predict.gnls
Predictions from a gnls Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
splitFormula
Split a Formula
pdSymm
General Positive-Definite Matrix
lmeControl
Specifying Control Values for lme Fit
plot.ACF
Plot an ACF Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
plot.nffGroupedData
Plot an nffGroupedData Object
random.effects
Extract Random Effects
predict.lmList
Predictions from an lmList Object
lmeObject
Fitted lme Object
logLik.gnls
Log-Likelihood of a gnls Object
nlme
Nonlinear Mixed-Effects Models
summary.corStruct
Summarize a corStruct Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
plot.lme
Plot an lme or nls object
recalc.modelStruct
Recalculate for a modelStruct Object
plot.Variogram
Plot a Variogram Object
pairs.compareFits
Pairs Plot of compareFits Object
plot.augPred
Plot an augPred Object
predict.gls
Predictions from a gls Object
recalc.corStruct
Recalculate for corStruct Object
logLik.lme
Log-Likelihood of an lme Object
pooledSD
Extract Pooled Standard Deviation
pairs.lmList
Pairs Plot of an lmList Object
recalc.reStruct
Recalculate for an reStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
recalc.varFunc
Recalculate for varFunc Object
varIdent
Constant Variance Function
summary.lme
Summarize an lme Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
quinModel
Model function for the Quinidine data
varPower
Power Variance Function
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
residuals.lmList
Extract lmList Residuals
varConstPower
Constant Plus Power Variance Function
pdConstruct.pdBlocked
Construct pdBlocked Objects
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
varClasses
Variance Function Classes
summary.nlsList
Summarize an nlsList Object
varComb
Combination of Variance Functions
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
summary.modelStruct
Summarize a modelStruct Object
nlsList
List of nls Objects with a Common Model
plot.gls
Plot a gls Object
varWeights
Extract Variance Function Weights
pdFactor
Square-Root Factor of a Positive-Definite Matrix
plot.compareFits
Plot a compareFits Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
nlsList.selfStart
nlsList Fit from a selfStart Function
plot.nmGroupedData
Plot an nmGroupedData Object
ranef.lme
Extract lme Random Effects
print.summary.pdMat
Print a summary.pdMat Object
pdDiag
Diagonal Positive-Definite Matrix
reStruct
Random Effects Structure
pdMat
Positive-Definite Matrix
print.varFunc
Print a varFunc Object
predict.lme
Predictions from an lme Object
ranef.lmList
Extract lmList Random Effects
varExp
Exponential Variance Function
plot.ranef.lme
Plot a ranef.lme Object
pdLogChol
General Positive-Definite Matrix
plot.nfnGroupedData
Plot an nfnGroupedData Object
residuals.lme
Extract lme Residuals
varFunc
Variance Function Structure
residuals.lmeStruct
Calculate lmeStruct Residuals
recalc
Recalculate Condensed Linear Model Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
plot.intervals.lmList
Plot lmList Confidence Intervals
predict.nlme
Predictions from an nlme Object
summary.pdMat
Summarize a pdMat Object
residuals.glsStruct
Calculate glsStruct Residuals
plot.ranef.lmList
Plot a ranef.lmList Object
residuals.gls
Extract gls Residuals
simulate.lme
Simulate Results from
lme
Models
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
update.modelStruct
Update a modelStruct Object
plot.lmList
Plot an lmList Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
summary.varFunc
Summarize varFunc Object
summary.lmList
Summarize an lmList Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
varFixed
Fixed Variance Function
solve.reStruct
Apply Solve to an reStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
Covariate.varFunc
Assign varFunc Covariate
Coef
Assign Values to Coefficients
Covariate
Assign Covariate Values