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nlme (version 3.1-117)
Linear and Nonlinear Mixed Effects Models
Description
Fit and compare Gaussian linear and nonlinear mixed-effects models.
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Install
install.packages('nlme')
Monthly Downloads
98,563
Version
3.1-117
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
March 31st, 2014
Functions in nlme (3.1-117)
Search functions
BodyWeight
Rat weight over time for different diets
Dim.corSpatial
Dimensions of a corSpatial Object
Coef
Assign Values to Coefficients
MathAchieve
Mathematics achievement scores
Dim
Extract Dimensions from an Object
PBG
Effect of Phenylbiguanide on Blood Pressure
Names.pdBlocked
Names of a pdBlocked Object
Glucose
Glucose levels over time
Tetracycline1
Pharmacokinetics of tetracycline
Matrix.reStruct
Assign reStruct Matrices
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
coef.pdMat
pdMat Object Coefficients
Wheat2
Wheat Yield Trials
Rail
Evaluation of Stress in Railway Rails
Covariate.varFunc
Assign varFunc Covariate
Dim.pdMat
Dimensions of a pdMat Object
Initialize
Initialize Object
Oats
Split-plot Experiment on Varieties of Oats
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Earthquake
Earthquake Intensity
asTable
Convert groupedData to a matrix
Names.pdMat
Names of a pdMat Object
compareFits
Compare Fitted Objects
ACF
Autocorrelation Function
Initialize.glsStruct
Initialize a glsStruct Object
Assay
Bioassay on Cell Culture Plate
Soybean
Growth of soybean plants
LDEsysMat
Generate system matrix for LDEs
Phenobarb
Phenobarbitol Kinetics
Gun
Methods for firing naval guns
Fatigue
Cracks caused by metal fatigue
Machines
Productivity Scores for Machines and Workers
IGF
Radioimmunoassay of IGF-I Protein
Meat
Tenderness of meat
Muscle
Contraction of heart muscle sections
Gasoline
Refinery yield of gasoline
getCovariate.data.frame
Extract Data Frame Covariate
Names.reStruct
Names of an reStruct Object
bdf
Language scores
corSpatial
Spatial Correlation Structure
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
corGaus
Gaussian Correlation Structure
Tetracycline2
Pharmacokinetics of tetracycline
corMatrix.corStruct
Matrix of a corStruct Object
coef.gnls
Extract gnls Coefficients
corSpher
Spherical Correlation Structure
getData.lme
Extract lme Object Data
Variogram
Calculate Semi-variogram
fixef.lmList
Extract lmList Fixed Effects
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
balancedGrouped
Create a groupedData object from a matrix
asOneFormula
Combine Formulas of a Set of Objects
Matrix
Assign Matrix Values
coef.modelStruct
Extract modelStruct Object Coefficients
Initialize.varFunc
Initialize varFunc Object
MathAchSchool
School demographic data for MathAchieve
getGroups.data.frame
Extract Groups from a Data Frame
Matrix.pdMat
Assign Matrix to a pdMat Object
corNatural
General correlation in natural parameterization
Spruce
Growth of Spruce Trees
Pixel
X-ray pixel intensities over time
ACF.gls
Autocorrelation Function for gls Residuals
collapse.groupedData
Collapse a groupedData Object
comparePred
Compare Predictions
Variogram.corExp
Calculate Semi-variogram for a corExp Object
gnlsControl
Control Values for gnls Fit
coef.lme
Extract lme Coefficients
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Oxboys
Heights of Boys in Oxford
getCovariate.varFunc
Extract varFunc Covariate
corFactor.corStruct
Factor of a corStruct Object Matrix
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
getData
Extract Data from an Object
getGroupsFormula
Extract Grouping Formula
Initialize.lmeStruct
Initialize an lmeStruct Object
glsObject
Fitted gls Object
lmeStruct
Linear Mixed-Effects Structure
anova.gls
Compare Likelihoods of Fitted Objects
Names
Names Associated with an Object
Ovary
Counts of Ovarian Follicles
formula.reStruct
Extract reStruct Object Formula
RatPupWeight
The weight of rat pups
Oxide
Variability in Semiconductor Manufacturing
Glucose2
Glucose Levels Following Alcohol Ingestion
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
Remifentanil
Pharmacokinetics of remifentanil
Variogram.corLin
Calculate Semi-variogram for a corLin Object
ACF.lme
Autocorrelation Function for lme Residuals
fdHess
Finite difference Hessian
Milk
Protein content of cows' milk
ergoStool
Ergometrics experiment with stool types
Nitrendipene
Assay of nitrendipene
plot.compareFits
Plot a compareFits Object
logDet.corStruct
Extract corStruct Log-Determinant
logLik.gnls
Log-Likelihood of a gnls Object
nlsList
List of nls Objects with a Common Model
logDet.pdMat
Extract Log-Determinant from a pdMat Object
nlsList.selfStart
nlsList Fit from a selfStart Function
getGroups
Extract Grouping Factors from an Object
Quinidine
Quinidine Kinetics
getResponseFormula
Extract Formula Specifying Response Variable
anova.lme
Compare Likelihoods of Fitted Objects
corAR1
AR(1) Correlation Structure
nlme
Nonlinear Mixed-Effects Models
logDet
Extract the Logarithm of the Determinant
summary.lme
Summarize an lme Object
Orthodont
Growth curve data on an orthdontic measurement
gapply
Apply a Function by Groups
Variogram.default
Calculate Semi-variogram
VarCorr
Extract variance and correlation components
logLik.glsStruct
Log-Likelihood of a glsStruct Object
groupedData
Construct a groupedData Object
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
getCovariate.corStruct
Extract corStruct Object Covariate
Wafer
Modeling of Analog MOS Circuits
pdConstruct
Construct pdMat Objects
coef.lmList
Extract lmList Coefficients
logLik.lmList
Log-Likelihood of an lmList Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
coef.reStruct
reStruct Object Coefficients
gsummary
Summarize by Groups
allCoef
Extract Coefficients from a Set of Objects
as.matrix.pdMat
Matrix of a pdMat Object
coef.corStruct
Coefficients of a corStruct Object
lmeObject
Fitted lme Object
augPred
Augmented Predictions
getCovariateFormula
Extract Covariates Formula
coef.varFunc
varFunc Object Coefficients
model.matrix.reStruct
reStruct Model Matrix
pdSymm
General Positive-Definite Matrix
pairs.lme
Pairs Plot of an lme Object
nlmeControl
Control Values for nlme Fit
lmeControl
Control Values for lme Fit
pooledSD
Extract Pooled Standard Deviation
getData.gls
Extract gls Object Data
pdClasses
Positive-Definite Matrix Classes
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
residuals.gls
Extract gls Residuals
plot.gls
Plot a gls Object
corRatio
Rational Quadratic Correlation Structure
Names.formula
Extract Names from a formula
logLik.varFunc
Extract varFunc logLik
logLik.reStruct
Calculate reStruct Log-Likelihood
varPower
Power Variance Function
corSymm
General Correlation Structure
corCAR1
Continuous AR(1) Correlation Structure
summary.corStruct
Summarize a corStruct Object
print.varFunc
Print a varFunc Object
splitFormula
Split a Formula
nlme.nlsList
NLME fit from nlsList Object
corFactor
Factor of a Correlation Matrix
fitted.lmList
Extract lmList Fitted Values
fitted.glsStruct
Calculate glsStruct Fitted Values
logDet.reStruct
Extract reStruct Log-Determinants
lme.lmList
LME fit from lmList Object
formula.pdBlocked
Extract pdBlocked Formula
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
recalc.modelStruct
Recalculate for a modelStruct Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
summary.nlsList
Summarize an nlsList Object
fitted.lme
Extract lme Fitted Values
getGroups.gls
Extract gls Object Groups
gnlsObject
Fitted gnls Object
logLik.lme
Log-Likelihood of an lme Object
reStruct
Random Effects Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
ranef.lmList
Extract lmList Random Effects
pairs.compareFits
Pairs Plot of compareFits Object
gls-internal
Auxiliary functions used by gls
ranef.lme
Extract lme Random Effects
varExp
Exponential Variance Function
getGroups.corStruct
Extract corStruct Groups
nlmeObject
Fitted nlme Object
plot.augPred
Plot an augPred Object
getCovariate
Extract Covariate from an Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
plot.ranef.lme
Plot a ranef.lme Object
predict.nlme
Predictions from an nlme Object
corMatrix
Extract Correlation Matrix
glsControl
Control Values for gls Fit
print.summary.pdMat
Print a summary.pdMat Object
intervals.lmList
Confidence Intervals on lmList Coefficients
Dialyzer
High-Flux Hemodialyzer
lme
Linear Mixed-Effects Models
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
predict.gls
Predictions from a gls Object
intervals
Confidence Intervals on Coefficients
glsStruct
Generalized Least Squares Structure
formula.pdMat
Extract pdMat Formula
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
recalc
Recalculate Condensed Linear Model Object
isBalanced
Check a Design for Balance
residuals.glsStruct
Calculate glsStruct Residuals
needUpdate
Check if Update is Needed
predict.gnls
Predictions from a gnls Object
getGroups.lmList
Extract lmList Object Groups
summary.varFunc
Summarize varFunc Object
varComb
Combination of Variance Functions
qqnorm.gls
Normal Plot of Residuals from a gls Object
logLik.corStruct
Extract corStruct Log-Likelihood
predict.lme
Predictions from an lme Object
getResponse
Extract Response Variable from an Object
varIdent
Constant Variance Function
getGroups.lme
Extract lme Object Groups
plot.ranef.lmList
Plot a ranef.lmList Object
quinModel
Model function for the Quinidine data
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pdMat
Positive-Definite Matrix
pdLogChol
General Positive-Definite Matrix
intervals.gls
Confidence Intervals on gls Parameters
collapse
Collapse According to Groups
corClasses
Correlation Structure Classes
recalc.varFunc
Recalculate for varFunc Object
plot.lmList
Plot an lmList Object
summary.gls
Summarize a gls Object
pdDiag
Diagonal Positive-Definite Matrix
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
plot.intervals.lmList
Plot lmList Confidence Intervals
random.effects
Extract Random Effects
varWeights.lmeStruct
Variance Weights for lmeStruct Object
plot.ACF
Plot an ACF Object
solve.reStruct
Apply Solve to an reStruct Object
varFunc
Variance Function Structure
residuals.lme
Extract lme Residuals
summary.modelStruct
Summarize a modelStruct Object
varConstPower
Constant Plus Power Variance Function
nlmeStruct
Nonlinear Mixed-Effects Structure
varClasses
Variance Function Classes
residuals.lmList
Extract lmList Residuals
residuals.gnlsStruct
Calculate gnlsStruct Residuals
plot.nmGroupedData
Plot an nmGroupedData Object
predict.lmList
Predictions from an lmList Object
phenoModel
Model function for the Phenobarb data
summary.pdMat
Summarize a pdMat Object
varFixed
Fixed Variance Function
residuals.nlmeStruct
Calculate nlmeStruct Residuals
varWeights
Extract Variance Function Weights
residuals.lmeStruct
Calculate lmeStruct Residuals
update.modelStruct
Update a modelStruct Object
gnlsStruct
Generalized Nonlinear Least Squares Structure
getData.lmList
Extract lmList Object Data
update.varFunc
Update varFunc Object
lmList
List of lm Objects with a Common Model
lme.groupedData
LME fit from groupedData Object
intervals.lme
Confidence Intervals on lme Parameters
getVarCov
Extract variance-covariance matrix
fixed.effects
Extract Fixed Effects
plot.Variogram
Plot a Variogram Object
plot.lme
Plot an lme or nls object
summary.lmList
Summarize an lmList Object
corARMA
ARMA(p,q) Correlation Structure
gls
Fit Linear Model Using Generalized Least Squares
Cefamandole
Pharmacokinetics of Cefamandole
recalc.reStruct
Recalculate for an reStruct Object
simulate.lme
Simulate Results from
lme
Models
corExp
Exponential Correlation Structure
Relaxin
Assay for Relaxin
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
recalc.corStruct
Recalculate for corStruct Object
lmList.groupedData
lmList Fit from a groupedData Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
isInitialized
Check if Object is Initialized
as.matrix.reStruct
Matrices of an reStruct Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
Wheat
Yields by growing conditions
Initialize.corStruct
Initialize corStruct Object
getGroups.varFunc
Extract varFunc Groups
corLin
Linear Correlation Structure
varWeights.glsStruct
Variance Weights for glsStruct Object
Covariate
Assign Covariate Values
corCompSymm
Compound Symmetry Correlation Structure
[.pdMat
Subscript a pdMat Object
pdBlocked
Positive-Definite Block Diagonal Matrix
plot.nffGroupedData
Plot an nffGroupedData Object
Dim.corStruct
Dimensions of a corStruct Object
Initialize.reStruct
Initialize reStruct Object
as.matrix.corStruct
Matrix of a corStruct Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pairs.lmList
Pairs Plot of an lmList Object