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nlme (version 3.1-140)
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
3.1-140
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
May 12th, 2019
Functions in nlme (3.1-140)
Search functions
Assay
Bioassay on Cell Culture Plate
ACF.gls
Autocorrelation Function for gls Residuals
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
ACF.lme
Autocorrelation Function for lme Residuals
IGF
Radioimmunoassay of IGF-I Protein
Dialyzer
High-Flux Hemodialyzer
BodyWeight
Rat weight over time for different diets
[.pdMat
Subscript a pdMat Object
Initialize
Initialize Object
Covariate
Assign Covariate Values
Fatigue
Cracks caused by metal fatigue
Dim
Extract Dimensions from an Object
Meat
Tenderness of meat
Covariate.varFunc
Assign varFunc Covariate
Gasoline
Refinery yield of gasoline
Milk
Protein content of cows' milk
Oxboys
Heights of Boys in Oxford
Pixel
X-ray pixel intensities over time
Quinidine
Quinidine Kinetics
bdf
Language scores
Glucose2
Glucose Levels Following Alcohol Ingestion
Oxide
Variability in Semiconductor Manufacturing
Tetracycline1
Pharmacokinetics of tetracycline
Cefamandole
Pharmacokinetics of Cefamandole
Gun
Methods for firing naval guns
Coef
Assign Values to Coefficients
Muscle
Contraction of heart muscle sections
Glucose
Glucose levels over time
coef.corStruct
Coefficients of a corStruct Object
Initialize.corStruct
Initialize corStruct Object
collapse.groupedData
Collapse a groupedData Object
compareFits
Compare Fitted Objects
Orthodont
Growth curve data on an orthdontic measurement
Ovary
Counts of Ovarian Follicles
Names
Names Associated with an Object
Rail
Evaluation of Stress in Railway Rails
RatPupWeight
The weight of rat pups
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Tetracycline2
Pharmacokinetics of tetracycline
corLin
Linear Correlation Structure
corMatrix
Extract Correlation Matrix
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
anova.lme
Compare Likelihoods of Fitted Objects
Variogram.default
Calculate Semi-variogram
Dim.pdMat
Dimensions of a pdMat Object
Earthquake
Earthquake Intensity
corSymm
General Correlation Structure
corSpher
Spherical Correlation Structure
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Initialize.varFunc
Initialize varFunc Object
Dim.corSpatial
Dimensions of a corSpatial Object
LDEsysMat
Generate system matrix for LDEs
Dim.corStruct
Dimensions of a corStruct Object
MathAchieve
Mathematics achievement scores
formula.pdMat
Extract pdMat Formula
formula.pdBlocked
Extract pdBlocked Formula
getCovariate.data.frame
Extract Data Frame Covariate
getCovariate.varFunc
Extract varFunc Covariate
Initialize.glsStruct
Initialize a glsStruct Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Initialize.lmeStruct
Initialize an lmeStruct Object
asOneFormula
Combine Formulas of a Set of Objects
gls-internal
Auxiliary functions used by gls
asTable
Convert groupedData to a matrix
coef.pdMat
pdMat Object Coefficients
as.matrix.corStruct
Matrix of a corStruct Object
balancedGrouped
Create a groupedData object from a matrix
coef.reStruct
reStruct Object Coefficients
augPred
Augmented Predictions
corExp
Exponential Correlation Structure
Matrix
Assign Matrix Values
corFactor
Factor of a Correlation Matrix
gls
Fit Linear Model Using Generalized Least Squares
Matrix.reStruct
Assign reStruct Matrices
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
coef.lme
Extract lme Coefficients
Names.pdMat
Names of a pdMat Object
Nitrendipene
Assay of nitrendipene
Relaxin
Assay for Relaxin
Oats
Split-plot Experiment on Varieties of Oats
corNatural
General correlation in natural parameterization
intervals.gls
Confidence Intervals on gls Parameters
intervals.lmList
Confidence Intervals on lmList Coefficients
Names.reStruct
Names of an reStruct Object
Remifentanil
Pharmacokinetics of remifentanil
fitted.lmList
Extract lmList Fitted Values
Initialize.reStruct
Initialize reStruct Object
Soybean
Growth of soybean plants
Spruce
Growth of Spruce Trees
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Machines
Productivity Scores for Machines and Workers
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
coef.modelStruct
Extract modelStruct Object Coefficients
fitted.lme
Extract lme Fitted Values
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
MathAchSchool
School demographic data for MathAchieve
getCovariate
Extract Covariate from an Object
logLik.lmList
Log-Likelihood of an lmList Object
nlmeObject
Fitted nlme Object
Wheat
Yields by growing conditions
getCovariate.corStruct
Extract corStruct Object Covariate
nlmeStruct
Nonlinear Mixed-Effects Structure
Names.formula
Extract Names from a formula
getGroups.lme
Extract lme Object Groups
Wheat2
Wheat Yield Trials
getGroups.varFunc
Extract varFunc Groups
allCoef
Extract Coefficients from a Set of Objects
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Names.pdBlocked
Names of a pdBlocked Object
anova.gls
Compare Likelihoods of Fitted Objects
coef.gnls
Extract gnls Coefficients
coef.varFunc
varFunc Object Coefficients
glsControl
Control Values for gls Fit
collapse
Collapse According to Groups
PBG
Effect of Phenylbiguanide on Blood Pressure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
coef.lmList
Extract lmList Coefficients
pairs.compareFits
Pairs Plot of compareFits Object
corClasses
Correlation Structure Classes
pairs.lmList
Pairs Plot of an lmList Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
corARMA
ARMA(p,q) Correlation Structure
corCAR1
Continuous AR(1) Correlation Structure
corMatrix.corStruct
Matrix of a corStruct Object
plot.intervals.lmList
Plot lmList Confidence Intervals
getCovariateFormula
Extract Covariates Formula
corCompSymm
Compound Symmetry Correlation Structure
glsObject
Fitted gls Object
plot.lmList
Plot an lmList Object
predict.lme
Predictions from an lme Object
intervals.lme
Confidence Intervals on lme Parameters
isBalanced
Check a Design for Balance
lmeControl
Specifying Control Values for lme Fit
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getData
Extract Data from an Object
getData.gls
Extract gls Object Data
Phenobarb
Phenobarbitol Kinetics
ergoStool
Ergometrics experiment with stool types
getGroups.corStruct
Extract corStruct Groups
lmeObject
Fitted lme Object
getData.lmList
Extract lmList Object Data
getGroups.data.frame
Extract Groups from a Data Frame
fdHess
Finite difference Hessian
VarCorr
Extract variance and correlation components
gnlsControl
Control Values for gnls Fit
predict.nlme
Predictions from an nlme Object
nlme.nlsList
NLME fit from nlsList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
nlmeControl
Control Values for nlme Fit
pdClasses
Positive-Definite Matrix Classes
fixed.effects
Extract Fixed Effects
getData.lme
Extract lme Object Data
qqnorm.gls
Normal Plot of Residuals from a gls Object
Variogram
Calculate Semi-variogram
getGroups
Extract Grouping Factors from an Object
glsStruct
Generalized Least Squares Structure
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
print.summary.pdMat
Print a summary.pdMat Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
fixef.lmList
Extract lmList Fixed Effects
Wafer
Modeling of Analog MOS Circuits
getGroupsFormula
Extract Grouping Formula
print.varFunc
Print a varFunc Object
as.matrix.pdMat
Matrix of a pdMat Object
reStruct
Random Effects Structure
residuals.lmList
Extract lmList Residuals
gsummary
Summarize by Groups
as.matrix.reStruct
Matrices of an reStruct Object
gnlsObject
Fitted gnls Object
isInitialized
Check if Object is Initialized
comparePred
Compare Predictions
getResponse
Extract Response Variable from an Object
lmList
List of lm Objects with a Common Model
solve.reStruct
Apply Solve to an reStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
varFunc
Variance Function Structure
varIdent
Constant Variance Function
logDet.corStruct
Extract corStruct Log-Determinant
lmList.groupedData
lmList Fit from a groupedData Object
intervals
Confidence Intervals on Coefficients
lme.groupedData
LME fit from groupedData Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logLik.reStruct
Calculate reStruct Log-Likelihood
logLik.gnls
Log-Likelihood of a gnls Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
lme
Linear Mixed-Effects Models
lme.lmList
LME fit from lmList Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
pdConstruct
Construct pdMat Objects
logLik.varFunc
Extract varFunc logLik
recalc
Recalculate Condensed Linear Model Object
corAR1
AR(1) Correlation Structure
pdConstruct.pdBlocked
Construct pdBlocked Objects
corGaus
Gaussian Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
nlme
Nonlinear Mixed-Effects Models
pdNatural
General Positive-Definite Matrix in Natural Parametrization
varComb
Combination of Variance Functions
logLik.lme
Log-Likelihood of an lme Object
pdSymm
General Positive-Definite Matrix
pairs.lme
Pairs Plot of an lme Object
corRatio
Rational Quadratic Correlation Structure
pdBlocked
Positive-Definite Block Diagonal Matrix
varConstPower
Constant Plus Power Variance Function
plot.lme
Plot an lme or nls object
phenoModel
Model function for the Phenobarb data
plot.ACF
Plot an ACF Object
plot.nffGroupedData
Plot an nffGroupedData Object
plot.compareFits
Plot a compareFits Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
plot.gls
Plot a gls Object
plot.ranef.lmList
Plot a ranef.lmList Object
ranef.lmList
Extract lmList Random Effects
ranef.lme
Extract lme Random Effects
plot.ranef.lme
Plot a ranef.lme Object
residuals.lme
Extract lme Residuals
corSpatial
Spatial Correlation Structure
nlsList
List of nls Objects with a Common Model
residuals.lmeStruct
Calculate lmeStruct Residuals
summary.nlsList
Summarize an nlsList Object
fitted.glsStruct
Calculate glsStruct Fitted Values
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
formula.reStruct
Extract reStruct Object Formula
summary.pdMat
Summarize a pdMat Object
gapply
Apply a Function by Groups
varPower
Power Variance Function
getGroups.gls
Extract gls Object Groups
getGroups.lmList
Extract lmList Object Groups
varWeights
Extract Variance Function Weights
residuals.nlmeStruct
Calculate nlmeStruct Residuals
nlsList.selfStart
nlsList Fit from a selfStart Function
getResponseFormula
Extract Formula Specifying Response Variable
getVarCov
Extract variance-covariance matrix
gnlsStruct
Generalized Nonlinear Least Squares Structure
pdDiag
Diagonal Positive-Definite Matrix
simulate.lme
Simulate Results from
lme
Models
pdFactor
Square-Root Factor of a Positive-Definite Matrix
groupedData
Construct a groupedData Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
summary.lmList
Summarize an lmList Object
update.varFunc
Update varFunc Object
varClasses
Variance Function Classes
pdLogChol
General Positive-Definite Matrix
lmeStruct
Linear Mixed-Effects Structure
logDet
Extract the Logarithm of the Determinant
pdMat
Positive-Definite Matrix
logDet.reStruct
Extract reStruct Log-Determinants
logLik.corStruct
Extract corStruct Log-Likelihood
model.matrix.reStruct
reStruct Model Matrix
needUpdate
Check if Update is Needed
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
plot.Variogram
Plot a Variogram Object
plot.nmGroupedData
Plot an nmGroupedData Object
pooledSD
Extract Pooled Standard Deviation
plot.augPred
Plot an augPred Object
predict.gls
Predictions from a gls Object
predict.gnls
Predictions from a gnls Object
recalc.corStruct
Recalculate for corStruct Object
predict.lmList
Predictions from an lmList Object
recalc.modelStruct
Recalculate for a modelStruct Object
recalc.reStruct
Recalculate for an reStruct Object
recalc.varFunc
Recalculate for varFunc Object
splitFormula
Split a Formula
quinModel
Model function for the Quinidine data
summary.corStruct
Summarize a corStruct Object
summary.varFunc
Summarize varFunc Object
update.modelStruct
Update a modelStruct Object
random.effects
Extract Random Effects
residuals.gls
Extract gls Residuals
varWeights.glsStruct
Variance Weights for glsStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
residuals.glsStruct
Calculate glsStruct Residuals
summary.lme
Summarize an lme Object
summary.modelStruct
Summarize a modelStruct Object
varExp
Exponential Variance Function
varFixed
Fixed Variance Function
ACF
Autocorrelation Function