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nlme (version 3.1-157)
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
124,627
Version
3.1-157
License
GPL (>= 2)
Maintainer
R-core R-core@R-project.org
Last Published
March 25th, 2022
Functions in nlme (3.1-157)
Search functions
[.pdMat
Subscript a pdMat Object
Ovary
Counts of Ovarian Follicles
Covariate
Assign Covariate Values
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Matrix.reStruct
Assign reStruct Matrices
Fatigue
Cracks caused by metal fatigue
Initialize.corStruct
Initialize corStruct Object
Orthodont
Growth curve data on an orthdontic measurement
Initialize.glsStruct
Initialize a glsStruct Object
VarCorr
Extract variance and correlation components
Phenobarb
Phenobarbitol Kinetics
PBG
Effect of Phenylbiguanide on Blood Pressure
Dim
Extract Dimensions from an Object
Initialize.reStruct
Initialize reStruct Object
Gasoline
Refinery yield of gasoline
corExp
Exponential Correlation Structure
Variogram
Calculate Semi-variogram
coef.pdMat
pdMat Object Coefficients
corLin
Linear Correlation Structure
bdf
Language scores
ACF.gls
Autocorrelation Function for gls Residuals
corFactor
Factor of a Correlation Matrix
Glucose
Glucose levels over time
coef.reStruct
reStruct Object Coefficients
corMatrix
Extract Correlation Matrix
anova.lme
Compare Likelihoods of Fitted Objects
Dialyzer
High-Flux Hemodialyzer
nlmeControl
Control Values for nlme Fit
Machines
Productivity Scores for Machines and Workers
ACF
Autocorrelation Function
Names.reStruct
Names of an reStruct Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
fixed.effects
Extract Fixed Effects
corNatural
General correlation in natural parameterization
MathAchieve
Mathematics achievement scores
fixef.lmList
Extract lmList Fixed Effects
varFunc
Variance Function Structure
Coef
Assign Values to Coefficients
getCovariate
Extract Covariate from an Object
pdDiag
Diagonal Positive-Definite Matrix
lme.groupedData
LME fit from groupedData Object
Matrix
Assign Matrix Values
corAR1
AR(1) Correlation Structure
logLik.reStruct
Calculate reStruct Log-Likelihood
corRatio
Rational Quadratic Correlation Structure
getCovariate.corStruct
Extract corStruct Object Covariate
Assay
Bioassay on Cell Culture Plate
Initialize.lmeStruct
Initialize an lmeStruct Object
pairs.compareFits
Pairs Plot of compareFits Object
getResponseFormula
Extract Formula Specifying Response Variable
getVarCov
Extract variance-covariance matrix
ergoStool
Ergometrics experiment with stool types
gnlsStruct
Generalized Nonlinear Least Squares Structure
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Remifentanil
Pharmacokinetics of Remifentanil
corClasses
Correlation Structure Classes
isBalanced
Check a Design for Balance
BodyWeight
Rat weight over time for different diets
Glucose2
Glucose Levels Following Alcohol Ingestion
gsummary
Summarize by Groups
glsStruct
Generalized Least Squares Structure
lme.lmList
LME fit from lmList Object
Nitrendipene
Assay of nitrendipene
corSpher
Spherical Correlation Structure
getGroupsFormula
Extract Grouping Formula
Milk
Protein content of cows' milk
plot.compareFits
Plot a compareFits Object
intervals
Confidence Intervals on Coefficients
Oats
Split-plot Experiment on Varieties of Oats
Meat
Tenderness of meat
logLik.varFunc
Extract varFunc logLik
fitted.lmList
Extract lmList Fitted Values
as.matrix.corStruct
Matrix of a corStruct Object
getGroups.lmList
Extract lmList Object Groups
pairs.lmList
Pairs Plot of an lmList Object
nlme.nlsList
NLME fit from nlsList Object
lmeStruct
Linear Mixed-Effects Structure
gnls
Fit Nonlinear Model Using Generalized Least Squares
coef.corStruct
Coefficients of a corStruct Object
ranef.lme
Extract lme Random Effects
ranef.lmList
Extract lmList Random Effects
Rail
Evaluation of Stress in Railway Rails
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Gun
Methods for firing naval guns
Dim.corSpatial
Dimensions of a corSpatial Object
Dim.pdMat
Dimensions of a pdMat Object
predict.gls
Predictions from a gls Object
pooledSD
Extract Pooled Standard Deviation
plot.gls
Plot a gls Object
lmeObject
Fitted lme Object
Dim.corStruct
Dimensions of a corStruct Object
asOneFormula
Combine Formulas of a Set of Objects
summary.gls
Summarize a Generalized Least Squares
gls
Object
balancedGrouped
Create a groupedData object from a matrix
RatPupWeight
The weight of rat pups
residuals.gls
Extract gls Residuals
lmList
List of lm Objects with a Common Model
getResponse
Extract Response Variable from an Object
getCovariate.data.frame
Extract Data Frame Covariate
IGF
Radioimmunoassay of IGF-I Protein
Tetracycline2
Pharmacokinetics of tetracycline
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
logDet.reStruct
Extract reStruct Log-Determinants
corSymm
General Correlation Structure
Soybean
Growth of soybean plants
Muscle
Contraction of heart muscle sections
fitted.lme
Extract lme Fitted Values
nlsList
List of nls Objects with a Common Model
Wheat
Yields by growing conditions
summary.lmList
Summarize an lmList Object
residuals.glsStruct
Calculate glsStruct Residuals
Names.pdMat
Names of a pdMat Object
Wheat2
Wheat Yield Trials
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Relaxin
Assay for Relaxin
predict.gnls
Predictions from a gnls Object
coef.modelStruct
Extract modelStruct Object Coefficients
gnlsControl
Control Values for gnls Fit
corGaus
Gaussian Correlation Structure
Initialize
Initialize Object
logLik.corStruct
Extract corStruct Log-Likelihood
anova.gls
Compare Likelihoods of Fitted Objects
varFixed
Fixed Variance Function
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
isInitialized
Check if Object is Initialized
as.matrix.pdMat
Matrix of a pdMat Object
getCovariate.varFunc
Extract varFunc Covariate
Cefamandole
Pharmacokinetics of Cefamandole
asTable
Convert groupedData to a matrix
nlsList.selfStart
nlsList Fit from a selfStart Function
augPred
Augmented Predictions
allCoef
Extract Coefficients from a Set of Objects
corCompSymm
Compound Symmetry Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
predict.lme
Predictions from an lme Object
varWeights
Extract Variance Function Weights
plot.intervals.lmList
Plot lmList Confidence Intervals
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
plot.lmList
Plot an lmList Object
predict.nlme
Predictions from an nlme Object
logDet
Extract the Logarithm of the Determinant
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
reStruct
Random Effects Structure
Names
Names Associated with an Object
Names.pdBlocked
Names of a pdBlocked Object
getGroups.gls
Extract gls Object Groups
recalc
Recalculate Condensed Linear Model Object
Oxboys
Heights of Boys in Oxford
Tetracycline1
Pharmacokinetics of tetracycline
formula.reStruct
Extract reStruct Object Formula
getGroups.data.frame
Extract Groups from a Data Frame
as.matrix.reStruct
Matrices of an reStruct Object
Names.formula
Extract Names from a formula
summary.varFunc
Summarize "varFunc" Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
coef.lme
Extract lme Coefficients
corMatrix.corStruct
Matrix of a corStruct Object
compareFits
Compare Fitted Objects
Variogram.default
Calculate Semi-variogram
fitted.lmeStruct
Calculate lmeStruct Fitted Values
Spruce
Growth of Spruce Trees
print.varFunc
Print a varFunc Object
comparePred
Compare Predictions
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
solve.reStruct
Apply Solve to an reStruct Object
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
formula.pdBlocked
Extract pdBlocked Formula
formula.pdMat
Extract pdMat Formula
update.modelStruct
Update a modelStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
groupedData
Construct a groupedData Object
getGroups.corStruct
Extract corStruct Groups
Earthquake
Earthquake Intensity
intervals.gls
Confidence Intervals on gls Parameters
getGroups
Extract Grouping Factors from an Object
getData.lme
Extract lme Object Data
pdConstruct.pdBlocked
Construct pdBlocked Objects
lmeControl
Specifying Control Values for lme Fit
gnlsObject
Fitted gnls Object
intervals.lme
Confidence Intervals on lme Parameters
Wafer
Modeling of Analog MOS Circuits
logLik.lme
Log-Likelihood of an lme Object
collapse.groupedData
Collapse a groupedData Object
gapply
Apply a Function by Groups
ACF.lme
Autocorrelation Function for lme Residuals
pairs.lme
Pairs Plot of an lme Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
LDEsysMat
Generate system matrix for LDEs
Initialize.varFunc
Initialize varFunc Object
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
model.matrix.reStruct
reStruct Model Matrix
getCovariateFormula
Extract Covariates Formula
pdMat
Positive-Definite Matrix
MathAchSchool
School demographic data for MathAchieve
corSpatial
Spatial Correlation Structure
gls-internal
Auxiliary functions used by gls
getData
Extract Data from an Object
logDet.corStruct
Extract corStruct Log-Determinant
residuals.lme
Extract lme Residuals
summary.modelStruct
Summarize a modelStruct Object
plot.ranef.lme
Plot a ranef.lme Object
plot.ACF
Plot an ACF Object
pdConstruct
Construct pdMat Objects
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
plot.nmGroupedData
Plot an nmGroupedData Object
simulate.lme
Simulate Results from
lme
Models
random.effects
Extract Random Effects
phenoModel
Model function for the Phenobarb data
plot.ranef.lmList
Plot a ranef.lmList Object
gls
Fit Linear Model Using Generalized Least Squares
nlmeObject
Fitted nlme Object
Pixel
X-ray pixel intensities over time
coef.varFunc
varFunc Object Coefficients
summary.nlsList
Summarize an nlsList Object
predict.lmList
Predictions from an lmList Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
Oxide
Variability in Semiconductor Manufacturing
nlmeStruct
Nonlinear Mixed-Effects Structure
pdLogChol
General Positive-Definite Matrix
print.summary.pdMat
Print a summary.pdMat Object
pdBlocked
Positive-Definite Block Diagonal Matrix
intervals.lmList
Confidence Intervals on lmList Coefficients
fdHess
Finite difference Hessian
needUpdate
Check if Update is Needed
Variogram.corExp
Calculate Semi-variogram for a corExp Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
quinModel
Model function for the Quinidine data
plot.nfnGroupedData
Plot an nfnGroupedData Object
logLik.lmList
Log-Likelihood of an lmList Object
Quinidine
Quinidine Kinetics
coef.lmList
Extract lmList Coefficients
pdNatural
General Positive-Definite Matrix in Natural Parametrization
corARMA
ARMA(p,q) Correlation Structure
coef.gnls
Extract gnls Coefficients
getData.lmList
Extract lmList Object Data
collapse
Collapse According to Groups
residuals.gnlsStruct
Calculate gnlsStruct Residuals
pdFactor
Square-Root Factor of a Positive-Definite Matrix
lme
Linear Mixed-Effects Models
plot.nffGroupedData
Plot an nffGroupedData Object
plot.lme
Plot an lme or nls object
pdSymm
General Positive-Definite Matrix
residuals.lmeStruct
Calculate lmeStruct Residuals
summary.lme
Summarize an lme Object
recalc.modelStruct
Recalculate for a modelStruct Object
summary.pdMat
Summarize a pdMat Object
fitted.glsStruct
Calculate glsStruct Fitted Values
update.varFunc
Update varFunc Object
recalc.corStruct
Recalculate for corStruct Object
varClasses
Variance Function Classes
residuals.lmList
Extract lmList Residuals
plot.Variogram
Plot a Variogram Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
logLik.glsStruct
Log-Likelihood of a glsStruct Object
corCAR1
Continuous AR(1) Correlation Structure
getGroups.varFunc
Extract varFunc Groups
lmList.groupedData
lmList Fit from a groupedData Object
glsControl
Control Values for gls Fit
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getData.gls
Extract gls Object Data
varExp
Exponential Variance Function
varConstProp
Constant Plus Proportion Variance Function
pdClasses
Positive-Definite Matrix Classes
getGroups.lme
Extract lme Object Groups
qqnorm.gls
Normal Plot of Residuals from a gls Object
glsObject
Fitted gls Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
logLik.gnls
Log-Likelihood of a gnls Object
summary.corStruct
Summarize a corStruct Object
nlme
Nonlinear Mixed-Effects Models
pdIdent
Multiple of the Identity Positive-Definite Matrix
plot.augPred
Plot an augPred Object
recalc.varFunc
Recalculate for varFunc Object
recalc.reStruct
Recalculate for an reStruct Object
varIdent
Constant Variance Function
varComb
Combination of Variance Functions
splitFormula
Split a Formula
varConstPower
Constant Plus Power Variance Function
varPower
Power Variance Function
Covariate.varFunc
Assign varFunc Covariate