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nlme (version 3.1-150)
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
149,202
Version
3.1-150
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
October 24th, 2020
Functions in nlme (3.1-150)
Search all functions
Coef
Assign Values to Coefficients
BodyWeight
Rat weight over time for different diets
Cefamandole
Pharmacokinetics of Cefamandole
Covariate.varFunc
Assign varFunc Covariate
Assay
Bioassay on Cell Culture Plate
ACF
Autocorrelation Function
ACF.gls
Autocorrelation Function for gls Residuals
Covariate
Assign Covariate Values
ACF.lme
Autocorrelation Function for lme Residuals
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Dialyzer
High-Flux Hemodialyzer
[.pdMat
Subscript a pdMat Object
Muscle
Contraction of heart muscle sections
LDEsysMat
Generate system matrix for LDEs
Dim.corStruct
Dimensions of a corStruct Object
Initialize.varFunc
Initialize varFunc Object
Dim.corSpatial
Dimensions of a corSpatial Object
Names
Names Associated with an Object
Dim.pdMat
Dimensions of a pdMat Object
Fatigue
Cracks caused by metal fatigue
Glucose2
Glucose Levels Following Alcohol Ingestion
Initialize.corStruct
Initialize corStruct Object
Nitrendipene
Assay of nitrendipene
Oats
Split-plot Experiment on Varieties of Oats
MathAchieve
Mathematics achievement scores
PBG
Effect of Phenylbiguanide on Blood Pressure
Initialize.reStruct
Initialize reStruct Object
Earthquake
Earthquake Intensity
Initialize.lmeStruct
Initialize an lmeStruct Object
Meat
Tenderness of meat
Dim
Extract Dimensions from an Object
Gasoline
Refinery yield of gasoline
Glucose
Glucose levels over time
Phenobarb
Phenobarbitol Kinetics
Matrix
Assign Matrix Values
Orthodont
Growth curve data on an orthdontic measurement
Machines
Productivity Scores for Machines and Workers
Initialize.glsStruct
Initialize a glsStruct Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Milk
Protein content of cows' milk
Matrix.reStruct
Assign reStruct Matrices
Names.pdBlocked
Names of a pdBlocked Object
MathAchSchool
School demographic data for MathAchieve
Names.formula
Extract Names from a formula
Gun
Methods for firing naval guns
IGF
Radioimmunoassay of IGF-I Protein
Variogram.default
Calculate Semi-variogram
bdf
Language scores
Initialize
Initialize Object
coef.corStruct
Coefficients of a corStruct Object
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Names.pdMat
Names of a pdMat Object
Relaxin
Assay for Relaxin
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Ovary
Counts of Ovarian Follicles
Remifentanil
Pharmacokinetics of Remifentanil
Tetracycline1
Pharmacokinetics of tetracycline
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
Tetracycline2
Pharmacokinetics of tetracycline
Wheat
Yields by growing conditions
Names.reStruct
Names of an reStruct Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Wheat2
Wheat Yield Trials
Spruce
Growth of Spruce Trees
Oxide
Variability in Semiconductor Manufacturing
Oxboys
Heights of Boys in Oxford
Soybean
Growth of soybean plants
Wafer
Modeling of Analog MOS Circuits
RatPupWeight
The weight of rat pups
Rail
Evaluation of Stress in Railway Rails
coef.lme
Extract lme Coefficients
VarCorr
Extract variance and correlation components
corMatrix
Extract Correlation Matrix
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
Pixel
X-ray pixel intensities over time
coef.modelStruct
Extract modelStruct Object Coefficients
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Quinidine
Quinidine Kinetics
corLin
Linear Correlation Structure
Variogram
Calculate Semi-variogram
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
fixed.effects
Extract Fixed Effects
corNatural
General correlation in natural parameterization
asTable
Convert groupedData to a matrix
comparePred
Compare Predictions
asOneFormula
Combine Formulas of a Set of Objects
anova.lme
Compare Likelihoods of Fitted Objects
as.matrix.corStruct
Matrix of a corStruct Object
corAR1
AR(1) Correlation Structure
augPred
Augmented Predictions
allCoef
Extract Coefficients from a Set of Objects
corMatrix.corStruct
Matrix of a corStruct Object
coef.gnls
Extract gnls Coefficients
anova.gls
Compare Likelihoods of Fitted Objects
as.matrix.pdMat
Matrix of a pdMat Object
coef.varFunc
varFunc Object Coefficients
as.matrix.reStruct
Matrices of an reStruct Object
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
getData.gls
Extract gls Object Data
fixef.lmList
Extract lmList Fixed Effects
fitted.glsStruct
Calculate glsStruct Fitted Values
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getData.lmList
Extract lmList Object Data
balancedGrouped
Create a groupedData object from a matrix
corExp
Exponential Correlation Structure
corFactor
Factor of a Correlation Matrix
getData
Extract Data from an Object
getCovariateFormula
Extract Covariates Formula
collapse.groupedData
Collapse a groupedData Object
getGroups.corStruct
Extract corStruct Groups
gls-internal
Auxiliary functions used by gls
gls
Fit Linear Model Using Generalized Least Squares
getGroups.varFunc
Extract varFunc Groups
getGroups.lme
Extract lme Object Groups
coef.lmList
Extract lmList Coefficients
ergoStool
Ergometrics experiment with stool types
groupedData
Construct a groupedData Object
compareFits
Compare Fitted Objects
gnlsStruct
Generalized Nonlinear Least Squares Structure
coef.reStruct
reStruct Object Coefficients
getGroups.data.frame
Extract Groups from a Data Frame
corCompSymm
Compound Symmetry Correlation Structure
coef.pdMat
pdMat Object Coefficients
corClasses
Correlation Structure Classes
corFactor.corStruct
Factor of a corStruct Object Matrix
lme.groupedData
LME fit from groupedData Object
corRatio
Rational Quadratic Correlation Structure
corSpatial
Spatial Correlation Structure
corGaus
Gaussian Correlation Structure
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
lme.lmList
LME fit from lmList Object
fdHess
Finite difference Hessian
formula.reStruct
Extract reStruct Object Formula
formula.pdBlocked
Extract pdBlocked Formula
fitted.lmeStruct
Calculate lmeStruct Fitted Values
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
gapply
Apply a Function by Groups
gnlsControl
Control Values for gnls Fit
getResponseFormula
Extract Formula Specifying Response Variable
getVarCov
Extract variance-covariance matrix
corSpher
Spherical Correlation Structure
corSymm
General Correlation Structure
getGroups.gls
Extract gls Object Groups
getCovariate.data.frame
Extract Data Frame Covariate
getGroups.lmList
Extract lmList Object Groups
fitted.lme
Extract lme Fitted Values
getCovariate.varFunc
Extract varFunc Covariate
formula.pdMat
Extract pdMat Formula
fitted.lmList
Extract lmList Fitted Values
getCovariate
Extract Covariate from an Object
corARMA
ARMA(p,q) Correlation Structure
getCovariate.corStruct
Extract corStruct Object Covariate
logLik.lmList
Log-Likelihood of an lmList Object
gnlsObject
Fitted gnls Object
intervals
Confidence Intervals on Coefficients
nlme.nlsList
NLME fit from nlsList Object
glsControl
Control Values for gls Fit
gsummary
Summarize by Groups
corCAR1
Continuous AR(1) Correlation Structure
lmList.groupedData
lmList Fit from a groupedData Object
logDet
Extract the Logarithm of the Determinant
lmeStruct
Linear Mixed-Effects Structure
nlmeControl
Control Values for nlme Fit
glsObject
Fitted gls Object
pairs.lme
Pairs Plot of an lme Object
nlsList
List of nls Objects with a Common Model
logDet.reStruct
Extract reStruct Log-Determinants
nlsList.selfStart
nlsList Fit from a selfStart Function
logLik.corStruct
Extract corStruct Log-Likelihood
pdDiag
Diagonal Positive-Definite Matrix
getResponse
Extract Response Variable from an Object
getGroupsFormula
Extract Grouping Formula
glsStruct
Generalized Least Squares Structure
pdBlocked
Positive-Definite Block Diagonal Matrix
lme
Linear Mixed-Effects Models
getData.lme
Extract lme Object Data
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
intervals.lme
Confidence Intervals on lme Parameters
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.lme
Log-Likelihood of an lme Object
gnls
Fit Nonlinear Model Using Generalized Least Squares
predict.gnls
Predictions from a gnls Object
pairs.compareFits
Pairs Plot of compareFits Object
plot.intervals.lmList
Plot lmList Confidence Intervals
plot.lmList
Plot an lmList Object
pdNatural
General Positive-Definite Matrix in Natural Parametrization
needUpdate
Check if Update is Needed
model.matrix.reStruct
reStruct Model Matrix
isBalanced
Check a Design for Balance
quinModel
Model function for the Quinidine data
predict.lmList
Predictions from an lmList Object
pdSymm
General Positive-Definite Matrix
isInitialized
Check if Object is Initialized
lmeControl
Specifying Control Values for lme Fit
lmList
List of lm Objects with a Common Model
getGroups
Extract Grouping Factors from an Object
intervals.lmList
Confidence Intervals on lmList Coefficients
random.effects
Extract Random Effects
lmeObject
Fitted lme Object
intervals.gls
Confidence Intervals on gls Parameters
logLik.reStruct
Calculate reStruct Log-Likelihood
logLik.varFunc
Extract varFunc logLik
plot.ranef.lmList
Plot a ranef.lmList Object
pairs.lmList
Pairs Plot of an lmList Object
pdLogChol
General Positive-Definite Matrix
pdMat
Positive-Definite Matrix
recalc
Recalculate Condensed Linear Model Object
plot.ranef.lme
Plot a ranef.lme Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
reStruct
Random Effects Structure
plot.lme
Plot an lme or nls object
summary.lme
Summarize an lme Object
plot.nffGroupedData
Plot an nffGroupedData Object
predict.lme
Predictions from an lme Object
summary.modelStruct
Summarize a modelStruct Object
logDet.corStruct
Extract corStruct Log-Determinant
residuals.lmList
Extract lmList Residuals
plot.ACF
Plot an ACF Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
phenoModel
Model function for the Phenobarb data
summary.corStruct
Summarize a corStruct Object
splitFormula
Split a Formula
nlme
Nonlinear Mixed-Effects Models
pdConstruct.pdBlocked
Construct pdBlocked Objects
varComb
Combination of Variance Functions
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
varConstPower
Constant Plus Power Variance Function
pdConstruct
Construct pdMat Objects
logLik.glsStruct
Log-Likelihood of a glsStruct Object
update.varFunc
Update varFunc Object
varClasses
Variance Function Classes
varWeights.glsStruct
Variance Weights for glsStruct Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
plot.Variogram
Plot a Variogram Object
nlmeObject
Fitted nlme Object
logLik.gnls
Log-Likelihood of a gnls Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
nlmeStruct
Nonlinear Mixed-Effects Structure
residuals.nlmeStruct
Calculate nlmeStruct Residuals
predict.nlme
Predictions from an nlme Object
plot.nmGroupedData
Plot an nmGroupedData Object
pdClasses
Positive-Definite Matrix Classes
plot.augPred
Plot an augPred Object
simulate.lme
Simulate Results from
lme
Models
print.summary.pdMat
Print a summary.pdMat Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
residuals.lme
Extract lme Residuals
pooledSD
Extract Pooled Standard Deviation
predict.gls
Predictions from a gls Object
residuals.lmeStruct
Calculate lmeStruct Residuals
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
ranef.lmList
Extract lmList Random Effects
print.varFunc
Print a varFunc Object
solve.reStruct
Apply Solve to an reStruct Object
varFunc
Variance Function Structure
summary.pdMat
Summarize a pdMat Object
varIdent
Constant Variance Function
pdIdent
Multiple of the Identity Positive-Definite Matrix
recalc.corStruct
Recalculate for corStruct Object
plot.gls
Plot a gls Object
summary.nlsList
Summarize an nlsList Object
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
plot.compareFits
Plot a compareFits Object
summary.varFunc
Summarize varFunc Object
recalc.reStruct
Recalculate for an reStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
ranef.lme
Extract lme Random Effects
update.modelStruct
Update a modelStruct Object
recalc.varFunc
Recalculate for varFunc Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
summary.lmList
Summarize an lmList Object
varExp
Exponential Variance Function
residuals.gls
Extract gls Residuals
residuals.glsStruct
Calculate glsStruct Residuals
varFixed
Fixed Variance Function
varPower
Power Variance Function
varWeights
Extract Variance Function Weights
collapse
Collapse According to Groups