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nlme (version 3.1-148)
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
85,005
Version
3.1-148
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
May 24th, 2020
Functions in nlme (3.1-148)
Search all functions
Glucose
Glucose levels over time
Assay
Bioassay on Cell Culture Plate
BodyWeight
Rat weight over time for different diets
Gasoline
Refinery yield of gasoline
Initialize.varFunc
Initialize varFunc Object
Glucose2
Glucose Levels Following Alcohol Ingestion
Dim.pdMat
Dimensions of a pdMat Object
Coef
Assign Values to Coefficients
Earthquake
Earthquake Intensity
Gun
Methods for firing naval guns
Cefamandole
Pharmacokinetics of Cefamandole
Matrix.reStruct
Assign reStruct Matrices
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
LDEsysMat
Generate system matrix for LDEs
PBG
Effect of Phenylbiguanide on Blood Pressure
Covariate
Assign Covariate Values
Initialize
Initialize Object
MathAchieve
Mathematics achievement scores
ACF.gls
Autocorrelation Function for gls Residuals
Matrix
Assign Matrix Values
Names.formula
Extract Names from a formula
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
Pixel
X-ray pixel intensities over time
Quinidine
Quinidine Kinetics
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
ACF
Autocorrelation Function
IGF
Radioimmunoassay of IGF-I Protein
Names.pdBlocked
Names of a pdBlocked Object
Covariate.varFunc
Assign varFunc Covariate
Phenobarb
Phenobarbitol Kinetics
Dim.corSpatial
Dimensions of a corSpatial Object
Wheat
Yields by growing conditions
Initialize.reStruct
Initialize reStruct Object
Wheat2
Wheat Yield Trials
Dim.corStruct
Dimensions of a corStruct Object
coef.gnls
Extract gnls Coefficients
coef.lmList
Extract lmList Coefficients
Initialize.lmeStruct
Initialize an lmeStruct Object
Variogram.corExp
Calculate Semi-variogram for a corExp Object
coef.pdMat
pdMat Object Coefficients
coef.reStruct
reStruct Object Coefficients
[.pdMat
Subscript a pdMat Object
Muscle
Contraction of heart muscle sections
Machines
Productivity Scores for Machines and Workers
Fatigue
Cracks caused by metal fatigue
augPred
Augmented Predictions
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Oxboys
Heights of Boys in Oxford
Variogram.default
Calculate Semi-variogram
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
MathAchSchool
School demographic data for MathAchieve
Initialize.corStruct
Initialize corStruct Object
Relaxin
Assay for Relaxin
balancedGrouped
Create a groupedData object from a matrix
Oxide
Variability in Semiconductor Manufacturing
coef.varFunc
varFunc Object Coefficients
Nitrendipene
Assay of nitrendipene
Initialize.glsStruct
Initialize a glsStruct Object
Soybean
Growth of soybean plants
Names
Names Associated with an Object
Oats
Split-plot Experiment on Varieties of Oats
Orthodont
Growth curve data on an orthdontic measurement
Remifentanil
Pharmacokinetics of Remifentanil
Ovary
Counts of Ovarian Follicles
RatPupWeight
The weight of rat pups
Rail
Evaluation of Stress in Railway Rails
Variogram.corLin
Calculate Semi-variogram for a corLin Object
collapse
Collapse According to Groups
fixed.effects
Extract Fixed Effects
corCAR1
Continuous AR(1) Correlation Structure
fixef.lmList
Extract lmList Fixed Effects
corGaus
Gaussian Correlation Structure
corFactor.corStruct
Factor of a corStruct Object Matrix
getCovariate
Extract Covariate from an Object
corARMA
ARMA(p,q) Correlation Structure
corRatio
Rational Quadratic Correlation Structure
Tetracycline1
Pharmacokinetics of tetracycline
Spruce
Growth of Spruce Trees
anova.lme
Compare Likelihoods of Fitted Objects
Tetracycline2
Pharmacokinetics of tetracycline
allCoef
Extract Coefficients from a Set of Objects
anova.gls
Compare Likelihoods of Fitted Objects
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
corLin
Linear Correlation Structure
corAR1
AR(1) Correlation Structure
comparePred
Compare Predictions
getCovariate.corStruct
Extract corStruct Object Covariate
as.matrix.corStruct
Matrix of a corStruct Object
corMatrix
Extract Correlation Matrix
corNatural
General correlation in natural parameterization
getGroups.corStruct
Extract corStruct Groups
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
bdf
Language scores
fitted.glsStruct
Calculate glsStruct Fitted Values
gnlsControl
Control Values for gnls Fit
gnlsObject
Fitted gnls Object
getGroups.data.frame
Extract Groups from a Data Frame
corSpatial
Spatial Correlation Structure
getData
Extract Data from an Object
getCovariateFormula
Extract Covariates Formula
coef.corStruct
Coefficients of a corStruct Object
collapse.groupedData
Collapse a groupedData Object
compareFits
Compare Fitted Objects
lmList
List of lm Objects with a Common Model
getGroups.gls
Extract gls Object Groups
isInitialized
Check if Object is Initialized
logDet.corStruct
Extract corStruct Log-Determinant
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
formula.pdMat
Extract pdMat Formula
formula.pdBlocked
Extract pdBlocked Formula
fdHess
Finite difference Hessian
ergoStool
Ergometrics experiment with stool types
logDet.pdMat
Extract Log-Determinant from a pdMat Object
getCovariate.data.frame
Extract Data Frame Covariate
VarCorr
Extract variance and correlation components
glsControl
Control Values for gls Fit
intervals
Confidence Intervals on Coefficients
glsObject
Fitted gls Object
gsummary
Summarize by Groups
getGroups.lmList
Extract lmList Object Groups
getCovariate.varFunc
Extract varFunc Covariate
formula.reStruct
Extract reStruct Object Formula
lmList.groupedData
lmList Fit from a groupedData Object
needUpdate
Check if Update is Needed
gapply
Apply a Function by Groups
model.matrix.reStruct
reStruct Model Matrix
Variogram
Calculate Semi-variogram
lme
Linear Mixed-Effects Models
nlmeStruct
Nonlinear Mixed-Effects Structure
gls-internal
Auxiliary functions used by gls
pdConstruct
Construct pdMat Objects
nlmeObject
Fitted nlme Object
pdClasses
Positive-Definite Matrix Classes
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
logLik.glsStruct
Log-Likelihood of a glsStruct Object
logLik.gnls
Log-Likelihood of a gnls Object
pdConstruct.pdBlocked
Construct pdBlocked Objects
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pdSymm
General Positive-Definite Matrix
asOneFormula
Combine Formulas of a Set of Objects
plot.ACF
Plot an ACF Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
plot.nffGroupedData
Plot an nffGroupedData Object
phenoModel
Model function for the Phenobarb data
quinModel
Model function for the Quinidine data
random.effects
Extract Random Effects
plot.lme
Plot an lme or nls object
getGroups.lme
Extract lme Object Groups
asTable
Convert groupedData to a matrix
ACF.lme
Autocorrelation Function for lme Residuals
residuals.lmList
Extract lmList Residuals
gls
Fit Linear Model Using Generalized Least Squares
getGroups.varFunc
Extract varFunc Groups
residuals.gnlsStruct
Calculate gnlsStruct Residuals
coef.lme
Extract lme Coefficients
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
getResponseFormula
Extract Formula Specifying Response Variable
plot.nmGroupedData
Plot an nmGroupedData Object
coef.modelStruct
Extract modelStruct Object Coefficients
summary.lme
Summarize an lme Object
corClasses
Correlation Structure Classes
corSymm
General Correlation Structure
logDet.reStruct
Extract reStruct Log-Determinants
corCompSymm
Compound Symmetry Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
getVarCov
Extract variance-covariance matrix
logLik.corStruct
Extract corStruct Log-Likelihood
summary.modelStruct
Summarize a modelStruct Object
corSpher
Spherical Correlation Structure
plot.ranef.lme
Plot a ranef.lme Object
varComb
Combination of Variance Functions
plot.ranef.lmList
Plot a ranef.lmList Object
nlme.nlsList
NLME fit from nlsList Object
nlmeControl
Control Values for nlme Fit
plot.augPred
Plot an augPred Object
Dialyzer
High-Flux Hemodialyzer
plot.Variogram
Plot a Variogram Object
intervals.lmList
Confidence Intervals on lmList Coefficients
lmeControl
Specifying Control Values for lme Fit
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getResponse
Extract Response Variable from an Object
pdBlocked
Positive-Definite Block Diagonal Matrix
intervals.gls
Confidence Intervals on gls Parameters
predict.lmList
Predictions from an lmList Object
predict.gnls
Predictions from a gnls Object
varConstPower
Constant Plus Power Variance Function
getGroupsFormula
Extract Grouping Formula
reStruct
Random Effects Structure
Dim
Extract Dimensions from an Object
lmeObject
Fitted lme Object
pairs.lme
Pairs Plot of an lme Object
recalc
Recalculate Condensed Linear Model Object
intervals.lme
Confidence Intervals on lme Parameters
logLik.varFunc
Extract varFunc logLik
ranef.lmList
Extract lmList Random Effects
isBalanced
Check a Design for Balance
ranef.lme
Extract lme Random Effects
logLik.reStruct
Calculate reStruct Log-Likelihood
residuals.nlmeStruct
Calculate nlmeStruct Residuals
residuals.gls
Extract gls Residuals
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
Meat
Tenderness of meat
nlme
Nonlinear Mixed-Effects Models
lme.groupedData
LME fit from groupedData Object
residuals.glsStruct
Calculate glsStruct Residuals
simulate.lme
Simulate Results from
lme
Models
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
pairs.compareFits
Pairs Plot of compareFits Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
print.summary.pdMat
Print a summary.pdMat Object
pairs.lmList
Pairs Plot of an lmList Object
Milk
Protein content of cows' milk
summary.gls
Summarize a Generalized Least Squares
gls
Object
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Names.pdMat
Names of a pdMat Object
splitFormula
Split a Formula
Wafer
Modeling of Analog MOS Circuits
lme.lmList
LME fit from lmList Object
Names.reStruct
Names of an reStruct Object
varWeights.glsStruct
Variance Weights for glsStruct Object
logLik.lme
Log-Likelihood of an lme Object
as.matrix.reStruct
Matrices of an reStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
nlsList.selfStart
nlsList Fit from a selfStart Function
nlsList
List of nls Objects with a Common Model
pdIdent
Multiple of the Identity Positive-Definite Matrix
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
as.matrix.pdMat
Matrix of a pdMat Object
summary.corStruct
Summarize a corStruct Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
summary.lmList
Summarize an lmList Object
plot.compareFits
Plot a compareFits Object
print.varFunc
Print a varFunc Object
plot.gls
Plot a gls Object
pooledSD
Extract Pooled Standard Deviation
update.varFunc
Update varFunc Object
predict.gls
Predictions from a gls Object
corFactor
Factor of a Correlation Matrix
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
corExp
Exponential Correlation Structure
fitted.lmList
Extract lmList Fitted Values
corMatrix.corStruct
Matrix of a corStruct Object
residuals.lme
Extract lme Residuals
recalc.corStruct
Recalculate for corStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
varClasses
Variance Function Classes
getData.gls
Extract gls Object Data
getData.lmList
Extract lmList Object Data
getGroups
Extract Grouping Factors from an Object
getData.lme
Extract lme Object Data
fitted.lme
Extract lme Fitted Values
glsStruct
Generalized Least Squares Structure
varPower
Power Variance Function
varFunc
Variance Function Structure
gnls
Fit Nonlinear Model Using Generalized Least Squares
varIdent
Constant Variance Function
gnlsStruct
Generalized Nonlinear Least Squares Structure
residuals.lmeStruct
Calculate lmeStruct Residuals
groupedData
Construct a groupedData Object
recalc.varFunc
Recalculate for varFunc Object
recalc.reStruct
Recalculate for an reStruct Object
lmeStruct
Linear Mixed-Effects Structure
varWeights
Extract Variance Function Weights
logLik.lmList
Log-Likelihood of an lmList Object
pdDiag
Diagonal Positive-Definite Matrix
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
logDet
Extract the Logarithm of the Determinant
update.modelStruct
Update a modelStruct Object
summary.varFunc
Summarize varFunc Object
solve.reStruct
Apply Solve to an reStruct Object
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
pdFactor
Square-Root Factor of a Positive-Definite Matrix
plot.intervals.lmList
Plot lmList Confidence Intervals
predict.lme
Predictions from an lme Object
pdMat
Positive-Definite Matrix
plot.lmList
Plot an lmList Object
pdLogChol
General Positive-Definite Matrix
predict.nlme
Predictions from an nlme Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
summary.nlsList
Summarize an nlsList Object
summary.pdMat
Summarize a pdMat Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
varExp
Exponential Variance Function
varFixed
Fixed Variance Function