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nlme (version 3.1-141)
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
3.1-141
License
GPL (>= 2) | file LICENCE
Maintainer
R-core R-core@R-project.org
Last Published
August 1st, 2019
Functions in nlme (3.1-141)
Search functions
Coef
Assign Values to Coefficients
Covariate.varFunc
Assign varFunc Covariate
BodyWeight
Rat weight over time for different diets
ACF.gls
Autocorrelation Function for gls Residuals
Cefamandole
Pharmacokinetics of Cefamandole
Assay
Bioassay on Cell Culture Plate
Covariate
Assign Covariate Values
ACF
Autocorrelation Function
ACF.lme
Autocorrelation Function for lme Residuals
Alfalfa
Split-Plot Experiment on Varieties of Alfalfa
Dialyzer
High-Flux Hemodialyzer
Names
Names Associated with an Object
Initialize
Initialize Object
Muscle
Contraction of heart muscle sections
IGF
Radioimmunoassay of IGF-I Protein
Dim
Extract Dimensions from an Object
Gun
Methods for firing naval guns
Milk
Protein content of cows' milk
Meat
Tenderness of meat
Glucose2
Glucose Levels Following Alcohol Ingestion
[.pdMat
Subscript a pdMat Object
Oxboys
Heights of Boys in Oxford
Gasoline
Refinery yield of gasoline
Glucose
Glucose levels over time
Initialize.lmeStruct
Initialize an lmeStruct Object
Dim.corSpatial
Dimensions of a corSpatial Object
Variogram.corGaus
Calculate Semi-variogram for a corGaus Object
Relaxin
Assay for Relaxin
Variogram.corExp
Calculate Semi-variogram for a corExp Object
Dim.corStruct
Dimensions of a corStruct Object
Remifentanil
Pharmacokinetics of remifentanil
Oxide
Variability in Semiconductor Manufacturing
allCoef
Extract Coefficients from a Set of Objects
RatPupWeight
The weight of rat pups
anova.gls
Compare Likelihoods of Fitted Objects
Rail
Evaluation of Stress in Railway Rails
Initialize.reStruct
Initialize reStruct Object
Names.pdBlocked
Names of a pdBlocked Object
Matrix
Assign Matrix Values
MathAchieve
Mathematics achievement scores
Names.formula
Extract Names from a formula
PBG
Effect of Phenylbiguanide on Blood Pressure
Phenobarb
Phenobarbitol Kinetics
as.matrix.corStruct
Matrix of a corStruct Object
coef.varFunc
varFunc Object Coefficients
anova.lme
Compare Likelihoods of Fitted Objects
collapse
Collapse According to Groups
Initialize.varFunc
Initialize varFunc Object
Machines
Productivity Scores for Machines and Workers
Fatigue
Cracks caused by metal fatigue
LDEsysMat
Generate system matrix for LDEs
Names.pdMat
Names of a pdMat Object
Names.reStruct
Names of an reStruct Object
Initialize.glsStruct
Initialize a glsStruct Object
Earthquake
Earthquake Intensity
Dim.pdMat
Dimensions of a pdMat Object
Initialize.corStruct
Initialize corStruct Object
Matrix.pdMat
Assign Matrix to a pdMat or pdBlocked Object
Oats
Split-plot Experiment on Varieties of Oats
Nitrendipene
Assay of nitrendipene
Matrix.reStruct
Assign reStruct Matrices
corARMA
ARMA(p,q) Correlation Structure
corCAR1
Continuous AR(1) Correlation Structure
MathAchSchool
School demographic data for MathAchieve
VarCorr
Extract variance and correlation components
Pixel
X-ray pixel intensities over time
Variogram.lme
Calculate Semi-variogram for Residuals from an lme Object
Variogram
Calculate Semi-variogram
Variogram.corRatio
Calculate Semi-variogram for a corRatio Object
bdf
Language scores
Variogram.gls
Calculate Semi-variogram for Residuals from a gls Object
Variogram.corLin
Calculate Semi-variogram for a corLin Object
Variogram.default
Calculate Semi-variogram
ergoStool
Ergometrics experiment with stool types
coef.corStruct
Coefficients of a corStruct Object
coef.gnls
Extract gnls Coefficients
Wafer
Modeling of Analog MOS Circuits
fdHess
Finite difference Hessian
Ovary
Counts of Ovarian Follicles
Orthodont
Growth curve data on an orthdontic measurement
comparePred
Compare Predictions
corExp
Exponential Correlation Structure
corAR1
AR(1) Correlation Structure
corFactor
Factor of a Correlation Matrix
corSpher
Spherical Correlation Structure
Quinidine
Quinidine Kinetics
fitted.lme
Extract lme Fitted Values
fitted.lmList
Extract lmList Fitted Values
formula.reStruct
Extract reStruct Object Formula
as.matrix.pdMat
Matrix of a pdMat Object
corSymm
General Correlation Structure
Soybean
Growth of soybean plants
collapse.groupedData
Collapse a groupedData Object
as.matrix.reStruct
Matrices of an reStruct Object
Spruce
Growth of Spruce Trees
Variogram.corSpatial
Calculate Semi-variogram for a corSpatial Object
corMatrix.reStruct
Extract Correlation Matrix from Components of an reStruct Object
compareFits
Compare Fitted Objects
gapply
Apply a Function by Groups
formula.pdMat
Extract pdMat Formula
formula.pdBlocked
Extract pdBlocked Formula
corNatural
General correlation in natural parameterization
Tetracycline2
Pharmacokinetics of tetracycline
Tetracycline1
Pharmacokinetics of tetracycline
getCovariate
Extract Covariate from an Object
corMatrix.corStruct
Matrix of a corStruct Object
corFactor.corStruct
Factor of a corStruct Object Matrix
corGaus
Gaussian Correlation Structure
coef.lmList
Extract lmList Coefficients
corMatrix.pdMat
Extract Correlation Matrix from a pdMat Object
fixef.lmList
Extract lmList Fixed Effects
getCovariate.data.frame
Extract Data Frame Covariate
fixed.effects
Extract Fixed Effects
Variogram.corSpher
Calculate Semi-variogram for a corSpher Object
getCovariate.varFunc
Extract varFunc Covariate
getData.gls
Extract gls Object Data
glsControl
Control Values for gls Fit
getCovariate.corStruct
Extract corStruct Object Covariate
getData.lmList
Extract lmList Object Data
getGroups.lme
Extract lme Object Groups
getGroups.varFunc
Extract varFunc Groups
getResponseFormula
Extract Formula Specifying Response Variable
lmeControl
Specifying Control Values for lme Fit
getData.lme
Extract lme Object Data
lmeObject
Fitted lme Object
intervals
Confidence Intervals on Coefficients
getGroups
Extract Grouping Factors from an Object
getVarCov
Extract variance-covariance matrix
gsummary
Summarize by Groups
getGroupsFormula
Extract Grouping Formula
Wheat
Yields by growing conditions
Wheat2
Wheat Yield Trials
coef.modelStruct
Extract modelStruct Object Coefficients
balancedGrouped
Create a groupedData object from a matrix
corCompSymm
Compound Symmetry Correlation Structure
fitted.lmeStruct
Calculate lmeStruct Fitted Values
coef.lme
Extract lme Coefficients
corClasses
Correlation Structure Classes
augPred
Augmented Predictions
glsStruct
Generalized Least Squares Structure
gnls
Fit Nonlinear Model Using Generalized Least Squares
logLik.glsStruct
Log-Likelihood of a glsStruct Object
getResponse
Extract Response Variable from an Object
asTable
Convert groupedData to a matrix
asOneFormula
Combine Formulas of a Set of Objects
gnlsControl
Control Values for gnls Fit
gnlsStruct
Generalized Nonlinear Least Squares Structure
gnlsObject
Fitted gnls Object
groupedData
Construct a groupedData Object
intervals.gls
Confidence Intervals on gls Parameters
intervals.lmList
Confidence Intervals on lmList Coefficients
glsObject
Fitted gls Object
lme.groupedData
LME fit from groupedData Object
corMatrix
Extract Correlation Matrix
coef.reStruct
reStruct Object Coefficients
corSpatial
Spatial Correlation Structure
corLin
Linear Correlation Structure
corRatio
Rational Quadratic Correlation Structure
coef.pdMat
pdMat Object Coefficients
lmeStruct
Linear Mixed-Effects Structure
model.matrix.reStruct
reStruct Model Matrix
logDet
Extract the Logarithm of the Determinant
fitted.glsStruct
Calculate glsStruct Fitted Values
logLik.gnls
Log-Likelihood of a gnls Object
logLik.gnlsStruct
Log-Likelihood of a gnlsStruct Object
lme.lmList
LME fit from lmList Object
nlme.nlsList
NLME fit from nlsList Object
logLik.lmList
Log-Likelihood of an lmList Object
fitted.gnlsStruct
Calculate gnlsStruct Fitted Values
getGroups.lmList
Extract lmList Object Groups
gls
Fit Linear Model Using Generalized Least Squares
getGroups.gls
Extract gls Object Groups
gls-internal
Auxiliary functions used by gls
isInitialized
Check if Object is Initialized
needUpdate
Check if Update is Needed
getCovariateFormula
Extract Covariates Formula
fitted.nlmeStruct
Calculate nlmeStruct Fitted Values
getData
Extract Data from an Object
getGroups.corStruct
Extract corStruct Groups
lmList
List of lm Objects with a Common Model
logLik.reStruct
Calculate reStruct Log-Likelihood
nlmeObject
Fitted nlme Object
nlmeStruct
Nonlinear Mixed-Effects Structure
pdFactor.reStruct
Extract Square-Root Factor from Components of an reStruct Object
logDet.pdMat
Extract Log-Determinant from a pdMat Object
logDet.corStruct
Extract corStruct Log-Determinant
logLik.lme
Log-Likelihood of an lme Object
pairs.compareFits
Pairs Plot of compareFits Object
logLik.lmeStruct
Log-Likelihood of an lmeStruct Object
logLik.varFunc
Extract varFunc logLik
nlsList
List of nls Objects with a Common Model
nlsList.selfStart
nlsList Fit from a selfStart Function
plot.lme
Plot an lme or nls object
predict.gnls
Predictions from a gnls Object
pairs.lmList
Pairs Plot of an lmList Object
plot.nffGroupedData
Plot an nffGroupedData Object
pdClasses
Positive-Definite Matrix Classes
plot.Variogram
Plot a Variogram Object
plot.augPred
Plot an augPred Object
pdIdent
Multiple of the Identity Positive-Definite Matrix
nlmeControl
Control Values for nlme Fit
pdConstruct
Construct pdMat Objects
isBalanced
Check a Design for Balance
intervals.lme
Confidence Intervals on lme Parameters
getGroups.data.frame
Extract Groups from a Data Frame
lmList.groupedData
lmList Fit from a groupedData Object
lme
Linear Mixed-Effects Models
predict.lmList
Predictions from an lmList Object
pdCompSymm
Positive-Definite Matrix with Compound Symmetry Structure
ranef.lmList
Extract lmList Random Effects
pdConstruct.pdBlocked
Construct pdBlocked Objects
phenoModel
Model function for the Phenobarb data
plot.lmList
Plot an lmList Object
pdFactor
Square-Root Factor of a Positive-Definite Matrix
pdSymm
General Positive-Definite Matrix
plot.intervals.lmList
Plot lmList Confidence Intervals
pdNatural
General Positive-Definite Matrix in Natural Parametrization
pdDiag
Diagonal Positive-Definite Matrix
plot.ACF
Plot an ACF Object
plot.nfnGroupedData
Plot an nfnGroupedData Object
pdMatrix
Extract Matrix or Square-Root Factor from a pdMat Object
predict.lme
Predictions from an lme Object
predict.nlme
Predictions from an nlme Object
summary.varFunc
Summarize varFunc Object
residuals.lme
Extract lme Residuals
solve.pdMat
Calculate Inverse of a Positive-Definite Matrix
varWeights.glsStruct
Variance Weights for glsStruct Object
solve.reStruct
Apply Solve to an reStruct Object
varWeights.lmeStruct
Variance Weights for lmeStruct Object
update.modelStruct
Update a modelStruct Object
residuals.lmeStruct
Calculate lmeStruct Residuals
ranef.lme
Extract lme Random Effects
pdMatrix.reStruct
Extract Matrix or Square-Root Factor from Components of an reStruct Object
residuals.nlmeStruct
Calculate nlmeStruct Residuals
logLik.corStruct
Extract corStruct Log-Likelihood
logDet.reStruct
Extract reStruct Log-Determinants
simulate.lme
Simulate Results from
lme
Models
varClasses
Variance Function Classes
summary.lmList
Summarize an lmList Object
update.varFunc
Update varFunc Object
summary.gls
Summarize a Generalized Least Squares
gls
Object
plot.ranef.lmList
Plot a ranef.lmList Object
pooledSD
Extract Pooled Standard Deviation
nlme
Nonlinear Mixed-Effects Models
pairs.lme
Pairs Plot of an lme Object
needUpdate.modelStruct
Check if a modelStruct Object Needs Updating
quinModel
Model function for the Quinidine data
summary.lme
Summarize an lme Object
residuals.gls
Extract gls Residuals
plot.ranef.lme
Plot a ranef.lme Object
random.effects
Extract Random Effects
residuals.glsStruct
Calculate glsStruct Residuals
summary.modelStruct
Summarize a modelStruct Object
pdBlocked
Positive-Definite Block Diagonal Matrix
pdMat
Positive-Definite Matrix
pdLogChol
General Positive-Definite Matrix
plot.compareFits
Plot a compareFits Object
plot.gls
Plot a gls Object
predict.gls
Predictions from a gls Object
reStruct
Random Effects Structure
print.summary.pdMat
Print a summary.pdMat Object
plot.nmGroupedData
Plot an nmGroupedData Object
print.varFunc
Print a varFunc Object
residuals.gnlsStruct
Calculate gnlsStruct Residuals
recalc
Recalculate Condensed Linear Model Object
residuals.lmList
Extract lmList Residuals
recalc.corStruct
Recalculate for corStruct Object
recalc.modelStruct
Recalculate for a modelStruct Object
recalc.reStruct
Recalculate for an reStruct Object
summary.nlsList
Summarize an nlsList Object
qqnorm.gls
Normal Plot of Residuals from a gls Object
varFunc
Variance Function Structure
varPower
Power Variance Function
varWeights
Extract Variance Function Weights
varIdent
Constant Variance Function
splitFormula
Split a Formula
recalc.varFunc
Recalculate for varFunc Object
summary.corStruct
Summarize a corStruct Object
qqnorm.lme
Normal Plot of Residuals or Random Effects from an lme Object
varComb
Combination of Variance Functions
varConstPower
Constant Plus Power Variance Function
varFixed
Fixed Variance Function
varExp
Exponential Variance Function
summary.pdMat
Summarize a pdMat Object