nlmeObject {nlme}R Documentation

Fitted nlme Object

Description

An object returned by the nlme function, inheriting from class nlme, also inheriting from class lme, and representing a fitted nonlinear mixed-effects model. Objects of this class have methods for the generic functions anova, coef, fitted, fixed.effects, formula, getGroups, getResponse, intervals, logLik, pairs, plot, predict, print, random.effects, residuals, summary, and update.

Value

The following components must be included in a legitimate nlme object.

apVar an approximate covariance matrix for the variance-covariance coefficients. If apVar = FALSE in the list of control values used in the call to nlme, this component is equal to NULL.
call a list containing an image of the nlme call that produced the object.
coefficients a list with two components, fixed and random, where the first is a vector containing the estimated fixed effects and the second is a list of matrices with the estimated random effects for each level of grouping. For each matrix in the random list, the columns refer to the random effects and the rows to the groups.
contrasts a list with the contrasts used to represent factors in the fixed effects formula and/or random effects formula. This information is important for making predictions from a new data frame in which not all levels of the original factors are observed. If no factors are used in the nlme model, this component will be an empty list.
dims a list with basic dimensions used in the nlme fit, including the components N - the number of observations in the data, Q - the number of grouping levels, qvec - the number of random effects at each level from innermost to outermost (last two values are equal to zero and correspond to the fixed effects and the response), ngrps - the number of groups at each level from innermost to outermost (last two values are one and correspond to the fixed effects and the response), and ncol - the number of columns in the model matrix for each level of grouping from innermost to outermost (last two values are equal to the number of fixed effects and one).
fitted a data frame with the fitted values as columns. The leftmost column corresponds to the population fixed effects (corresponding to the fixed effects only) and successive columns from left to right correspond to increasing levels of grouping.
fixDF a list with components X and terms specifying the denominator degrees of freedom for, respectively, t-tests for the individual fixed effects and F-tests for the fixed-effects terms in the models.
groups a data frame with the grouping factors as columns. The grouping level increases from left to right.
logLik the (restricted) log-likelihood at convergence.
map a list with components fmap, rmap, rmapRel, and bmap, specifying various mappings for the fixed and random effects, used to generate predictions from the fitted object.
method the estimation method: either "ML" for maximum likelihood, or "REML" for restricted maximum likelihood.
modelStruct an object inheriting from class nlmeStruct, representing a list of mixed-effects model components, such as reStruct, corStruct, and varFunc objects.
numIter the number of iterations used in the iterative algorithm.
residuals a data frame with the residuals as columns. The leftmost column corresponds to the population residuals and successive columns from left to right correspond to increasing levels of grouping.
sigma the estimated within-group error standard deviation.
varFix an approximate covariance matrix of the fixed effects estimates.

Author(s)

Jose Pinheiro Jose.Pinheiro@pharma.novartis.com and Douglas Bates bates@stat.wisc.edu

See Also

nlme, nlmeStruct


[Package nlme version 3.1-80 Index]