plot.nmGroupedData: Plot an nmGroupedData Object

In nlme: Linear and Nonlinear Mixed Effects Models

Plot an nmGroupedData Object

Description

The groupedData object is summarized by the values of the displayLevel grouping factor (or the combination of its values and the values of the covariate indicated in preserve, if any is present). The collapsed data is used to produce a new groupedData object, with grouping factor given by the displayLevel factor, which is plotted using the appropriate plot method for groupedData objects with single level of grouping.

Usage

## S3 method for class 'nmGroupedData'
plot(x, collapseLevel, displayLevel, outer, inner,
    preserve, FUN, subset, key, grid, ...)

Arguments

x	an object inheriting from class nmGroupedData, representing a groupedData object with multiple grouping factors.
collapseLevel	an optional positive integer or character string indicating the grouping level to use when collapsing the data. Level values increase from outermost to innermost grouping. Default is the highest or innermost level of grouping.
displayLevel	an optional positive integer or character string indicating the grouping level to use for determining the panels in the Trellis display, when outer is missing. Default is collapseLevel.
outer	an optional logical value or one-sided formula, indicating covariates that are outer to the displayLevel grouping factor, which are used to determine the panels of the Trellis plot. If equal to TRUE, the displayLevel element attr(object, "outer") is used to indicate the outer covariates. An outer covariate is invariant within the sets of rows defined by the grouping factor. Ordering of the groups is done in such a way as to preserve adjacency of groups with the same value of the outer variables. Defaults to NULL, meaning that no outer covariates are to be used.
inner	an optional logical value or one-sided formula, indicating a covariate that is inner to the displayLevel grouping factor, which is used to associate points within each panel of the Trellis plot. If equal to TRUE, attr(object, "outer") is used to indicate the inner covariate. An inner covariate can change within the sets of rows defined by the grouping factor. Defaults to NULL, meaning that no inner covariate is present.
preserve	an optional one-sided formula indicating a covariate whose levels should be preserved when collapsing the data according to the collapseLevel grouping factor. The collapsing factor is obtained by pasting together the levels of the collapseLevel grouping factor and the values of the covariate to be preserved. Default is NULL, meaning that no covariates need to be preserved.
FUN	an optional summary function or a list of summary functions to be used for collapsing the data. The function or functions are applied only to variables in object that vary within the groups defined by collapseLevel. Invariant variables are always summarized by group using the unique value that they assume within that group. If FUN is a single function it will be applied to each non-invariant variable by group to produce the summary for that variable. If FUN is a list of functions, the names in the list should designate classes of variables in the data such as ordered, factor, or numeric. The indicated function will be applied to any non-invariant variables of that class. The default functions to be used are mean for numeric factors, and Mode for both factor and ordered. The Mode function, defined internally in gsummary, returns the modal or most popular value of the variable. It is different from the mode function that returns the S-language mode of the variable.
subset	an optional named list. Names can be either positive integers representing grouping levels, or names of grouping factors. Each element in the list is a vector indicating the levels of the corresponding grouping factor to be used for plotting the data. Default is NULL, meaning that all levels are used.
key	an optional logical value, or list. If TRUE, a legend is included at the top of the plot indicating which symbols (colors) correspond to which prediction levels. If FALSE, no legend is included. If given as a list, key is passed down as an argument to the trellis function generating the plots (xyplot). Defaults to TRUE.
grid	an optional logical value indicating whether a grid should be added to plot. Default is TRUE.
...	optional arguments passed to the Trellis plot function.

Value

a Trellis display of the data collapsed over the values of the collapseLevel grouping factor and grouped according to the displayLevel grouping factor.

Author(s)

José Pinheiro and Douglas Bates [e-mail]

References

Bates, D.M. and Pinheiro, J.C. (1997), "Software Design for Longitudinal Data", in "Modelling Longitudinal and Spatially Correlated Data: Methods, Applications and Future Directions", T.G. Gregoire (ed.), Springer-Verlag, New York.

See Also

groupedData, collapse.groupedData, plot.nfnGroupedData, plot.nffGroupedData

Examples

# no collapsing, panels by Dog
plot(Pixel, display = "Dog", inner = ~Side)
# collapsing by Dog, preserving day
plot(Pixel, collapse = "Dog", preserve = ~day)

nlme documentation built on Nov. 27, 2023, 5:09 p.m.