collapse.groupedData {nlme}R Documentation

Collapse a groupedData Object

Description

If object has a single grouping factor, it is returned unchanged. Else, it 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.

Usage

## S3 method for class 'groupedData':
collapse(object, collapseLevel, displayLevel,
       outer, inner, preserve, FUN, subset, ...)

Arguments

object an object inheriting from class groupedData, generally 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 as the grouping factor for the collapsed data. Default is collapseLevel.
outer an optional logical value or one-sided formula, indicating covariates that are outer to the displayLevel grouping factor. 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. 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 preserved in the collapsed data. Default is NULL, meaning that all levels are used.
... some methods for this generic require additional arguments. None are used in this method.

Value

a groupedData object with a single grouping factor given by the displayLevel grouping factor, resulting from collapsing object over the levels of the collapseLevel grouping factor.

Author(s)

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

References

Pinheiro, J.C. and Bates, D.M. (1997) "Future Directions in Mixed-Effects Software: Design of NLME 3.0" available at http://franz.stat.wisc.edu/pub/NLME.

See Also

groupedData, plot.nmGroupedData

Examples

# collapsing by Dog
collapse(Pixel, collapse = 1)  # same as collapse(Pixel, collapse = "Dog")

[Package nlme version 3.1-80 Index]