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 3.1-73 Index]