nlme: plot.nmGroupedData – R documentation

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plot.nmGroupedData

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 bates@stat.wisc.edu

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.

Examples

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

nlme

Linear and Nonlinear Mixed Effects Models

v3.1-152

GPL (>= 2) | file LICENCE

Authors

José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R-core [aut, cre]

Initial release

2021-02-03