plot.ranef.lme {nlme} | R Documentation

## Plot a ranef.lme Object

### Description

If `form` is missing, or is given as a one-sided formula, a Trellis dot-plot of the random effects is generated, with a different panel for each random effect (coefficient). Rows in the dot-plot are determined by the `form` argument (if not missing) or by the row names of the random effects (coefficients). If a single factor is specified in `form`, its levels determine the dot-plot rows (with possibly multiple dots per row); otherwise, if `form` specifies a crossing of factors, the dot-plot rows are determined by all combinations of the levels of the individual factors in the formula. The Trellis function `dotplot` is used in this method function.

If `form` is a two-sided formula, a Trellis display is generated, with a different panel for each variable listed in the right hand side of `form`. Scatter plots are generated for numeric variables and boxplots are generated for categorical (`factor` or `ordered`) variables.

### Usage

    ## S3 method for class 'ranef.lme':
    plot(x, form, omitFixed, level, grid, control, ...)

### Arguments

`x` | an object inheriting from class `ranef.lme`, representing the estimated coefficients or estimated random effects for the `lme` object from which it was produced.
`form` | an optional formula specifying the desired type of plot. If given as a one-sided formula, a `dotplot` of the estimated random effects (coefficients) grouped according to all combinations of the levels of the factors named in `form` is returned. Single factors (`~g`) or crossed factors (`~g1*g2`) are allowed. If given as a two-sided formula, the left hand side must be a single random effects (coefficient) and the right hand side is formed by covariates in `x` separated by `+`. A Trellis display of the random effect (coefficient) versus the named covariates is returned in this case. Default is `NULL`, in which case the row names of the random effects (coefficients) are used.
`omitFixed` | an optional logical value indicating whether columns with values that are constant across groups should be omitted. Default is `TRUE`.
`level` | an optional integer value giving the level of grouping to be used for `x`. Only used when `x` is a list with different components for each grouping level. Defaults to the highest or innermost level of grouping.
`grid` | an optional logical value indicating whether a grid should be added to plot. Only applies to plots associated with two-sided formulas in `form`. Default is `FALSE`.
`control` | an optional list with control values for the plot, when `form` is given as a two-sided formula. The control values are referenced by name in the `control` list and only the ones to be modified from the default need to be specified. Available values include: `drawLine`, a logical value indicating whether a `loess` smoother should be added to the scatter plots and a line connecting the medians should be added to the boxplots (default is `TRUE`); `span.loess`, used as the `span` argument in the call to `panel.loess` (default is `2/3`); `degree.loess`, used as the `degree` argument in the call to `panel.loess` (default is `1`); `cex.axis`, the character expansion factor for the x-axis (default is `0.8`); `srt.axis`, the rotation factor for the x-axis (default is `0`); and `mgp.axis`, the margin parameters for the x-axis (default is `c(2, 0.5, 0)`).
`...` | optional arguments passed to the Trellis `dotplot` function.

### Value

a Trellis plot of the estimated random-effects (coefficients) versus covariates, or groups.

### Author(s)

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

### See Also

`ranef.lme`, `lme`, `dotplot`

### Examples

    ## Not run:
    data(Orthodont)
    fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject)
    plot(ranef(fm1))
    fm1RE <- ranef(fm1, aug = TRUE)
    plot(fm1RE, form = ~ Sex)
    plot(fm1RE, form = age ~ Sex)
    ## End(Not run)

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