nlme: plot.ranef.lme – R documentation

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plot.ranef.lme

Plot a ranef.lme Object

Description

Plots (class "Trellis" from package lattice) of the random effects from linear mixed effects model, i.e., the result of ranef(lme(*)) (of class "ranef.lme").

Usage

## S3 method for class 'ranef.lme'
plot(x, form = NULL, omitFixed = TRUE, level = Q,
     grid = TRUE, control, xlab, ylab, strip,
     ...)

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. If given as a two-sided formula (or by default, `NULL`), an `xyplot()` Trellis display of the random effect (coefficient) versus the named covariates is returned. In `NULL` case the row names of the random effects (coefficients) are used (as covariates). See also ‘Details:’.
`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 `TRUE`.
`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)`).
`xlab, ylab`	axis labels, each with a sensible default.
`strip`	a `function` or `FALSE`, see `dotplot()` from package lattice.
`...`	optional arguments passed to the Trellis `dotplot` function.

Details

If form is missing, or is given as a one-sided formula, a Trellis dot-plot (via dotplot() from pkg lattice) 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). Single factors (~g) or crossed factors (~g1*g2) are allowed. For a single factor, 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.

If form is a two-sided formula, the left hand side must be a single random effect (coefficient) and the right hand side is formed by covariates in x separated by +. An xyplot() 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.

Value

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

Author(s)

José Pinheiro and Douglas Bates bates@stat.wisc.edu

Examples

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) # "connected" boxplots

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