plot.ranef.lme {nlme}R Documentation

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

See Also

ranef.lme, lme, dotplot.

Examples

fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject)
plot(ranef(fm1))
fm1RE <- ranef(fm1, augFrame = TRUE)
plot(fm1RE, form = ~ Sex)
plot(fm1RE, form = age ~ Sex) # "connected" boxplots
[Package nlme version 3.1-168 Index]