forest.default {metafor}R Documentation

Forest Plots

Description

Function to create forest plots for a given set of data.

Usage

## Default S3 method:
forest(x, vi, sei, annotate=TRUE, xlim=NULL, alim=NULL, ylim=NULL, 
       at=NULL, steps=5, level=95, digits=2, refline=0, xlab=NULL, 
       slab=NULL, ilab=NULL, ilab.xpos=NULL, ilab.pos=NULL, 
       subset=NULL, transf=FALSE, atransf=FALSE, targs=NULL, 
       addrows=0, efac=1, pch=15, psize=NULL, 
       cex=NULL, cex.lab=NULL, cex.axis=NULL, ...)

Arguments

x a vector of length k with the observed effect sizes or outcomes.
vi a vector of length k with the corresponding sampling variances.
sei a vector of length k with the corresponding standard errors.
(note: only one of the two, vi or sei, needs to be specified)
annotate logical specifying whether annotations should be added to the plot (default is TRUE).
xlim horizontal limits of the plot region. Defaults to NULL, which means that the function tries to set the horizontal plot limits to some sensible values.
alim the actual x axis limits. Defaults to NULL, which means that the function tries to set the x axis limits to some sensible values.
ylim the y limits of the plot. Defaults to NULL, which means that the function tries to set the y axis limits to some sensible values.
at position of the x axis tick marks and corresponding labels. Defaults to NULL, which means that the function tries to set the tick mark positions/labels to some sensible values.
steps the number of tick marks and corresponding labels for the x axis (default is 5). Ignored when the user specifies the positions via the at argument.
level numerical value between 0 and 100 specifying the confidence interval level (default is 95).
digits integer value specifying the number of decimal places to which the tick mark labels and annotations should be rounded (default is 2).
refline value at which a vertical ‘reference’ line should be drawn (default is 0). The line can be suppressed by setting this argument to NA.
xlab title for the x axis (NULL by default, which suppresses the title).
slab an optional vector with unique labels for the k studies. Defaults to NULL, which means that simple labels are created within the function. To suppress labels, set this argument to NA.
ilab an optional vector or matrix of character strings providing additional information about the studies.
ilab.xpos numerical value(s) specifying the x axis position(s) of the character vector(s) given via ilab.
ilab.pos integer(s) (either 1, 2, 3, or 4) specifying the alignment of the character vector(s) given via ilab (2 means right, 4 mean left aligned). The default is to center the labels.
subset an optional vector indicating the subset of studies that should be used for the plot. This can be a logical vector of length k or a numeric vector indicating the indices of the observations to include. Note that this argument can also be used for reordering the studies.
transf an optional argument specifying the name of a function that should be used to transform the observed effect sizes and corresponding confidence interval bounds (e.g., transf=exp). Defaults to FALSE, which means that no transformation is used.
atransf an optional argument specifying the name of a function that should be used to transform the x axis labels and annotations (e.g., transf=exp). Defaults to FALSE, which means that no transformation is used.
targs optional arguments needed by the function specified via transf or atransf.
addrows number of extra rows that should be added at the bottom of the forest plot (default is 0).
efac vertical expansion factor for arrows, confidence interval limits, and the symbol used to denote summary estimates. The default value of 1 should usually work okay.
pch plotting symbol to use for the observed effect sizes or outcomes. By default, a filled square is used. See points for other options.
psize an optional vector with point sizes for the observed effect sizes or outcomes. Default is NULL, which means that the point sizes are drawn proportional to the inverse of the sampling variances.
cex an optional character and symbol expansion factor. If NULL (default), the function tries to set this to a sensible value.
cex.lab an optional expansion factor for the x axis titel. If NULL (default), the function tries to set this to a sensible value.
cex.axis an optional expansion factor for x axis labels. If NULL (default), the function tries to set this to a sensible value.
... other arguments.

Details

The plot shows the individual observed effect sizes or outcomes with corresponding confidence intervals.

With the transf argument, the observed effect sizes and corresponding confidence interval bounds can be transformed with an arbitrary function. For example, if log odds ratios are provided to the function, then one could use transf=exp to obtain a forest plot showing the odds ratios. Alternatively, one can use the atransf argument to transform the x axis labels and annotations. The examples below illustrate the use of these arguments.

Summary estimates can also be added to the plot with the addpoly function. See the documentation for that function for examples.

Note

The function tries to set some sensible values for the optional arguments, but it may be necessary to tweak these in certain circumstances. In particular, if the number of studies is quite large, the labels, annotations, and symbols may become quite small and impossible to read. Stretching the plot window vertically may then provide a more readable figure (you will have to call the function again after the stretching, so that the label/symbol sizes are properly adjusted).

If the horizontal plot and/or x axis limits are set by the user, then the horizontal plot limits (xlim) must be at least as wide as the x axis limits (alim). Moreover, the x axis limits must encompass the observed effect sizes or outcomes. These restrictions are enforced inside the function.

Author(s)

Wolfgang Viechtbauer; wvb@www.wvbauer.com; http://www.wvbauer.com/

See Also

forest, addpoly

Examples

### load BCG vaccine data
data(dat.bcg)

### calculate log risk ratios and corresponding sampling variances
dat <- escalc(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg)
dat <- cbind(dat.bcg, dat)

### forest plot of the observed risk ratios
forest(dat$yi, dat$vi, slab=paste(dat.bcg$author, dat$year), 
       atransf=exp, xlab="Risk Ratio (log scale)")

[Package metafor version 0.5-5 Index]