metafor (version 1.9-2)

forest.default: Forest Plots

Description

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

Usage

## S3 method for class 'default':
forest(x, vi, sei, ci.lb, ci.ub, annotate=TRUE, showweight=FALSE,
       xlim, alim, ylim, at, steps=5,
       level=95, digits=2, refline=0, xlab,
       slab, ilab, ilab.xpos, ilab.pos,
       subset, transf=FALSE, atransf=FALSE, targs, rows,
       efac=1, pch=15, psize, cex, cex.lab, cex.axis, \dots)

Arguments

x

vector of length $k$ with the observed effect sizes or outcomes.

vi

vector of length $k$ with the corresponding sampling variances.

sei

vector of length $k$ with the corresponding standard errors. (note: only one of the two, vi or sei, needs to be specified)

ci.lb

vector of length $k$ with the corresponding lower confidence intervals bounds. Not needed if vi or sei is specified. See Details.

ci.ub

vector of length $k$ with the corresponding upper confidence intervals bounds. Not needed if vi or sei is specified. See Details.

annotate

logical specifying whether annotations should be added to the plot (default is TRUE).

showweight

logical specifying whether the annotations should also include inverse variance weights (default is FALSE).

xlim

horizontal limits of the plot region. If unspecified, the function tries to set the horizontal plot limits to some sensible values.

alim

the actual x-axis limits. If unspecified, the function tries to set the x-axis limits to some sensible values.

ylim

the y limits of the plot. If unspecified, the function tries to set the y-axis limits to some sensible values.

at

position of the x-axis tick marks and corresponding labels. If unspecified, the function tries to set the tick mark positions/labels to some sensible values.

steps

the number of tick marks 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 specifying the number of decimal places to which the tick mark labels of the x-axis and the annotations should be rounded (default is 2). Can also be a vector of two integers, the first specifying the number of decimal places for the annotations,

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. If unspecified, the function tries to set an appropriate axis title.

slab

optional vector with unique labels for the $k$ studies. If unspecified, simple labels are created within the function. To suppress labels, set this argument to NA.

ilab

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 (must be specified if ilab is specified).

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). If unspecified, the default is to center the labels.

subset

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 reorderin

transf

optional argument specifying the name of a function that should be used to transform the observed effect sizes or outcomes and corresponding confidence interval bounds (e.g., transf=exp). Defaults to FALSE, which means that no tr

atransf

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.

rows

optional vector specifying the rows (or more generally, the horizontal positions) for plotting the outcomes. If unspecified, the function sets this value automatically. Can also be a single value specifying the row (horizontal position) of the first outco

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. Can also be a vector of values.

psize

optional vector with point sizes for the observed effect sizes or outcomes. If unspecified, the point sizes are drawn proportional to the precision of the estimates.

cex

optional character and symbol expansion factor. If unspecified, the function tries to set this to a sensible value.

cex.lab

optional expansion factor for the x-axis titel. If unspecified, the function tries to set this to a sensible value.

cex.axis

optional expansion factor for the x-axis labels. If unspecified, 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. To use the function, one should specify the observed effect sizes or outcomes (via the x argument) together with the corresponding sampling variances (via the vi argument) or with the corresponding standard errors (via the sei argument). Alternatively, one can specify the observed effect sizes or outcomes together with the corresponding confidence interval bounds (via the ci.lb and ci.ub arguments). With the transf argument, the observed effect sizes or outcomes and corresponding confidence interval bounds can be transformed with an arbitrary function. For example, when plotting log odds ratios, 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 (e.g., atransf=exp). The examples below illustrate the use of these arguments. By default, the studies are ordered from top to bottom (i.e., the first study in the dataset will be placed in row $k$, the second study in row $k-1$, and so on, until the last study, which is placed in the first row). The studies can be reordered with the subset argument (by specifying a vector with indices with the desired order). Summary estimates can also be added to the plot with the addpoly function. See the documentation for that function for examples.

References

Lewis, S., & Clarke, M. (2001). Forest plots: Trying to see the wood and the trees. British Medical Journal, 322, 1479--1480. Viechtbauer, W. (2010). Conducting meta-analyses in R with the metafor package. Journal of Statistical Software, 36(3), 1--48. http://www.jstatsoft.org/v36/i03/.

See Also

forest, forest.rma, addpoly

Examples

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

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

### default forest plot of the observed log relative risks
forest(dat$yi, dat$vi)

### forest plot of the observed relative risks
forest(dat$yi, dat$vi, slab=paste(dat$author, dat$year, sep=", "), transf=exp,
       alim=c(0,2), steps=5, xlim=c(-2,3.5), refline=1)

### forest plot of the observed relative risks
forest(dat$yi, dat$vi, slab=paste(dat$author, dat$year, sep=", "), atransf=exp,
       at=log(c(.05,.25,1,4,20)), xlim=c(-10,8))

### see also examples for the forest.rma function