forest.cumul.rma: Forest Plots (Method for 'cumul.rma' Objects)

Description

Function to create forest plots for objects of class "cumul.rma".

Usage

"forest"(x, annotate=TRUE, xlim, alim, clim, ylim, at, steps=5, level=x$level, refline=0, digits=2L, width, xlab, ilab, ilab.xpos, ilab.pos, transf, atransf, targs, rows, efac=1, pch=15, psize=1, lty, cex, cex.lab, cex.axis, ...)

Arguments

an object of class "cumul.rma".

annotate

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

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.

clim

limits for the confidence intervals. If unspecified, no limits are used.

ylim

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

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 (the 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 (the default is to take the value from the object).

refline

value at which a vertical ‘reference’ line should be drawn (the default is 0). The line can be suppressed by setting this argument to NA.

digits

integer specifying the number of decimal places to which the tick mark labels of the x-axis and the annotations should be rounded (the default is 2L). Can also be a vector of two integers, the first specifying the number of decimal places for the annotations, the second for the x-axis labels. When specifying an integer (e.g., 2L), trailing zeros after the decimal mark are dropped for the x-axis labels. When specifying a numerical value (e.g., 2), trailing zeros are retained.

width

optional integer to manually adjust the width of the columns for the annotations.

xlab

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

ilab

optional vector, matrix, or data frame providing additional information about the studies that should be added to the plot.

ilab.xpos

vector of numerical value(s) specifying the x-axis position(s) of the variable(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 vector(s) given via ilab (2 means right, 4 mean left aligned). If unspecified, the default is to center the labels.

transf

optional argument specifying the name of a function that should be used to transform the observed effect sizes, summary estimates, fitted values, and confidence interval bounds (e.g., transf=exp; see also transf). If unspecified, no transformation is used.

atransf

optional argument specifying the name of a function that should be used to transform the x-axis labels and annotations (e.g., atransf=exp; see also transf). If unspecified, 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 outcome (the remaining outcomes are then plotted below this starting row).

efac

vertical expansion factor for confidence interval limits and arrows. The default value of 1 should usually work okay. Can also be a vector of two numbers, the first for CI limits, the second for arrows.

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. Default is 1.

lty

optional character string specifying the line type for the confidence intervals (if unspecified, the function sets this to "solid" by default).

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 estimated (average) outcome with corresponding confidence interval as one study at a time is added to the analysis.

References

Chalmers, T. C., & Lau, J. (1993). Meta-analytic stimulus for changes in clinical trials. Statistical Methods in Medical Research, 2, 161--172.

Lau, J., Schmid, C. H., & Chalmers, T. C. (1995). Cumulative meta-analysis of clinical trials builds evidence for exemplary medical care. Journal of Clinical Epidemiology, 48, 45--57.

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/.

Examples

Run this code

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

### random-effects model
res <- rma(yi, vi, data=dat, slab=paste(author, year, sep=", "))

x <- cumul(res, order=order(dat$year))
forest(x, cex=.8)
forest(x, alim=c(-2,1), cex=.8)

### meta-analysis of the (log) relative risks using the Mantel-Haenszel method
res <- rma.mh(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg,
              slab=paste(author, year, sep=", "))
x <- cumul(res, order=order(dat$year))
forest(x, alim=c(-2,1), cex=.8)