addpoly.rma: Add Polygons to Forest Plots (Method for 'rma' Objects)

In metafor: Meta-Analysis Package for R

Add Polygons to Forest Plots (Method for 'rma' Objects)

Description

Function to add a polygon to a forest plot showing the summary estimate with corresponding confidence interval based on an object of class "rma".

Usage

## S3 method for class 'rma'
addpoly(x, row=-2, level=x$level, annotate,
        addpred=FALSE, digits, width, mlab, transf, atransf, targs,
        efac, col, border, lty, fonts, cex, ...)

Arguments

x	an object of class "rma".
row	numeric value to specify the row (or more generally, the horizontal position) for plotting the polygon (the default is -2).
level	numeric value between 0 and 100 to specify the confidence interval level (see here for details). The default is to take the value from the object.
annotate	optional logical to specify whether annotations for the summary estimate should be added to the plot.
addpred	logical to specify whether the bounds of the prediction interval should be added to the plot (the default is FALSE).
digits	optional integer to specify the number of decimal places to which the annotations should be rounded.
width	optional integer to manually adjust the width of the columns for the annotations.
mlab	optional character string giving a label for the summary estimate polygon. If unspecified, the function sets a default label.
transf	optional argument to specify a function to transform the summary estimate and confidence interval bound (e.g., transf=exp; see also transf).
atransf	optional argument to specify a function to transform the annotations (e.g., atransf=exp; see also transf).
targs	optional arguments needed by the function specified via transf or atransf.
efac	optional vertical expansion factor for the polygon.
col	optional character string to specify the color of the polygon.
border	optional character string to specify the border color of the polygon.
lty	optional character string to specify the line type for the prediction interval.
fonts	optional character string to specify the font for the label and annotations.
cex	optional symbol expansion factor.
...	other arguments.

Details

The function can be used to add a four-sided polygon, sometimes called a summary ‘diamond’, to an existing forest plot created with the forest function. The polygon shows the summary estimate (with its confidence interval bounds) based on an equal- or a random-effects model. Using this function, summary estimates based on different types of models can be shown in the same plot. Also, summary estimates based on a subgrouping of the studies can be added to the plot this way. See ‘Examples’.

If unspecified, arguments annotate, digits, width, transf, atransf, targs, efac (only if the forest plot was created with forest.rma), fonts, cex, annosym, and textpos are automatically set equal to the same values that were used when creating the forest plot.

Author(s)

Wolfgang Viechtbauer [e-mail] https://www.metafor-project.org

References

Viechtbauer, W. (2010). Conducting meta-analyses in R with the metafor package. Journal of Statistical Software, 36(3), 1–48. ⁠https://doi.org/10.18637/jss.v036.i03⁠

See Also

forest for functions to draw forest plots to which polygons can be added.

Examples

### meta-analysis of the log risk ratios 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=", "))

### forest plot of the observed risk ratios with summary estimate
forest(res, atransf=exp, xlim=c(-8,6), ylim=c(-2.5,15), header=TRUE, top=2)

### meta-analysis of the log risk ratios using a random-effects model
res <- rma(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg)

### add the summary estimate from the random-effects model to the forest plot
addpoly(res)

### forest plot with subgrouping of studies and summaries per subgroup
res <- rma(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg,
           slab=paste(author, year, sep=", "))
tmp <- forest(res, xlim=c(-16, 4.6), at=log(c(0.05, 0.25, 1, 4)), atransf=exp,
              ilab=cbind(tpos, tneg, cpos, cneg), ilab.xpos=c(-9.5,-8,-6,-4.5),
              cex=0.75, ylim=c(-1, 27), order=alloc, rows=c(3:4,9:15,20:23),
              mlab="RE Model for All Studies", header="Author(s) and Year")
op <- par(cex=0.75, font=2)
text(c(-9.5,-8,-6,-4.5), tmp$ylim[2]-1, c("TB+", "TB-", "TB+", "TB-"))
text(c(-8.75,-5.25),     tmp$ylim[2],   c("Vaccinated", "Control"))
par(font=4)
text(-16, c(24,16,5), c("Systematic Allocation", "Random Allocation",
                        "Alternate Allocation"), pos=4)
par(op)
res <- rma(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg,
           subset=(alloc=="systematic"))
addpoly(res, row=18.5, mlab="RE Model for Subgroup")
res <- rma(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg,
           subset=(alloc=="random"))
addpoly(res, row=7.5, mlab="RE Model for Subgroup")
res <- rma(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg,
           subset=(alloc=="alternate"))
addpoly(res, row=1.5, mlab="RE Model for Subgroup")

metafor documentation built on May 29, 2024, 7:44 a.m.