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Here is another example of a contour-enhanced funnel plot (Peters et al., 2008) (see here for a brief discussion of the idea behind such plots). This one is a very close re-creation of Figure 2(b) from Peters et al. (2008). Note that the values for
ylim technically have to be greater than 0 when using the inverse standard error on the y-axis, but we can get essentially the same limits by using a very small value for the lower limit.
library(metafor) ### decrease margins so the full space is used par(mar=c(5,4,1,2)) ### calculate log odds ratios and corresponding sampling variances dat <- escalc(measure="OR", ai=ai, n1i=n1i, ci=ci, n2i=n2i, data=dat.graves2010) ### create contour enhanced funnel plot funnel(dat$yi, dat$vi, yaxis="seinv", xlim=c(-3,2), ylim=c(.00001,8), xaxs="i", yaxs="i", las=1, level=c(.10, .05, .01), shade=c("white", "gray55", "gray75"), legend=TRUE, back="gray90", ylab="Precision (1/se)")
Peters, J. L., Sutton, A. J., Jones, D. R., Abrams, K. R., & Rushton, L. (2008). Contour-enhanced meta-analysis funnel plots help distinguish publication bias from other causes of asymmetry. Journal of Clinical Epidemiology, 61(10), 991–996.