plots:forest_plot_with_subgroups
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Table of Contents
Forest Plot with Subgroups
Description
Below is an example of a forest plot with three subgroups. The results of the individual studies are shown grouped together according to their subgroup. Below each subgroup, a summary polygon shows the results when fitting a random-effects model just to the studies within that group. The summary polygon at the bottom of the plot shows the results from a random-effects model when analyzing all 13 studies.
Plot
Code
library(metafor) ### copy BCG vaccine meta-analysis data into 'dat' dat <- dat.bcg ### calculate log risk ratios and corresponding sampling variances (and use ### the 'slab' argument to store study labels as part of the data frame) dat <- escalc(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat, slab=paste(author, year, sep=", ")) ### fit random-effects model res <- rma(yi, vi, data=dat) ### set up forest plot (with 2x2 table counts added; the 'rows' argument is ### used to specify in which rows the outcomes will be plotted) forest(res, xlim=c(-16, 6), at=log(c(0.05, 0.25, 1, 4)), atransf=exp, ilab=cbind(dat$tpos, dat$tneg, dat$cpos, dat$cneg), ilab.xpos=c(-9.5,-8,-6,-4.5), cex=0.75, ylim=c(-1, 27), order=order(dat$alloc), rows=c(3:4,9:15,20:23), xlab="Risk Ratio", mlab="", psize=1, header="Author(s) and Year") ### add text with Q-value, dfs, p-value, and I^2 statistic text(-16, -1, pos=4, cex=0.75, bquote(paste("RE Model for All Studies (Q = ", .(formatC(res$QE, digits=2, format="f")), ", df = ", .(res$k - res$p), ", p = ", .(formatC(res$QEp, digits=2, format="f")), "; ", I^2, " = ", .(formatC(res$I2, digits=1, format="f")), "%)"))) ### fit meta-regression model to test for subgroup differences res <- rma(yi, vi, mods = ~ alloc, data=dat) ### add text for the test of subgroup differences text(-16, -1.8, pos=4, cex=0.75, bquote(paste("Test for Subgroup Differences: ", Q[M], " = ", .(formatC(res$QM, digits=2, format="f")), ", df = ", .(res$p - 1), ", p = ", .(formatC(res$QMp, digits=2, format="f"))))) ### set font expansion factor (as in forest() above) and use bold italic ### font and save original settings in object 'op' op <- par(cex=0.75, font=4) ### add text for the subgroups text(-16, c(24,16,5), pos=4, c("Systematic Allocation", "Random Allocation", "Alternate Allocation")) ### switch to bold font par(font=2) ### add column headings to the plot text(c(-9.5,-8,-6,-4.5), 26, c("TB+", "TB-", "TB+", "TB-")) text(c(-8.75,-5.25), 27, c("Vaccinated", "Control")) ### set par back to the original settings par(op) ### fit random-effects model in the three subgroups res.s <- rma(yi, vi, subset=(alloc=="systematic"), data=dat) res.r <- rma(yi, vi, subset=(alloc=="random"), data=dat) res.a <- rma(yi, vi, subset=(alloc=="alternate"), data=dat) ### add summary polygons for the three subgroups addpoly(res.s, row=18.5, cex=0.75, atransf=exp, mlab="") addpoly(res.r, row= 7.5, cex=0.75, atransf=exp, mlab="") addpoly(res.a, row= 1.5, cex=0.75, atransf=exp, mlab="") ### add text with Q-value, dfs, p-value, and I^2 statistic for subgroups text(-16, 18.5, pos=4, cex=0.75, bquote(paste("RE Model for Subgroup (Q = ", .(formatC(res.s$QE, digits=2, format="f")), ", df = ", .(res.s$k - res.s$p), ", p = ", .(formatC(res.s$QEp, digits=2, format="f")), "; ", I^2, " = ", .(formatC(res.s$I2, digits=1, format="f")), "%)"))) text(-16, 7.5, pos=4, cex=0.75, bquote(paste("RE Model for Subgroup (Q = ", .(formatC(res.r$QE, digits=2, format="f")), ", df = ", .(res.r$k - res.r$p), ", p = ", .(formatC(res.r$QEp, digits=2, format="f")), "; ", I^2, " = ", .(formatC(res.r$I2, digits=1, format="f")), "%)"))) text(-16, 1.5, pos=4, cex=0.75, bquote(paste("RE Model for Subgroup (Q = ", .(formatC(res.a$QE, digits=2, format="f")), ", df = ", .(res.a$k - res.a$p), ", p = ", .(formatC(res.a$QEp, digits=2, format="f")), "; ", I^2, " = ", .(formatC(res.a$I2, digits=1, format="f")), "%)")))
plots/forest_plot_with_subgroups.1591169770.txt.gz ยท Last modified: 2020/06/03 07:36 by Wolfgang Viechtbauer