[R-meta] Appending a risk-of-bias traffic-light plot to a 'three-level' forest plot

Mon May 23 04:52:44 CEST 2022

Dear all,

After spending some more time on the issue, I have managed to find a
solution and indeed the vignette's instructions can be used directly,
with a little help of cbind(sav, dat$slab.ref)!

Thanks,
Josh

On Mon, May 23, 2022 at 2:02 AM Joshua Bernal <jdkb9701 using connect.hku.hk> wrote:
>
> Dear Dr. Viechtbauer and members,
>
> I was hoping to add numbered references to the forest plot using
> superscripts, as described by the vignette in the metafor website
> (https://www.metafor-project.org/doku.php/plots:forest_plot_with_superscripts).
> However, because of the 'dataframe transformation from rma.mv to
> rma.uni' following the workaround method to aggregate effect sizes as
> described in Source A
> (stat.ethz.ch/pipermail/r-sig-meta-analysis/2019-February/001423.html),
> I simply could not use the vignette's instructions directly. Your help
> on this would be highly appreciated!
>
> Thanks,
> Josh
>
>
> On Fri, Feb 18, 2022 at 5:51 PM Viechtbauer, Wolfgang (SP)
> <wolfgang.viechtbauer using maastrichtuniversity.nl> wrote:
> >
> > Dear Josh,
> >
> > See below for my responses.
> >
> > Best,
> > Wolfgang
> >
> > >-----Original Message-----
> > >From: R-sig-meta-analysis [mailto:r-sig-meta-analysis-bounces using r-project.org] On
> > >Behalf Of Joshua Bernal
> > >Sent: Friday, 18 February, 2022 3:07
> > >To: r-sig-meta-analysis using r-project.org
> > >Subject: [R-meta] Appending a risk-of-bias traffic-light plot to a 'three-level'
> > >forest plot
> > >
> > >Greetings Dr. Viechtbauer and members,
> > >
> > >I ran a three-level meta-analysis with rma.mv (due to multiple
> > >measures of a construct within-studies). I seek help on how to append
> > >a risk-of-bias traffic-light plot to an extension of the three-level
> > >forest plot, please find the query details below...
> > >
> > >Goal A (metafor):
> > >Create the three-level forest plot with each study's "aggregated"
> > >effect estimate and CI.
> > >(Source A: stat.ethz.ch/pipermail/r-sig-meta-analysis/2019-February/001423.html)
> > >
> > >Goal A Issues:
> > >1) Source A presents 2 ways to obtain "aggregated" effect sizes, with
> > >the second way getting "exactly the same results as those from the
> > >full model". Because the present rma.mv analysis uses the
> > >t-distribution (test = "t"), the p-values and summary CIs obtained are
> > >slightly different/larger. Is it possible to get the exact same
> > >results as when test = "t" for the rma.mv model? To see what this
> > >looks like, please find the metafor reprex below.
> >
> > I would suggest to do the following:
> >
> > 1) Use the 'contain' method for computing the dfs:
> >
> > res <- rma.mv(yi, vi, random = ~ 1 | author/outcome, data = dat, test = "t", dfs = "contain",
> >               method = "REML", slab = author)
> >
> > 2) Then use test="t" for rma():
> >
> > rma(yi, vi, data=sav, test="t")
> >
> > Then the results match up exactly.
> >
> > >2) After running the reprex, you will see that Study 6 contributes one
> > >effect size only, its CI from the "standard" rma.mv forest plot (where
> > >all effect sizes in each study are shown) vs its CI from the
> > >"aggregated" forest plot are different. If the argument
> > >"tau2=res$sigma2[2]" is omitted from the code of the "aggregated"
> > >forest plot, then the obtained summary CI for Study 6 then matches
> > >with that of the "standard" plot. Which would be considered the
> > >correct approach in this case?
> >
> > The first. If you want to show a forest plot of the aggregated data, then the aggregation involves adding the within-study variance (as you have done) and hence the CI will be wider also for study 6.
> >
> > >metafor reprex:
> > >###
> > >library(metafor)
> > >
> > >dat <- structure(list(author = c("Study 1", "Study 1", "Study 1", "Study 1",
> > >"Study 1", "Study 2", "Study 2", "Study 2", "Study 2", "Study 3",
> > >"Study 3", "Study 4", "Study 4", "Study 5", "Study 5", "Study 6"
> > >), study = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 4, 4, 5, 5, 6),
> > >    outcome = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
> > >    15, 16), yi = c(0.52, 0.256, 0.5003, 0.3131, -0.1019, 0.3591,
> > >    0.0341, 0.0357, 0.3942, -0.1503, 0.2671, 0.131, 0.1664, 1.1761,
> > >    0.5799, 0.406), vi = c(0.00926, 0.00199, 0.01171, 0.0171,
> > >    0.00524, 0.0712, 0.0971, 0.0823, 0.0912, 0.1204, 0.3536,
> > >    0.0655, 0.0607, 0.9571, 0.6617, 0.5139)), row.names = c(NA,
> > >16L), class = "data.frame")
> > >
> > >res <- rma.mv(yi, vi, random = ~ 1 | author/outcome, data = dat, test
> > >= "t", method = "REML", slab = author)
> > >res
> > >forest(res)
> > >
> > >sav <- lapply(split(dat, dat$author), function(x) {
> > >    res <- rma(yi, vi, data=x, tau2=res$sigma2[2])
> > >    return(c(coef(res), vcov(res)))
> > >})
> > >
> > >sav <- data.frame(do.call(rbind, sav))
> > >names(sav) <- c("yi", "vi")
> > >
> > >forest(sav$yi, sav$vi, slab=rownames(sav))
> > >
> > >rma(yi, vi, data=sav)
> > >res
> > >###
> > >
> > >Goal B (robvis, development version 0.3.0.900):
> > >Create a risk-of-bias traffic-light plot using the "Generic" (or aka
> > >"ROB1") template.
> > >(Source B: https://github.com/mcguinlu/robvis  ("Generic")  OR
> > >cran.r-project.org/web/packages/robvis/vignettes/Introduction_to_robvis.html#rob1
> > > ("ROB1"))
> > >
> > >Goal B Issues:
> > >After running the robvis reprex below, you will see that an extra
> > >judgment label ("Critical" or dark red circle with exclamation mark)
> > >is automatically added/cannot be removed (although only 5 judgment
> > >labels are relevant in the dataset, I am forced to specify 6 judgement
> > >labels). I am aware there is an argument "judgement_levels" under
> > >development, but do not know if it is relevant and if so how to take
> > >it from here...
> >
> > Can't help with this.
> >
> > >robvis reprex:
> > >###
> > >library(robvis)
> > >
> > >rp <- structure(list(Study = c("Study 1", "Study 2", "Study 3", "Study 4",
> > >"Study 5", "Study 6"), Bias.due.to.confounding. = c("Not applicable",
> > >"Not applicable", "Not applicable", "Some concerns", "Low", "No information"
> > >), Bias.in.selection.of.participants.into.the.study. = c("Not applicable",
> > >"Not applicable", "Not applicable", "Some concerns", "Low", "Low"
> > >), Bias.in.classification.of.interventions. = c("Not applicable",
> > >"Not applicable", "Not applicable", "Some concerns", "Low", "Low"
> > >), Bias.arising.from.the.randomization.process. = c("Some concerns",
> > >"Low", "Low", "Not applicable", "Not applicable", "Not applicable"
> > >), Bias.due.to.deviations.from.intended.intervention. = c("Low",
> > >"Some concerns", "Low", "Low", "Some concerns", "Low"),
> > >Bias.due.to.missing.outcome.data. = c("Some concerns",
> > >"Low", "No information", "Some concerns", "Low", "No information"
> > >), Bias.in.measurement.of.the.outcome. = c("Some concerns", "Low",
> > >"Some concerns", "Some concerns", "Low", "Some concerns"),
> > >Bias.due.to.selection.of.the.reported.result. = c("Some concerns",
> > >"Low", "High", "Some concerns", "Low", "High"), Overall = c("Some concerns",
> > >"Low", "High", "Some concerns", "Low", "High")), row.names = c(NA,
> > >6L), class = "data.frame")
> > >
> > >bor <- rob_traffic_light(rp, tool="Generic", colour="cochrane",
> > >psize=10, overall=TRUE, judgement_labels=c("","High","Some
> > >concerns","Low","No information","Not applicable"))
> > >
> > >bor
> > >###
> > >
> > >Goal C:
> > >Append the risk-of-bias traffic-light plot (from Goal B) to the forest
> > >plot (from Goal A).
> > >(Source C: mcguinlu.github.io/robvis/articles/metafor.html#appending-risk-of-
> > >bias-plots-to-forest-plots-1)
> > >
> > >Goal C Issues:
> > >Because the present analysis considers the bias domains of both
> > >randomized and non-randomized controlled intervention studies and risk
> > >of bias was respectively assessed by ROB2 and ROBINS-I, the "Generic"
> > >template is used because it allows modifying the number of domains so
> > >as to include the relevant domains of both tools in the traffic-light
> > >plot. However, according to "rob_tools(forest = TRUE)", robvis
> > >currently supports only "ROB2" and "ROBINS-I" templates for the
> > >"rob_append_to_forest()" function.
> >
> > Again, can't really help with robvis.
> >
> > As an alternative, you could also consider creating the traffic light part of the plot yourself. Then you have full control over what is shown and how. An example where I did this can be found here:
> >
> > https://www.metafor-project.org/doku.php/plots:forest_plot_revman
> >
> > >Other sub-goals:
> > >- Modify text of header from "Estimate [95% CI]" to "SMD [95% CI]".
> >
> > In forest(), see argument 'header'.
> >
> > >- Modify text of x-axis label from "Observed Outcome" to "Standardized
> > >Mean Difference".
> >
> > In forest(), see argument 'xlab'.
> >
> > >- To the right of "SMD [95% CI]", add a column with the header "No. of
> > >effect sizes" to display the number of effect sizes within each study.
> >
> > In forest(), you can use the 'textpos' argument to create space to the right of the annotations and then add this column either via the 'ilab' argument or with text(). In fact, the link above demonstrates this.
> >
> > >Many thanks in advance for your help...
> > >
> > >Sincerely,
> > >Josh