[R-meta] Mismatch between output from sub-group analysis and forest plot

[Viechtbauer, Wolfgang (SP)]

First of all, thanks, Joao, for posting in plain text.

I don't know whether this is relevant to the issue, but I can already tell you that the following makes no sense:

pes.da.lcm=rma(yi, vi, data=ies.da.lcmbi, mods=~lcmbi=="Records", method="DL")

(I am referring to the 'mods=~lcmbi=="Records"' part). What are you trying to do here? Maybe you were trying to use the 'subset' argument? Something like this:

pes.da.lcm=rma(yi, vi, data=ies.da.lcmbi, subset=lcmbi=="Records", method="DL")

But I am just guessing.

Best,
Wolfgang

-----Original Message-----
From: R-sig-meta-analysis [mailto:r-sig-meta-analysis-bounces using r-project.org] On Behalf Of Gerta Ruecker
Sent: Tuesday, 11 February, 2020 19:31
To: Joao Afonso; r-sig-meta-analysis using r-project.org
Subject: Re: [R-meta] Mismatch between output from sub-group analysis and forest plot

Dear Joao,

There is another problem. You say that the output and the forest plot 
"have different values for the pooled estimates", but you've sent us 
only the code, not the output or the forest plot, at least I didn't find 
either of them. Thus, if we are expected to see what's wrong here you 
have to send us your results and, even better, the data to reproduce the 
results.

One idea is that the results in the output may be transformed, while in 
the forest plot they are back-transformed, but I don't know.

Best,

Gerta

Am 11.02.2020 um 19:20 schrieb Joao Afonso:
> Dear all,
>
> Sorry for the double posting and previous "messy" message. I am
> conducting a meta-analysis on prevalence and incidence data. As there
> is plenty of heterogeneity I am doing a sub-group analysis. However I
> am finding the output of the same and forest plots produced to have
> different values for the pooled estimates. I am using the double
> arcsine transformation and then have the data back-transformed to
> produce the estimates. The model is the following:
>
> iies.da.lcmbi<-ies.da %>%
>    filter(is.na(lcmbi)==FALSE)
>
> subganal.lcmbi=rma(yi, vi, data=ies.da.lcmbi, mods=~lcmbi, method="DL")
> pes.da.lcm=rma(yi, vi, data=ies.da.lcmbi, mods=~lcmbi=="Records", method="DL")
> pes.da.records=rma(yi, vi, data=ies.da.lcmbi, mods=~lcmbi=="Locomotion
> Scoring Method", method="DL")
> pes.subg.lcmbi=predict(subganal.lcmbi,
> transf=transf.ipft.hm,
> targ=list(ni=prevalence_2020_cow_nomv$ssizeanimal))
> dat.samevar=data.frame(estimate=c((pes.da.lcm$b)[1], (pes.da.records$b)[1]),
> stderror=c((pes.da.lcm$se)[1], (pes.da.records$se)[1]),
> tau2=subganal.lcmbi$tau2)
> pes.da.lcmbi=rma(estimate, sei=stderror,
> method="DL",
> data=dat.samevar)
> pes.lcmbi=predict(pes.da.lcmbi, transf=transf.ipft.hm,
> targ=list(ni=prevalence_2020_cow_nomv$ssizeanimal))
> print(pes.da.lcm, digits=3)
> print(pes.da.records, digits=3)
> print(subganal.lcmbi, digits=3)
> print(pes.lcmbi, digits=3)
>
>
> And to produce the forest plot I use the following code:
>
> subganal.lcmbi=rma(yi, vi, data=ies.da.lcmbi, mods=~lcmbi, method="DL")
> pes.summary=metaprop(nlameanimal, ssizeanimal, author, data=ies.da.lcmbi,
>                       sm="PFT",
>                       method.tau="DL",
>                       method.ci="NAsm",
>                       byvar=lcmbi,
>                       tau.common=TRUE,
>                       tau.preset=sqrt(subganal.lcmbi$tau2))
> precision=sqrt(ies.da.lcmbi$vi)
> jpeg(file="forest_cow_cow_lcmbi.jpeg", width=11, height=12, units="in", res=300)
> forest(pes.summary,
>         xlim=c(0,1),
>         pscale=1,
>         rightcols=FALSE,
>         leftcols=c("studlab", "effect", "ci"),
>         leftlabs=c("Study", "Prevalence", "95% C.I."),
>         text.random="Prevalence of Lameness in British Dairy Cattle",
>         bylab = "Lameness Data Source",
>         print.byvar = TRUE,
>         xlab="Prevalence of Lameness", smlab="",
>         weight.study="random", squaresize=0.5, col.square="navy",
>         col.diamond="maroon", col.diamond.lines="maroon",
>         pooled.totals=FALSE,
>         comb.fixed=FALSE,
>         fs.hetstat=10,
>         print.tau2=TRUE,
>         print.Q=TRUE,
>         print.pval.Q=TRUE,
>         print.I2=TRUE,
>         digits=2,
>         sortvar = precision)
> dev.off()
>
> What could I be doing wrong? I will be extremely grateful for any help
> or guidance.
>
> Wishing all a great afternoon,
>
> Joao