[R] metafor package
John Peterson
john.peterson.can at gmail.com
Sat Dec 12 15:43:39 CET 2015
Hi Dr. Viechtbauer,
Thank you very much. Putting in sei=se in forest() fixed the problem.
Thanks for your help.
On 8 December 2015 at 08:37, Viechtbauer Wolfgang (STAT) <
wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:
> The first and second argument of forest() (or more precisely,
> forest.default()) are for the estimates and the corresponding sampling
> variances, respectively. So, if you do forest(rr, se, ...), then the
> function will interpret the standard errors as if they are variances. So,
> you should do forest(rr, sei=se, ...).
>
> And just in case: In all likelihood, those SEs are for the
> *log-transformed* risk ratios, so you should also pass log-transformed risk
> ratios to the function (and then use 'atransf=exp' so results are shown
> with back-transformed x-axis labels and annotations).
>
> Best,
> Wolfgang
>
> --
> Wolfgang Viechtbauer, Ph.D., Statistician | Department of Psychiatry and
> Neuropsychology | Maastricht University | P.O. Box 616 (VIJV1) | 6200 MD
> Maastricht, The Netherlands | +31 (43) 388-4170 | http://www.wvbauer.com
>
> > -----Original Message-----
> > From: John Peterson [mailto:john.peterson.can at gmail.com]
> > Sent: Tuesday, December 08, 2015 14:25
> > To: Viechtbauer Wolfgang (STAT)
> > Cc: R-help at r-project.org
> > Subject: Re: [R] metafor package
> >
> > Hi Dr. Viechtbauer,
> >
> > The code provided in the metafor projects website for subgroup includes
> > fitting a random effects model on the entire dataset and fitting a random
> > effects model within subgroups. When I exactly follow this code, my
> > estimates and confidence intervals for estimate within each subgroup
> > matches with what I get in STATA so it seems to be the correct estimate
> > (and CI). However, I don't want to present an overall effect and I want
> > to present only the effect within each subgroup. In my second attempt, I
> > did not run a random effects model within the entire dataset and only ran
> > the models within each subgroup. I generated a variable corresponding to
> > the estimate(risk ratio) and standard error which I plugged in the
> > forest() function (i.e. forest(rr, se, .....). When I run this code, the
> > estimate I get for each subgroup is slightly different than the estimate
> > I get for each subgroup in comparison to when I also included the random
> > effects model for the overall effect. (i.e. my first attempt). Is this
> > the right approach? I was not clear when you said passing the estimates
> > and sampling variances to the forest() function. I created a variable
> > corresponding to the estimate and standard error and plugged those in the
> > forest() function. I am not sure if this is the right approach. Thanks,
> >
> > John
> >
> > On 8 December 2015 at 03:47, Viechtbauer Wolfgang (STAT)
> > <wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:
> > Hi John,
> >
> > Please keep r-help copied on the reply.
> >
> > What's the 'previous model'? How do you get estimates within subgroups
> > that 'includes the overall effect'? I really cannot follow you here.
> >
> > Best,
> > Wolfgang
> >
> > --
> > Wolfgang Viechtbauer, Ph.D., Statistician | Department of Psychiatry and
> > Neuropsychology | Maastricht University | P.O. Box 616 (VIJV1) | 6200 MD
> > Maastricht, The Netherlands | +31 (43) 388-4170 | http://www.wvbauer.com
> >
> > > -----Original Message-----
> > > From: John Peterson [mailto:john.peterson.can at gmail.com]
> > > Sent: Monday, December 07, 2015 22:14
> > > To: Viechtbauer Wolfgang (STAT)
> > > Subject: Re: [R] metafor package
> > >
> > > Hi Dr. Viechtbauer,
> > > Thank you very much for your reply. I tried your advice and was able to
> > > make a forest plot with only the estimates for each subgroup.For the
> > > estiamte for each subgroup, similar to the previous model, I random
> > > effects model within each subgroup. However, I now find the result for
> > > the estiamte within subgroup to be different thant the result for the
> > > previous model. I have tried analyzing this in STATA and I get the same
> > > result as the model which includes the overall effect. Any advice on
> > what
> > > may be wrong here? Thanks greatly,
> > > John
> > >
> > > On 7 December 2015 at 04:02, Viechtbauer Wolfgang (STAT)
> > > <wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:
> > > The code you posted is totally mangled up, but it's just what can be
> > > found here:
> > >
> > > http://www.metafor-
> > project.org/doku.php/plots:forest_plot_with_subgroups
> > >
> > > If you don't want an overall estimate, just pass the estimates and
> > > corresponding sampling variances to the forest() function (and not the
> > > model object). Use the 'rows' argument to specify where the estimates
> > > will be placed and adjust 'ylim' so give you enough space to leave gaps
> > > for headings and the subgroup estimates. Then fit models within the
> > > subgroups (the 'subset' argument is useful here) and use addpoly() to
> > add
> > > the subgroup estimates in the appropriate rows. With text(), you can
> > add
> > > headings as needed.
> > >
> > > If you use weights() on each subgroup model object, you can get the
> > > subgroup weights (that add up to 100% within each subgroup). It's
> > > probably easiest to just add those values with text() in an appropriate
> > > place to the plot.
> > >
> > > Best,
> > > Wolfgang
> > >
> > > --
> > > Wolfgang Viechtbauer, Ph.D., Statistician | Department of Psychiatry
> > and
> > > Neuropsychology | Maastricht University | P.O. Box 616 (VIJV1) | 6200
> > MD
> > > Maastricht, The Netherlands | +31 (43) 388-4170 |
> > http://www.wvbauer.com
> > >
> > > > -----Original Message-----
> > > > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of John
> > > > Peterson
> > > > Sent: Monday, December 07, 2015 01:39
> > > > To: r-help at r-project.org
> > > > Subject: [R] metafor package
> > > >
> > > > Hi Everyone,
> > > >
> > > > I am conducting a meta-analysis using the metafor package. I am
> > > > interested
> > > > in obtaining an estimate by subgroup only without showing an overall
> > > > effect. This is directly from the metafor website. How would i modify
> > > > this
> > > > code to only show subgroup effects? Further, I want to show weights
> > by
> > > > subgroup. The option showweights=TRUE does not display weights by
> > > > subgroup
> > > > but by the weight of each study in comparison to all studies (and not
> > > the
> > > > subgroup). You help would be appreciated.
> >
> > [snip garbled code]
>
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