[R-meta] adapting forest plot visual

Michael Dewey ||@t@ @end|ng |rom dewey@myzen@co@uk
Thu Jun 4 11:15:08 CEST 2020 

Dear Norman

There are many packages which perform meta-analysis in one form or 
another, there are 100+ on CRAN, so it is unlikely that they will result 
in objects with the same format. Since the R way is to access the 
results of the fit using the extractor functions the authors are 
entitled to change the internals as much as they like. I suggest that 
for a given analysis you choose one of meta or metafor and stick to it 
as far as possible.

Michael

On 04/06/2020 07:18, Norman DAURELLE wrote:
> 
> Hello again everyone,
> 
> I tired to use the arguments that you suggested Gerta, (col.study, 
> col.square, col.square.lines and col.inside),
> but every time I got the same result, with nothing changed from the 
> original plot,
> and warnings that read "In segments(...) : "col.study" is not a 
> graphical parameter ".
> 
> I tried to run the example you gave me though, and it worked alright, 
> even though there were many lines not fitting in the plot I believe,
> but I could see the different colours for each effect size or for groups 
> of effect sizes.
> 
> Also, I am working with an object that is the result of using the rma 
> function from the package metafor, and I don't quite understand what 
> difference exists between rma, meta, and robu objects.
> I used the robu() function to have a result that accounts for the fact 
> that some of the studies I use provide multiple effect-sizes to my 
> meta-analysis,
> as shown in the youtube video by Daniel Quintana explaining his 2015 
> article,
> "From pre-registration to publication : a non-technical primer for 
> conducting a meta-analysis to synthesize correlational data".
> However, when I try to use the forest function with the robu object it 
> doesn't work.
> 
> Would you know what exactly differs between these rma, meta, and robu 
> objects ?
> I understand that they are the results of different functions, but they 
> are supposed to be meta-analysis results, so in my mind they should have 
> been of the same format,
> or at least I should still be able to use the robu object in the forest 
> function since the forest plot is the main result of the meta-analysis.
> 
> Do you have any advice ?
> 
> Thank you !
> 
> Norman
> 
> 
> 
> **//_^**//_^
> ----- Mail d'origine -----
> De: Norman DAURELLE <norman.daurelle using agroparistech.fr>
> À: r-sig-meta-analysis using r-project.org
> Cc: Michael Dewey <lists using dewey.myzen.co.uk>, ruecker using imbi.uni-freiburg.de
> Envoyé: Thu, 04 Jun 2020 01:12:06 +0200 (CEST)
> Objet: Re: [R-meta] adapting forest plot visual
> 
> 
> Dear all, dear Greta and Michael,
> 
> thank you for your answers, I am indeed using the function forest (or 
> forest.rma, which gives the same result I think when I look up the 
> documentation through "help") from the package meta.
> 
> I use the rma() function from the metafor package to perform the 
> meta-analysis. I have read about the forestplot function from the 
> package named the same, and I tried to use it, but the first plot I got 
> with it was not that nice, so I went back to digging deeper into the 
> forest function from the package meta.
> 
> Special thanks Greta for the advice about the arguments col.study, 
> col.square, col.square.lines and col.inside, I was trying to use the 
> argument leftcols, without much success.
> 
> Have a nice day !
> 
> Norman
> **//_^
> ----- Mail d'origine -----
> De: Gerta Ruecker <ruecker using imbi.uni-freiburg.de>
> À: Michael Dewey <lists using dewey.myzen.co.uk>, Norman DAURELLE 
> <norman.daurelle using agroparistech.fr>, r-sig-meta-analysis using r-project.org
> Envoyé: Wed, 03 Jun 2020 11:22:15 +0200 (CEST)
> Objet: Re: [R-meta] adapting forest plot visual
> 
> I think he mentioned the meta package, therefore I provided an example
> how to do it in meta. Disclaimer: I have often used it myself ;-)
> 
> Best,
> 
> Gerta
> 
> Am 03.06.2020 um 11:05 schrieb Michael Dewey:
>  > Dear Norman
>  >
>  > There is a package on CRAN called forestplot which claims to provide
>  > comprehensive options for controlling the forest plot so if you cannot
>  > find how to do it in your preferred package (which you do not name
>  > incidentally) then it might be worth investigating. Disclaimer: I have
>  > never used it myself.
>  >
>  > Michael
>  >
>  > On 02/06/2020 12:24, Norman DAURELLE wrote:
>  >>
>  >> Dear list,I have now run a meta-analysis based on relationship slopes
>  >> between two variables and I am trying to make the forest plot easily
>  >> readable and understandable.I used the "order" parameter of the
>  >> forest function to order outcomes from lowest estimate on the first
>  >> line to highest estimate on the last line, but I would like to
>  >> display the outcomes that share a characteristic in the same colour (
>  >> for example, all effect-sizes coming from studies conducted in the
>  >> same country displayed in one colour ). I have been looking for a way
>  >> to do that in the documentation of the forest function of the meta
>  >> package, but there are a lot of arguments to that function and I
>  >> can't find one that does what I would like to do. It doesn't
>  >> necessarily have to be based on colour but if I can change the shape
>  >> of the square representing the effect sizes that come from the same
>  >> place for example that would also do the trick, even though colour is
>  >> more direct.Would you know of a way to do that ? Thank
>  > yo
>  >>   u !Norman
>  >>     [[alternative HTML version deleted]]
>  >>
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>  >
> --
> 
> Dr. rer. nat. Gerta Rücker, Dipl.-Math.
> 
> Institute of Medical Biometry and Statistics,
> Faculty of Medicine and Medical Center - University of Freiburg
> 
> Stefan-Meier-Str. 26, D-79104 Freiburg, Germany
> 
> Phone: +49/761/203-6673
> Fax: +49/761/203-6680
> Mail: ruecker using imbi.uni-freiburg.de
> Homepage: https://www.uniklinik-freiburg.de/imbi.html
> 
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Michael
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