[R-meta] Jitter points in the contour-enhanced funnel plot

[Angeline Tsui]

Hello Michael,

Thank you very much for your reply. Yes, I did jitter the effect size or
variance before running rma. But I did not find difference of the funnel
plot plotted using this method.

I am sorry but I really have a question about jittering the points in the
function of "funnel plot". I tried to go through the arguments and I really
do not know where I can put the jitter function in the code. I can't jitter
the regression model itself (as it is an object) and I can't jitter other
arguments as well because the other arguments are related to the graph
itself, for example y-axis and x-axis. I would very much appreciate it if
you can give me more tips here. I am a beginner of R (only knowing how to
run several analyses in R, so my knowledge of creating a function in R is
very limited).

Thanks,
Angeline

On Fri, Jul 20, 2018 at 3:56 AM, Michael Dewey <lists using dewey.myzen.co.uk>
wrote:

> Dear Angeline
>
> Yes, that was what I meant. Of course then the result of rma.uni() will be
> very slightly different but you are using the funnel plot as what Tukey
> called an impact graphic as opposed to an archive graphic so the fact that
> the contours may not be in precisely the same place is not going to be
> critical to your purposes.
>
> If that does not work then I suggest going through the code of funnel.rma
> and finding where it plots the points and then making you own function with
> jitter added in to the call(s). That way you would still be using your
> original fit.
>
> Michael
>
> On 20/07/2018 00:39, Angeline Tsui wrote:
>
>> Dear Michael,
>>
>> Thank you very much for your reply. I actually tried different plot
>> symbol, but it didn't help much.
>>
>> For the jitter function, do you mean that I need to simply use the jitter
>> function with the effect size or var before running the regression and
>> later plot the regression model with funnel plot?
>>
>> Thanks again,
>> Angeline
>>
>> On Thu, Jul 19, 2018 at 5:41 AM, Michael Dewey <lists using dewey.myzen.co.uk
>> <mailto:lists using dewey.myzen.co.uk>> wrote:
>>
>>     Dear Angeline
>>
>>     The first thing I would try is using a different plot symbol. A
>>     hollow circle or a cross might help if the points are not absolutely
>>     identical. The second thing would be to re-run the meta-analysis
>>     with the values of yi and sei (or vi) with added jitter, perhaps
>>     using the jitter() function for that.
>>
>>     Michael
>>
>>     On 18/07/2018 14:58, Angeline Tsui wrote:
>>
>>         Dear all,
>>
>>         I plotted the studies in my meta-analysis in a contour-enhanced
>>         funnel
>>         plot. In my meta-analysis, I have about 140 studies. However,
>>         when I plot
>>         the funnel plot, I find that a number of studies (i.e., points)
>>         overlapped
>>         with each other in the plot and this leads to an illustration
>>         that I am not
>>         plotting all studies in the funnel plot.
>>
>>         So I am writing to ask if you can teach me how to jitter points
>>         in the
>>         funnel plot, so that there could be some spaces between studies
>> with
>>         similar effect size?
>>
>>         Thanks,
>>         Angeline
>>
>>
>>     --     Michael
>>     http://www.dewey.myzen.co.uk/home.html
>>     <http://www.dewey.myzen.co.uk/home.html>
>>
>>
>>
>>
>> --
>> Best Regards,
>> Angeline
>>
>
> --
> Michael
> http://www.dewey.myzen.co.uk/home.html
>



-- 
Best Regards,
Angeline

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