[R-meta] question on scatter plot of estimates (Fisher's Z) against the standard error
Michael Dewey
||@t@ @end|ng |rom dewey@myzen@co@uk
Thu Jul 20 15:51:15 CEST 2023
Dear Gabriel
Comments in-line
On 20/07/2023 05:55, Gabriel Cotlier wrote:
> Dear Michael,
>
> I think you are completely right, in the fact, the plot I am producing
> is indeed valid for the purpose for which I want to use it, meaning it
> is representative of the relationship I want to show. Therefore, I
> assume that the plot I am getting, is supposed to be sufficient.
>
> However, I receive from the function metafore:: funnel (model), for a
> model without modierators, a very nice representation of the scarring of
> the observed outcomes or the estimates (x axis), as a function of the SE
> (e.i., square root of the sampling variance, SE assumef to have a pseudo
> confidence interval region drawn around each of its values). While, when
> I plot by myself
> x = observed outcomes
> y = square root of the sampling variance,
>
> Then the plot shows that:
> a. the scattering of the points appears upside down with respect to the
> output of the function metafore:: funnel (model),
I have already answered that one in a previous post. It is just the
convention
> b. the scale of the y axis, instead of having a defined top at zero and
> from there values are represented downwards, the scale is different.
>
Without your code it is hard to tell but I suspect you are not plotting
what you think you are. Are you plotting the inverse of the se?
Michael
>
> Anyways, I started thinking that in any case, such a difference in the
> plot I am doing by myself is not necessarily wrong, but is just a
> different way of representing the data. Just the scattering of the
> points in one case looks like the upside down scattering of the other.
> And I assume this is because maybe the function metafore::funnel()
> applies some operation on the square root of the mean (y axis) that I
> presume is the calculation of the aforementioned pseudo confidence
> interval for each value, but I am not sure.
>
> Thanks a lot for your response.
> Kind regards,
> Gabriel
>
> On Wed, Jul 19, 2023 at 7:20 PM Michael Dewey <lists using dewey.myzen.co.uk
> <mailto:lists using dewey.myzen.co.uk>> wrote:
>
> I am sorry Gabriel but I do not understand why the plot you say you
> produced fails to do what you say you want.
>
> Michael
>
> On 19/07/2023 10:59, Gabriel Cotlier wrote:
> > Hello Michael,
> > Thank you very much for your response.
> > I just would like to show that the of data set I have has high
> > uncertainty given that no possible pattern is observable or
> detectable
> > and no order is possible to visulize in the scattering,
> > I thought that a plot with x axis = fisher's z observed
> > outcomes (estimates) and y axis = standard error or any
> other measure of
> > uncertainty could at least visually demostrate that assumption.
> > If such a lack of pattern or high uncertainty in the data set can
> also
> > be demonstrated numerically, even better.
> > Kind regards,
> > Gabriel
> >
> > On Wed, Jul 19, 2023 at 12:29 PM Michael Dewey
> <lists using dewey.myzen.co.uk <mailto:lists using dewey.myzen.co.uk>
> > <mailto:lists using dewey.myzen.co.uk
> <mailto:lists using dewey.myzen.co.uk>>> wrote:
> >
> > Dear Gabriel
> >
> > I am not realy sure what you are trying to do but one point which
> > occurs
> > to me is that forest plots are conventional plotted with small
> > values of
> > standard error at the top.
> >
> > Michael
> >
> > On 19/07/2023 06:07, Gabriel Cotlier via R-sig-meta-analysis
> wrote:
> > > Dear all,
> > >
> > > I have already posted this question with no response.
> > > Maybe this time I am luckier and someone with more
> knowledge than
> > me in the
> > > Metafor package can answer me.
> > >
> > > In a nutshell, what I would like is to be able to produce a
> > scatter plot of
> > > the observed oucomes or the estimates, in my case Fisher's
> z for
> > the x axis
> > > and the standard error in the y axis, with the standard error
> > (SE) the
> > > same as it appears when running the funnel() function for a
> > funnel plot
> > > with the model (without moderators) as the input argument.
> > Actually, it is
> > > a funnel plot without the background of the funnel
> distribution
> > but just
> > > the scatter of points, that is suppressing the funnel
> distribution on
> > > the background.
> > >
> > > I tried to do so in agreement with the definition of SE
> used for
> > the funnel
> > > plot in the package Vignette published at Journal of
> Scientific
> > software in
> > > page 26:
> > >
> > > "*For models without moderators, the figure shows the observed
> > outcomes on
> > > the horizontal axis against their corresponding standard
> errors
> > (i.e., the
> > > square root of the sampling variances) on the vertical axis. A
> > vertical
> > > line indicates the **estimate based on the model. A pseudo
> confidence
> > > interval region is drawn around this value with bounds
> equal to
> > ±1.96 · SE,
> > > where SE is the standard error value from the vertical axis.*"
> > >
> > >
> > > I tried to reproduce the vertical axis (y) using the
> square root
> > of the
> > > sampling variable, but the result was an upside down
> scaling of the
> > > observed outcomes or estimates on a different y scale for
> the x
> > ticks. The
> > > plot seems to have similarities with the funnel plot from the
> > funnel()
> > > function, but it is not exactly the same without the
> background
> > of the
> > > funnel distribution graphic. Maybe the problem could be
> that in the
> > > funnel() function, contrary to my simple attempt to imitate it
> > with the
> > > square root of the sampling variable, the pseudo confidence
> > interval is
> > > estimated for each value? Could this be the reason?
> > >
> > >
> > > If so, how could I reproduce the funnel () function plot
> without
> > the funnel
> > > distribution graphic in the background and just the
> scattering of the
> > > points using the same pseudo-confidence interval?
> > >
> > >
> > > Thanks a lot for your help and assistance.
> > >
> > > Kind regards,
> > >
> > > Gabriel
> > >
> > > [[alternative HTML version deleted]]
> > >
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> > --
> > Michael
> > http://www.dewey.myzen.co.uk/home.html
> <http://www.dewey.myzen.co.uk/home.html>
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