Message-ID: <2506d67e-e628-2609-7dc8-eb97bb74fbc7@dewey.myzen.co.uk>
Date: 2023-07-20T13:51:15Z
From: Michael Dewey
Subject: [R-meta] question on scatter plot of estimates (Fisher's Z) against the standard error
In-Reply-To: <CAAKwTDEDUX_iYAGSGs+-3Fh1imKRTHFQND3XwwCk2Vze9eEmXg@mail.gmail.com>
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 at dewey.myzen.co.uk
> <mailto:lists at 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 at dewey.myzen.co.uk <mailto:lists at dewey.myzen.co.uk>
> > <mailto:lists at dewey.myzen.co.uk
> <mailto:lists at 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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