[R-meta] question on scatter plot of estimates (Fisher's Z) against the standard error
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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>? ? ?--
>? ? ?Michael
> http://www.dewey.myzen.co.uk/home.html
>
>
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