[Biomod-commits] Comparison among variable importance

[Antonio Canepa]

Hi there!,
Many thanks for your help.
It's great that thsi list works so good.

Cheers,

Antonio


On 16 May 2013 18:34, Wilfried Thuiller
<wilfried.thuiller at ujf-grenoble.fr>wrote:

> Hi there all,
>
> This is, indeed, a tricky question.
> The way we perform variable importance, as do RandomForest, is really
> without unit. As Viorel mentioned, this is 1 minus the mean of correlations
> (depending on the number of variable importance runs). This is done
> independently (as Maxent is also doing as far as I understood). I do not
> think there is a sound statistical way of standardizing them. You may do as
> Damien suggest but I fear this is not really sound and should be
> interpreted without caution (but I am happy to be convinced otherwise).
> As Viorel suggested, box plots would do the same more or less the same but
> in a more sound way to me.
>
> Best,
> Wilfried
>
>
>
>
>
> Le 16 mai 2013 à 16:44, Viorel Popescu <vioreldpopescu at gmail.com> a écrit
> :
>
> > Hi everyone, I had a similar question a few weeks ago, and from my
> > understanding the varImportance scores are drawn from correlation
> > coefficients between different models (with and without the respective
> > variable permuted), namely, 1 minus the correlation (r). Hence, they
> cannot
> > add up to 1, the way variable importance is performed in MaxEnt. In that
> > case, standardizing the scores would not a be very good way to deal
> > with the varImportance. Am I missing something here?
> >
> > The way I dealt with them (with advice from Wilfried) was to show
> boxplots
> > of varImportance score for each variable across modeling techniques (and
> > taxa if you need to make such comparisons), and refer to median scores
> > (distribution of scores was far from normal).
> >
> > Cheers,
> > Viorel
> >
> >
> > On Thu, May 16, 2013 at 3:39 AM, Damien Georges
> > <damien.georges2 at gmail.com>wrote:
> >
> >> Dear Antonio,
> >>
> >> I guess you are right and you need to make  a kind of standardisation of
> >> scores to make them all comparable. Make them sum to 1 is a good way to
> do
> >> it.
> >>
> >> Cheers,
> >> Damien.
> >>
> >>
> >>
> >> On 16/05/2013 12:09, Antonio Canepa wrote:
> >>
> >>> Dear list,
> >>> I would like to know if you can directly compare among different models
> >>> the
> >>> variable importance of each variable selected?
> >>> My guess is not, because when I got the importance of each variable (
> >>> getModelsVarImport()), the sum of all of them for each model was not =
> 1.
> >>> I don't know if I'm doing something wrong or there is another way to
> >>> "standardise" the output from getModelsVarImport() and thus compare
> >>> throughout models ?
> >>>
> >>>
> >> ______________________________**_________________
> >> Biomod-commits mailing list
> >> Biomod-commits at lists.r-forge.**r-project.org<
> Biomod-commits at lists.r-forge.r-project.org>
> >> https://lists.r-forge.r-**project.org/cgi-bin/mailman/**
> >> listinfo/biomod-commits<
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits
> >
> >>
> >
> >
> >
> > --
> > Viorel D. Popescu
> > David H. Smith Conservation Research Fellow
> > University of California - Santa Cruz &
> > Simon Fraser University, Biological Sciences
> > (604) 340 4228
> > https://sites.google.com/site/vioreldpopescu/
> > _______________________________________________
> > Biomod-commits mailing list
> > Biomod-commits at lists.r-forge.r-project.org
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits
>
> -----------------------------
> Dr. Wilfried Thuiller
> Laboratoire d'Ecologie Alpine, UMR CNRS 5553
> Université Joseph Fourier
> BP53, 38041 Grenoble cedex 9, France
> tel: +33 (0)4 76 51 44 97
> fax: +33 (0)4 76 51 42 79
>
> Email: wilfried.thuiller at ujf-grenoble.fr
> Personal website: http://www.will.chez-alice.fr
> Team website: http://www-leca.ujf-grenoble.fr/equipes/emabio.htm
>
> ERC Starting Grant TEEMBIO project:
> http://www.will.chez-alice.fr/Research.html
>
> _______________________________________________
> Biomod-commits mailing list
> Biomod-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/biomod-commits
>



-- 
Antonio Canepa Oneto
PhD student
Dept. Biologia Marina i Oceanografia
Institut de Ciencies Del Mar CMIMA, CSIC
Ps. Marítim de la Barceloneta,37-49, c.p. 08003
BARCELONA, Catalunya,Spain
Phone: +34 932 30 9500  (ext. 6067)
Mobile: +34 628 320 778
e-mail: canepa at icm.csic.es
           ajcanepa at gmail.com