[R-sig-Geo] [R-sig-eco] Error in run GAM (Biomod 2)

[Lara Silva]

Thanks for the information.

Drew Tyre <atyre2 using unl.edu> escreveu no dia segunda, 18/03/2019 à(s) 11:48:

> I don't think the number of presences is the problem.
> "A term has fewer unique covariate combinations than specified maximum
> degrees of freedom"
> One of your covariates has a small number of unique values.
> lapply(your_data_frame, function(x)length(unique(x)))
> will print out the number of unique values in each variable. Values < 30
> could be problematic -- the docs are a bit ambiguous on the default values
> of k, the maximum degrees of freedom for a smooth term. Another approach to
> diagnose the problem is to set k to a low value, like 5, and see if that
> makes the problem go away. I'm not familiar with biomod2, but I think doing
> something like
> MO <- BIOMOD_ModelingOptions(GAM  = list(k = 5))
> BIOMOD_Modeling( ..., models.options = MO, ...)
>
> should do it. Note that setting k to a low value causes other problems, I
> would use mcgv::gam.check() to ensure k is large enough, but I don't know
> how to do that with biomod2.
>
> hth
>
> --
> Drew Tyre
>
> School of Natural Resources
> University of Nebraska-Lincoln
> 416 Hardin Hall, East Campus
> 3310 Holdrege Street
> Lincoln, NE 68583-0974
>
> phone: +1 402 472 4054
> fax: +1 402 472 2946
> email: atyre2 using unl.edu
> http://snr.unl.edu/tyre
> http://drewtyre.rbind.io
>     The point is that our true nature is not some ideal that we have to
> live up to. It’s who we are right now, and that’s what we can make friends
> with and celebrate.
> Excerpted from: Awakening Loving-Kindness by Pema Chödrön
>
>
> On 3/18/19, 6:28 AM, "R-sig-ecology on behalf of Lara Silva" <
> r-sig-ecology-bounces using r-project.org on behalf of lara.sfp.silva using gmail.com>
> wrote:
>
>     Hello
>
>     I am trying to run several algorithms in biomod 2 (GLM, GAM, ANN, SRE)
> but
>     I received the following menssage.
>
>     Model=GAM
>              GAM_mgcv algorithm chosen
>             Automatic formula generation...
>             > GAM (mgcv) modelling...Error in
>     smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) :
>       A term has fewer unique covariate combinations than specified maximum
>     degrees of freedom
>     Error in predict(model.bm, Data[, expl_var_names, drop = FALSE],
> on_0_1000
>     = TRUE) :
>       object 'model.bm' not found
>
>     *** inherits(g.pred,'try-error')
>        ! Note :  Lactuca.global_AllData_RUN1_GAM failed!
>
>     I have 19 presences and 1019 pseudo-absences ...
>     It is because the low number of presences?
>
>     Thanks
>
>     Lara
>
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