[R] Proportion data GAM
Rodrigo Tardin
rhtardin at gmail.com
Wed Oct 15 22:20:36 CEST 2014
Thanks Simon!
That worked!
I did not constrain my k as you suggested, but when I saw my results, my
degrees of freedom are not larger than 1, the REML is negative and all
covariates are not significant (what it does not make sense). Is there
something wrong?
Here's the results of summary (a2)
Family: Beta regression(76.885)
Link function: logit
Formula:
MDENS1 ~ s(DEPTH2) + s(DISTCOAST_1) + s(DIST_DIVE) + s(TOUR)
Parametric coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -6.7613 0.0252 -268.3 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Approximate significance of smooth terms:
edf Ref.df Chi.sq p-value
s(DEPTH2) 1.005 1.009 0.004 0.948
s(DISTCOAST_1) 1.004 1.008 0.077 0.785
s(DIST_DIVE) 1.004 1.008 0.065 0.801
s(TOUR) 1.004 1.008 0.010 0.922
R-sq.(adj) = -0.00255 Deviance explained = 11.7%
-REML = -19521 Scale est. = 1 n = 1560
Thanks a lot one more time!
Rodrigo Tardin
Shor Term Scholar - Duke Marine Lab. - Duke University
Doutorando em Ecologia e Evolução - IBRAG - UERJ
M.Sc em Biologia Animal - PPGBA - UFRRJ
Especialista em Docência do Ensino Superior - IAVM
Laboratório de Bioacústica e Ecologia de Cetáceos - UFRRJ/ IF/ DCA
2014-10-15 15:42 GMT-04:00 Simon Wood <s.wood at bath.ac.uk>:
> Rodrigo,
>
> OK, it looks as if your mgcv help files/manual are somehow out of sync
> with the package version you have loaded. 'betar' is only available from
> mgcv 1.8. If you update to the current mgcv from CRAN then this problem
> should be solved.
>
> best,
> Simon
>
> ps. beta regression is only available with REML (or ML) smoothness
> selection in mgcv, so the 'gamma' parameter will be ignored.
>
> pps. Do you really want to limit all your smooths to a maximum of 3
> degrees of freedom by setting k=?. I'd be inclined to allow the smoothing
> parameter selection do its thing with a higher k, and only get really
> restrictive on k if the resulting models somehow don't make sense.
>
>
> On 15/10/14 20:34, Rodrigo Tardin wrote:
>
>> Hi Simon,
>>
>> The result of sessionInfo() is:
>> R version 3.1.0 (2014-04-10)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252
>> [3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C
>> [5] LC_TIME=Portuguese_Brazil.1252
>>
>> attached base packages:
>> [1] splines stats graphics grDevices utils datasets methods
>> base
>>
>> other attached packages:
>> [1] gamlss_4.3-1 gamlss.dist_4.3-1 MASS_7.3-31
>> gamlss.data_4.2-7 MuMIn_1.10.0
>> [6] ggplot2_1.0.0 mgcv_1.7-29 nlme_3.1-117 betareg_3.0-5
>>
>> loaded via a namespace (and not attached):
>> [1] colorspace_1.2-4 digest_0.6.4 flexmix_2.3-12 Formula_1.1-2
>> [5] grid_3.1.0 gtable_0.1.2 lattice_0.20-29 lmtest_0.9-33
>> [9] Matrix_1.1-3 modeltools_0.2-21 munsell_0.4.2 nnet_7.3-8
>> [13] plyr_1.8.1 proto_0.3-10 Rcpp_0.11.2 reshape2_1.4
>> [17] sandwich_2.3-1 scales_0.2.4 stats4_3.1.0 stringr_0.6.2
>> [21] survival_2.37-7 tools_3.1.0 zoo_1.7-11
>>
>> Is this that you were asking or the sessionInfo() of the code (it would
>> be sessionInfo(a2))?
>>
>> If it is the sessionInfo(a2) the result is:
>> Error in if (pkg == "base") file.path(.Library, "base") else if (pkg
>> %in% :
>> missing value where TRUE/FALSE needed
>> In addition: There were 50 or more warnings (use warnings() to see the
>> first 50)
>>
>> Thanks
>>
>> Rodrigo Tardin
>>
>> Shor Term Scholar - Duke Marine Lab. - Duke University
>> Doutorando em Ecologia e Evolução - IBRAG - UERJ
>> M.Sc em Biologia Animal - PPGBA - UFRRJ
>> Especialista em Docência do Ensino Superior - IAVM
>> Laboratório de Bioacústica e Ecologia de Cetáceos - UFRRJ/ IF/ DCA
>>
>> 2014-10-15 15:22 GMT-04:00 Simon Wood <s.wood at bath.ac.uk
>> <mailto:s.wood at bath.ac.uk>>:
>>
>> Can you give the result of typing
>> sessionInfo()
>> in the session where this happens, please?
>>
>>
>> On 15/10/14 16:48, Rodrigo Tardin wrote:
>>
>> Hi all,
>>
>> I am not sure if this is the right place for this question or if
>> there is
>> one more specific.
>> Anyway, I hope somebody can help me.
>>
>> I am trying to run a GAM with beta distribution from mgcv package.
>> My dependent variable is a proportion continuously ranging from
>> 0 to 1
>> (whales density) and I have three co-variates Depth, Distance to
>> Coast and
>> Seabed Slope.
>>
>> From what I read, beta distribution is the most appropriate
>> for my response
>>
>> variable and not binomial.
>> According to mgcv manual, it is possible to specify beta
>> distribution on a
>> GAM with the "betar" function, but I get the following error:
>> could not find function "betar"
>>
>> My code is:
>> library(mgcv)
>> a2=gam(Density~s(DEPTH,k=4)+s(__DISTCOAST_1,k=4)+s(SLOPE,k=4),
>> family=betar(link="logit"),__data=misti,gamma=1.4)
>>
>> The beta family is specified exactly as it is shown in the manual:
>> bm <-
>> gam(y~s(x0)+s(x1)+s(x2)+s(x3),__family=betar(link="logit"),_
>> _data=dat)
>>
>> Does anyone know what it seems to be the problem?
>> Thanks in advance,
>> Rodrigo
>>
>>
>> Rodrigo Tardin
>>
>> Shor Term Scholar - Duke Marine Lab. - Duke University
>> Doutorando em Ecologia e Evolu��o - IBRAG - UERJ
>> M.Sc em Biologia Animal - PPGBA - UFRRJ
>> Especialista em Doc�ncia do Ensino Superior - IAVM
>> Laborat�rio de Bioac�stica e Ecologia de Cet�ceos - UFRRJ/ IF/ DCA
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
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>>
>>
>>
>> --
>> Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
>> +44 (0)1225 386603 <tel:%2B44%20%280%291225%20386603>
>> http://people.bath.ac.uk/sw283
>>
>> ________________________________________________
>> R-help at r-project.org <mailto:R-help at r-project.org> mailing list
>> https://stat.ethz.ch/mailman/__listinfo/r-help
>> <https://stat.ethz.ch/mailman/listinfo/r-help>
>> PLEASE do read the posting guide
>> http://www.R-project.org/__posting-guide.html
>> <http://www.R-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>>
>
> --
> Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
> +44 (0)1225 386603 http://people.bath.ac.uk/sw283
>
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