subject:"Re\: \[R\] Proportion data GAM"

Re: [R] Proportion data GAM

2014-10-15 Thread Rodrigo Tardin

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 :

> 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_2.3-12Formula_1.1-2
>>   [5] grid_3.1.0gtable_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_1.8.1proto_0.3-10  Rcpp_0.11.2   reshape2_1.4
>> [17] sandwich_2.3-1scales_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 > >:
>>
>> 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:
>> librar

Re: [R] Proportion data GAM

2014-10-15 Thread Rodrigo Tardin

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_2.3-12Formula_1.1-2
 [5] grid_3.1.0gtable_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_1.8.1proto_0.3-10  Rcpp_0.11.2   reshape2_1.4
[17] sandwich_2.3-1scales_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 :

> 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]]
>>
>>
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide 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
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Proportion data GAM

2014-10-15 Thread Simon Wood


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_2.3-12Formula_1.1-2
  [5] grid_3.1.0gtable_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_1.8.1proto_0.3-10  Rcpp_0.11.2   reshape2_1.4
[17] sandwich_2.3-1scales_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 mailto:s.w...@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]]




R-help@r-project.org  mailing list
https://stat.ethz.ch/mailman/__listinfo/r-help

PLEASE do read the posting guide
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


R-help@r-project.org  mailing list
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Re: [R] Proportion data GAM

2014-10-15 Thread Simon Wood


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]]



__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 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

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Proportion data GAM

Re: [R] Proportion data GAM

Re: [R] Proportion data GAM

Re: [R] Proportion data GAM

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