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.w...@bath.ac.uk
<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
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--
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+44 (0)1225 386603 http://people.bath.ac.uk/sw283
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