Trevor, Can I just check - were you using the new 'nb' from mgcv version
>= 1.8 or the old (and very slow) 'negbin' family? (Not that negative
binomial seems needed here, but just to know) best, Simon
On 16/07/14 21:16, Trevor Davies wrote:
Hi Simon,
Thank you so much for being active on this list, it really is
tremendously helpful.
Thanks you for your insights, I was wondering whether both terms were
necessary.
As for 'NB wouldn't work' it was a convergence problem (and tremendously
slow). There were also issues with the models not giving lack of
convergence warnings but then the model saying it was not converged and
vice versa. The QP seemed to fit the data well (and quickly) so we
switched to that.
Thanks again.
Trevor
On Wed, Jul 16, 2014 at 12:44 PM, Simon Wood <s.w...@bath.ac.uk
<mailto:s.w...@bath.ac.uk>> wrote:
Trevor,
It looks like you've added a parametric COR.YEARLY.MEAN in addition
to your s(cxe,cyn,by=COR.YEARLY.MEAN) term. Because the latter
includes a linear effect of COR.YEARLY.MEAN, then the parametric
COR.YEARLY.MEAN will not be identifiable, so gam has dropped it.
I guess from the scale parameter your data are, if anything,
under-dispersed relative to Poisson, but perhaps Poisson would have
been ok too.
Could you give a bit more detail on 'NB just wouldn't work' please?
What actually happened? (It's new functionality, so having reports
when stuff goes wrong is useful).
best,
Simon
On 16/07/14 20:25, Trevor Davies wrote:
I have run a quasipoisson spatial model via GAM (NB just
wouldn't work) and
I am getting the following output of one of my parameters
(COR.YEARLY.MEAN). Does this suggest an error in the model fit?
The model
seems to have converged. Apologies for the lack of reproducible
example
but it didn't really seem warranted in this case. Thank you for the
assistance.
Trevor
Parametric coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -3.7084 0.2185 -16.97 <2e-16 ***
COR.YEARLY.MEAN 0.0000 0.0000 NA NA
---
Approximate significance of smooth terms:
edf Ref.df F
p-value
s(PRED_cBOTTOM_TEMPERATURE.__std) 5.008 6.045 24.871
< 2e-16 ***
s(cxe,cyn) 28.999 29.000 13.951 <
2e-16 ***
s(cDMAX.std) 3.830 4.761 243.895 <
2e-16 ***
s(cxe,cyn):male.allyear.__intensity.std 8.053 9.923 4.486
2.8e-06 ***
s(cxe,cyn):female.allyear.__intensity.std 3.733 4.334 5.478
0.000149 ***
s(cxe,cyn):COR.YEARLY.MEAN 28.979 29.886 28.502 <
2e-16 ***
s(cxe,cyn):cFISHING_INTENSITY.__std 5.592 6.464 24.330
< 2e-16 ***
-
Rank: 1/169
R-sq.(adj) = 0.697 Deviance explained = 64.1%
GCV = 0.70372 Scale est. = 0.69061 n = 4575
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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
--
Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
+44 (0)1225 386603 http://people.bath.ac.uk/sw283
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