. You get an F-statistic for
> > each s() term by default and you are referred to saummary.gam for further
> > explanation.
> >
> > David Winsemius, MD
> > Heritage Laboratories
> > West Hartford, CT
>
> [[alternative HTML version deleted]]
>
>
://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 Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603
between
> two smooth terms, together with the interaction of this interaction with
> factor. Is model 2 reasonable? I find it is rather complicated to interpret
> the plot of model 2.
> Thank you very much for helping!
--
> Simon Wood, Mathematical Sciences, University of Bath, Bat
ces in DF(0.77246) and deviance (-0.02), these two models
>
> seem to be not significantly different. Isn't it?
> Thank you anyway!
>
> Simon Wood-4 wrote:
> > The simpler model has the lower deviance (marginally), so there is
> > nothing to
> > test here. This can
601.27
> 2 1201.43848 601.290.77246-0.02
>
> Thank you very much!
>
> Jianghua Liu, University of Sheffield
--
> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603 www.mat
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> PLEASE do read the posting guide
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> self-contained, reproducible code.
--
> Sim
an be
> found in here:
> myknots6 = c(20,24,34)
> p.spline8 = spm(accel ~
> f(times,basis="trunc.poly",degree=2,knots=myknots6))
>
> Can someone please help me with this task? I'm kind of desperate.
>
> Thank you!
--
>
th the package {mgcv}.
> >
> > My command is: gam(y~s(x1,bs="cr")+s(x2, bs="cr")).
> >
> > I need help to know what are the default basis funcitons for gam. I have
> > not found any detailed reference for this.
> >
> > Ca
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> PLEASE do read the posting guide
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> self-contained, reproducible code.
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> Simon Wood, Mathem
mgcv 1.5-0 is now on CRAN. Main changes are:
* REML and ML smoothness selection are now available.
* A Tweedie family has been added.
* `gam.method' has been replaced (see arguments `method' and `optimizer'
for `gam')
For other changes see the changeLog.
Si
sp = f.ug$sp,
> p = f.nofit$smooth[[1]]$xp,
> Ain = FF2$A,
> bin = FF2$b
> )
>
> p2 <- pcls(G2)
> fv2<-Predict.matrix(f.nofit$smooth[[1]],data.frame(x=x))%*%p2
>
>
>
> Many thanks
> -Ben
>
> __
for any response, M
>
> [[alternative HTML version deleted]]
>
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> PLEASE do read the posting guide
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gt;
>
>
>
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> PLEASE do read the posting guide
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talling a few
> times. __
> This is mgcv 1.4-1.1
> Error in runif(1) :
> .Random.seed is not an integer vector but of type 'list'
> Error : .onAttach failed in 'attachNamespace'
> Error: package/namespace load failed for 'mgcv'
> --
27;list'
> Error : .onAttach failed in 'attachNamespace'
> Error: package/namespace load failed for 'mgcv'
> -----
> Thanks.
> Chetty
--
> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603
all that lovely
sparcity in the MRF, :-( ).
Hope this helps.
best,
Simon
On Saturday 07 February 2009 21:00, Daniel Sabanés Bové wrote:
> Dear Mr. Simon Wood, dear list members,
>
> I am trying to fit a similar model with gam from mgcv compared to what I
> did with BayesX,
er)+s(lon,lat,k=c(4,4),fx=T),random=list
> >>(co de_tripnr=~1),family="poisson", niterPQL=200)
> >>
> >> Maximum number of PQL iterations: 200
> >>
> >> iteration 1
> >>
> >> iteration 2
> >>
> >> Error in MEestima
t;
> Diederik
>
> Diederik Strubbe
> Evolutionary Ecology Group
> Department of Biology, University of Antwerp
> Universiteitsplein 1
> B-2610 Antwerp, Belgium
> http://webhost.ua.ac.be/deco
> tel : 32 3 820 23 85
>
>
>
>
> [[alternative HTML version
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 Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 3
ontrol(nlmStepMax=0.0001))
>
> Maximum number of PQL iterations: 200
>
> iteration 1
>
> iteration 2
>
> Error in MEestimate(lmeSt, grps) :
>
>
> NA/NaN/Inf in foreign function call (arg 1)
>
>
>
>
> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),
>fa
y yours,
> > >
> > > Robbert Langenberg
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > __
> > > R-help@r-project.org mailing list
> > > https://stat.ethz.ch/m
_
> > > 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.
g 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 Scien
n passes basic model checking?).
>
> See Pinheiro and Bates (2000) for more info.
>
> hope this is some use,
> Simon
>
>
>
>
>
>
>
>
>
>
>
>
>
> David Warner
> Research Fishery Biologist
> USGS Great Lakes Science Center
> 1451 Green Road
> Ann Arbo
odel<-gam(Kept.CPUE~s(HOUR)+s(LAT_dec)+s(LONG_dec)+s(mea
>ntemp_C)+s(meandepth_fa)+s(change_depth)+s(seds),
> data=cod.fall.version2,family=poisson)
>
> In dpois(y, mu, log = TRUE) ... : non-integer x = 5.325517
>
> Thanks Sally
--
> Simon Wood, Mathematical Sciences, University o
Biologist
> USGS Great Lakes Science Center
> 1451 Green Road
> Ann Arbor MI 48105
> 734.214.9392
> [[alternative HTML version deleted]]
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r
-project.org/posting-guide.html and provide commented, minimal,
> self-contained, reproducible code.
--
> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603 www.maths.bath.ac.uk/~sw283
__
R-help@r-project
ted]]
>
> ______
> 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, reproduc
[[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 comme
> 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 Sciences, University of Bath, Bath, BA2
t; http://newton.ex.ac.uk/research/emag
> http://projects.ex.ac.uk/atto
>
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> PLEASE do read the posting gu
527
> 17 0.7251362 0.017382274 15531
> 18 1.1871948 0.025481173 15521
> 19 1.6495832 0.048264689 15524
> 20 5.1180227 0.131198022 15218
>
> > newdata
>
> tscore
> 1 0.5059341
> 2 0.4125522
> 3 1.4335818
> 4 0.7060673
> 5 0.3229316
>
> Thank
dified and
simplified. See ?smooth.construct.
A fuller list of changes is at
http://cran.r-project.org/web/packages/mgcv/ChangeLog
--
> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603 www.maths.b
ot;terms") ? Thanks in
> advance, Amandine.
> _
> Votre contact a choisi Hotmail, l'e-mail ultra s�curis�. Cr�ez un compte
> gratuitement !
>
> [[alternative HTML version deleted]]
--
> Simon Wood, Mathematical Sciences, Uni
0 and tmean by multiple imputation approach. Hope this information
> can also help identify the
> element of this problem.
>
> LC
>
> > From: Simon Wood <[EMAIL PROTECTED]>
> > To: r-help@r-project.org
> > Date: Wed, 21 May 2008 08:55:02 +0100
> > Subject
; iteration 6
> Error in `*tmp*`[[k]] : attempt to select less than one element
>
> I never saw this error message before, and there is also no related
> information about this error from the Internet. Hope some people who once
> encountered this problem can tell me what's wron
add an extra ridge penalty to a smooth and have mgcv::gam
estimate its smoothing parameter, then you would need to add write a smoother
class to do this (by modifying one of the existing ones). See ?p.spline, or
exercise 8, chapter 5 of Wood (2006) "GAMs:An Intro with R".
best,
S
hat is
> the advantage of the lpmatrix approach for prediction outside R? Thanks.
-- You can get standard errors on the predictions if you do the `lpmatrix'
interpolation thing.
best,
Simon
--
> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +
lues.
>
> Question: Have I overfitted the data?
>
> Feedback?
>
> Tom
> Thomas L. Jones, PhD, Computer Science
>
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weights, start = start, ... :
>fitted probabilities numerically 0 or 1 occurred
>
> ______
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> PLEASE do read the posting guide
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in order to estimate smoothing parameters via calls to lme... not a very
enticing prospect.
best,
Simon
>- Simon Wood, Mathematical Sciences, University of Bath, Bath BA2 7AY
>- +44 (0)1225 386603 www.maths.bath.ac.uk/~sw283/
__
fit(x = X, y = Y, weights = weights, start = start, ... :
>fitted probabilities numerically 0 or 1 occurred
> 4: In glm.fit(x = X, y = Y, weights = weights, start = start, ... :
>fitted probabilities numerically 0 or 1 occurred
>
> ______
> R-help@r-project
>
> > Because there is more than one way to handle rank deficiency. There are
> > two different 'gam' functions in contributed packages for R (and none in
> > R itself), so we need more details: see the footer of this message. In
> > glm() the NA estimates are
me book for the bases used.
>In my humble opinion, the '^4' in the first term
> of the second line of this equation should be '^3'.
--- Perhaps take a look at section 2.3.3 of Gu (2002) "Smoothing Spline ANOVA"
for a bit more detail on this/
>
>
gt; [1] 901
> [1] 1001
> warnings() over 50
>
> > warnings()
>
> 1: In gam.fit(G, family = G$family, control = control, gamma = gamma, ...
> : fitted probabilities numerically 0 or 1 occurred
> ......
> 14: In gam.fit(G, family = G$family, c
tted
> probabilities numerically 0 or 1 occurred" ? How can i solve it?
>
> I didn't try the possible solutions for them, because it took such a
> longer time to run the whole programs.
> Could anybody suggest their solutions?
> Any help or suggestions are greatly appr
basis for estimating f.
>- Simon Wood, Mathematical Sciences, University of Bath, Bath BA2 7AY
>- +44 (0)1225 386603 www.maths.bath.ac.uk/~sw283/
On Thu, 13 Dec 2007, zhijie zhang wrote:
> Dear all,
> Following the help from gam(mgcv) help page, i tried to a
with both of them, if smoothing
> parameters are given, should it not?
-- yes that's right
> Simon Wood-4 wrote:
> > `pcls' is really useful for the inequality constraint case (e.g. when you
> > want
> > shape preserving smooths). For fixed smoothing parameters you can
eed is to incorporate the constraints before calculating the
> penalties. Can this be done in R?
> Any help would be greately appreciated.
--
> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603 www.maths.bath.ac.uk/~sw283
__
hen determine the dimension of A, alternatively the
routine will attempt to determine the rank of B (and usually over-estimate it
slightly).
--
> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603 www.maths.bath.ac.uk/~sw283
_
t; __
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_
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> PLEASE do read the posting guide
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> self-contained, reproducible code.
--
> Simon Wood, Mathematical
t(x)) both failed.")
> if( verbose )print("svd(x) failed but svd(t(x)) worked.")
> temp= svdtx$u
> svdtx$u = svdtx$v
> svdtx$v = temp
> svdtx
> }
>
> __
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t;
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--
&
nson, Senior Population Biologist
> British Trust for Ornithology, The Nunnery, Thetford, Norfolk, IP24 2PU
> Ph: +44 (0)1842 750050 E: [EMAIL PROTECTED]
> Fx: +44 (0)1842 750030 W: http://www.bto.org
> eSafe scanned this email for viruses, vandals and malicious content (
proach?
>
> Julian
>
> Julian Burgos
> FAR lab
> University of Washington
>
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with MGCV package?
>
--- They'll always be somewhat different as the representation of the models
is slightly different in gam::gam and mgcv::gam. See ?gam
best,
Simon
--
> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603 www.maths.bath.ac.u
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> Simon Wood,
in gamm() ???
>
> --
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>
> "Here I try to mean by "overfitting" that GCV was significantly SMALLER
> than the mean square error of prediction of the validation data, which
> was randomly selected and not used for regression."
--- so you could try increasing gamma until this is no long
urself using the `sp' argument to `gam', or by using the `min.sp' argument
to set a lower bound on the smoothing parameter.
-- I'm suprised that `gamma' had no effect - how high did you try?
best,
Simon
> Thank you.
>
> Best Wishes,
>
> Ariyo
>
> 200
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> self-contained, reproducible code.
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> Simon Wood,
t; definite
> %%%
>
> Could be any problem in gamm() ???
>
> --
>
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