[R] convergence problem gamm / lme

Fri Jan 30 09:03:40 CET 2009

The previous message didn't came through properly, so here again.

problem solved: 
As is probably mostly the case, a convergence problem lies in the specification of the model or the data itself.

Some information: I was trying to model the spatial distribution of fish of a particular age. The raw observations consisted of the number of individuals of a particular length. We were interested in modelling the number of fish of age A per hour: Y*a/(t*s) where Y is the count, a is the probability that a fish of length l belongs to age A, t is the haul duration and s is the subsample factor (when not all fish caught are measured). So I decided to use Y as the response variable and log(t*s/a) as the model offset. In some cases a was 0, leading to a model offset of infinity. So I decided to replace those zeros (6 observations) by a small value, but apparently not large enough. This must have caused the convergence problems in gamm.

After some reflection, I believe that one should often include the offset as model weights as well. E.g. assume you treat the log(fishing duration) as a model offset. If the fishing duration is very small compared to the rest or even 0, you haven’t really made an observation, so it should receive a very small or zero model weight. In case of zero weight you might as well remove the observation from the analysis. At least that is how I see it.

So the solutions that worked:
1) Y*a as the response variable and log(t*s) as offset
2) Replacing the zero a’s by not such a small value
3) Removing the rows with zero a’s, using Y as the response variable and log(t*s/a) as the offset and weights. 

I believe that option 3 is most elegant.
Unfortunately it turned out that nobody could answer the question, because I didn't provided the data. Nevertheless, Simon thanks a lot for your replies!

Cheers Geert

>Geert,
>Sorry for slow reply... I don't see any obvious problems with what you've 
>done, so I guess it's the usual problem that PQL just doesn't *have* to 
>converge, and the bit of extra flexibility of using a smooth is too much for 
>it in this case. If you send me the data offline I can dig a little bit more 
>if you like (I'll only use the data for this purpose etc. etc.) 
>You are right that PQL does the same thing for Poisson and quasi-poisson. I 
>don't think there is an easy way to use the values for the reduced dataset 
>fit in the full dataset fitting, unfortunately. 
>Another option is to use `gam' to fit the random effects. It'll be a bit slow 
>with 70+ random effects, as you have, and it's a bit more work to set up, but 
>it should converge. See ?gam.models which has some examples showing how to do 
>this.
best,
Simon

On Thursday 29 January 2009 08:20, geert aarts wrote:
> Simon, thanks for your reply and your suggestions.
>
> I fitted the following glmm's
>
> gamm3<-try(glmmPQL(count~offset(offsetter)+poly(lon,3)*poly(lat,3),random=l
>ist(code_tripnr=~1),family="poisson"))
>
> Which worked OK (see summary below)
>
> I also fitted a model using quasipoisson, but that didn't help. I actually
> also thought that glmmPQL and gamm estimate the dispersion parameter and
> hence assumes a quasipoisson distribution, even if you specify poisson. Is
> that correct?
>
> Finally I tried fitting a model to less data, and sometimes gamm managed to
> converge (see summary below). So would it be possible to use the parameter
> estimates from the model fitted to less data as starting values for the
> gamm fitted to the full data set? Or do you have any other suggestions?
>
> Thanks.
> Cheers Geert
>
>
>
>
>
>
> gamm3<-try(glmmPQL(count~offset(offsetter)+poly(lon,3)*poly(lat,3),random=l
>ist(code_tripnr=~1),f
>
> amily="poisson"))
>
>
>
> iteration
> 1
>
> iteration
> 2
>
> iteration
> 3
>
>> detach(Disc_age)
>
> summary(gamm3)
>
> Linear
> mixed-effects model fit by maximum likelihood
>
> Data: NULL
>
> AIC BIC logLik
>
> NA NA
> NA
>
>
>
> Random
> effects:
>
> Formula: ~1 | code_tripnr
>
> (Intercept) Residual
>
> StdDev:
> 0.001391914 231.9744
>
>
>
> Variance
> function:
>
> Structure: fixed weights
>
> Formula: ~invwt
>
> Fixed
> effects: count ~ offset(offsetter) + poly(lon, 3) * poly(lat, 3)
>
> Value
> Std.Error DF t-value p-value
>
> (Intercept) -1.582 11.96 2024 -0.13232174 0.8947
>
> poly(lon,
> 3)1 -4.048 1397.33 2024 -0.00289673 0.9977
>
> poly(lon,
> 3)2 -22.013 699.71 2024 -0.03145996 0.9749
>
> poly(lon,
> 3)3 -8.538 593.87 2024 -0.01437683 0.9885
>
> poly(lat,
> 3)1 -109.624 666.05 2024 -0.16458856 0.8693
>
> poly(lat,
> 3)2 -104.179 381.37 2024 -0.27316977 0.7848
>
> poly(lat,
> 3)3 -10.661 221.93 2024 -0.04803585 0.9617
>
> poly(lon,
> 3)1:poly(lat, 3)1 4290.737 61369.98 2024
> 0.06991589 0.9443
>
> poly(lon,
> 3)2:poly(lat, 3)1 1853.559 36835.63 2024
> 0.05031972 0.9599
>
> poly(lon,
> 3)3:poly(lat, 3)1 -240.521 25771.80 2024 -0.00933272 0.9926
>
> poly(lon,
> 3)1:poly(lat, 3)2 2540.147 41378.38 2024
> 0.06138826 0.9511
>
> poly(lon,
> 3)1:poly(lat, 3)2 2540.147 41378.38 2024
> 0.06138826 0.9511
>
> poly(lon,
> 3)2:poly(lat, 3)2 -1803.911 21522.17
> 2024 -0.08381643 0.9332
>
> poly(lon,
> 3)3:poly(lat, 3)2 1040.858 16352.56 2024
> 0.06365109 0.9493
>
> poly(lon,
> 3)1:poly(lat, 3)3 632.587 12180.28 2024
> 0.05193535 0.9586
>
> poly(lon,
> 3)2:poly(lat, 3)3 -394.339 13088.72 2024 -0.03012818 0.9760
>
> poly(lon,
> 3)3:poly(lat, 3)3 -543.502 6221.71 2024 -0.08735569 0.9304
>
> Correlation:
>
> (Intr) ply(ln,3)1
> ply(ln,3)2 ply(ln,3)3 ply(lt,3)1
>
> poly(lon,
> 3)1 0.889
>
> poly(lon,
> 3)2 0.938 0.878
>
> poly(lon,
> 3)3 0.843 0.981
> 0.792
>
> poly(lat,
> 3)1 -0.829 -0.949 -0.906
> -0.882
>
> poly(lat,
> 3)2 0.859 0.578 0.742
> 0.538 -0.474
>
> poly(lat,
> 3)3 -0.552 -0.783 -0.579
> -0.756 0.837
>
> poly(lon,
> 3)1:poly(lat, 3)1 -0.947 -0.974
> -0.940 -0.940 0.925
>
> poly(lon,
> 3)2:poly(lat, 3)1 -0.934 -0.950
> -0.857 -0.929 0.881
>
> poly(lon,
> 3)3:poly(lat, 3)1 -0.818 -0.963
> -0.866 -0.945 0.931
>
> poly(lon,
> 3)1:poly(lat, 3)2 0.808 0.975
> 0.784 0.968 -0.928
>
> poly(lon,
> 3)2:poly(lat, 3)2 0.737 0.575
> 0.853 0.465 -0.659
>
> poly(lon,
> 3)3:poly(lat, 3)2 0.735 0.896
> 0.647 0.938 -0.765
>
> poly(lon,
> 3)1:poly(lat, 3)3 -0.794 -0.592
> -0.823 -0.518 0.591
>
> poly(lon,
> 3)2:poly(lat, 3)3 -0.542 -0.737
> -0.419 -0.781 0.635
>
> poly(lon,
> 3)3:poly(lat, 3)3 -0.398 -0.383
> -0.534 -0.334 0.425
>
> ply(lt,3)2
> ply(lt,3)3 p(,3)1:(,3)1 p(,3)2:(,3)1
>
> poly(lon,
> 3)1
>
> poly(lon,
> 3)2
>
> poly(lon,
> 3)3
>
> poly(lat,
> 3)1
>
> poly(lat,
> 3)2
>
> poly(lat,
> 3)3 -0.136
>
> poly(lon,
> 3)1:poly(lat, 3)1 -0.708 0.690
>
> poly(lon,
> 3)2:poly(lat, 3)1 -0.701 0.710 0.933
>
> poly(lon,
> 3)3:poly(lat, 3)1 -0.499 0.738 0.956 0.849
>
> poly(lon,
> 3)1:poly(lat, 3)2 0.458 -0.845
> -0.915 -0.934
>
> poly(lon,
> 3)2:poly(lat, 3)2 0.683 -0.344
> -0.719 -0.522
>
> poly(lon,
> 3)2:poly(lat, 3)2 0.683 -0.344
> -0.719 -0.522
>
> poly(lon,
> 3)3:poly(lat, 3)2 0.464 -0.655
> -0.834 -0.884
>
> poly(lon,
> 3)1:poly(lat, 3)3 -0.823 0.241 0.752 0.594
>
> poly(lon,
> 3)2:poly(lat, 3)3 -0.300 0.707 0.612 0.788
>
> poly(lon,
> 3)3:poly(lat, 3)3 -0.266 0.148 0.493 0.250
>
> p(,3)3:(,3)1
> p(,3)1:(,3)2 p(,3)2:(,3)2 p(,3)3:(,3)2
>
> poly(lon,
> 3)1
>
> poly(lon,
> 3)2
>
> poly(lon,
> 3)3
>
> poly(lat,
> 3)1
>
> poly(lat,
> 3)2
>
> poly(lat,
> 3)3
>
> poly(lon,
> 3)1:poly(lat, 3)1
>
> poly(lon,
> 3)2:poly(lat, 3)1
>
> poly(lon,
> 3)3:poly(lat, 3)1
>
> poly(lon,
> 3)1:poly(lat, 3)2 -0.928
>
> poly(lon,
> 3)2:poly(lat, 3)2 -0.637 0.432
>
> poly(lon,
> 3)3:poly(lat, 3)2 -0.851
> 0.935 0.245
>
> poly(lon,
> 3)1:poly(lat, 3)3 0.642 -0.482 -0.894 -0.410
>
> poly(lon,
> 3)2:poly(lat, 3)3 0.609 -0.822 0.007 -0.847
>
> poly(lon,
> 3)3:poly(lat, 3)3 0.551 -0.327 -0.637 -0.291
>
> p(,3)1:(,3)3
> p(,3)2:(,3)3
>
> poly(lon,
> 3)1
>
> poly(lon,
> 3)2
>
> poly(lon,
> 3)3
>
> poly(lat,
> 3)1
>
> poly(lat,
> 3)2
>
> poly(lat,
> 3)3
>
> poly(lon,
> 3)1:poly(lat, 3)1
>
> poly(lon,
> 3)2:poly(lat, 3)1
>
> poly(lon,
> 3)3:poly(lat, 3)1
>
> poly(lon,
> 3)1:poly(lat, 3)2
>
> poly(lon,
> 3)2:poly(lat, 3)2
>
> poly(lon,
> 3)3:poly(lat, 3)2
>
> poly(lon,
> 3)1:poly(lat, 3)3
>
> poly(lon,
> 3)3:poly(lat, 3)1
>
> poly(lon,
> 3)1:poly(lat, 3)2
>
> poly(lon,
> 3)2:poly(lat, 3)2
>
> poly(lon,
> 3)3:poly(lat, 3)2
>
> poly(lon,
> 3)1:poly(lat, 3)3
>
> poly(lon,
> 3)2:poly(lat, 3)3 0.080
>
> poly(lon,
> 3)3:poly(lat, 3)3 0.684 -0.180
>
>
>
> Standardized
> Within-Group Residuals:
>
> Min Q1 Med Q3 Max
>
> -0.504980771 -0.000866948
> 0.028470924 0.078583094
> 33.247831244
>
>
>
> Number
> of Observations: 2113
>
> Number
> of Groups: 74
>
>
>
>
>
>
>
> gamm3<-try(gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=
>~1),family="quasipoisson", niterPQL=200))
>
>
>
>
> summary(gamm3$gam)
>
>
>
> Family:
> quasipoisson
>
> Link
> function: log
>
>
>
> Formula:
>
> count
> ~ offset(offsetter) + s(lon, lat)
>
>
>
> Parametric
> coefficients:
>
> Estimate Std. Error t value Pr(>|t|)
>
> X 1.31370
> 0.09854 13.33
>
>
>
>
> summary(gamm3$lme)
>
> Linear
> mixed-effects model fit by maximum likelihood
>
> Data: data
>
> AIC
> BIC logLik
>
> 2808.398 2837.845 -1398.199
>
>
>
> Random
> effects:
>
> Formula: ~Xr.1 - 1 | g.1
>
> Structure: pdIdnot
>
> Xr.11 Xr.12
> Xr.13 Xr.14 Xr.15
> Xr.16 Xr.17 Xr.18
>
> StdDev:
> 12.49623 12.49623 12.49623 12.49623 12.49623 12.49623 12.49623 12.49623
>
> Xr.19 Xr.110
> Xr.111 Xr.112 Xr.113
> Xr.114 Xr.115 Xr.116
>
> StdDev:
> 12.49623 12.49623 12.49623 12.49623 12.49623 12.49623 12.49623 12.49623
>
> Xr.117 Xr.118
> Xr.119 Xr.120 Xr.121
> Xr.122 Xr.123 Xr.124
>
> StdDev:
> 12.49623 12.49623 12.49623 12.49623 12.49623 12.49623 12.49623 12.49623
>
> Xr.125 Xr.126
> Xr.127
>
> StdDev:
> 12.49623 12.49623 12.49623
>
>
>
> Formula: ~1 | code_tripnr %in% g.1
>
> (Intercept) Residual
>
> StdDev: 0.8132693 5.077804
>
>
>
> Variance
> function:
>
> Structure: fixed weights
>
> Formula: ~invwt
>
> Fixed
> effects: list(fixed)
>
> Value Std.Error
> DF t-value p-value
>
> XX 1.3137042 0.09863463 923
> 13.318894 0.0000
>
> Xs(lon,lat)Fx1
> -0.4406352 0.23114503 923 -1.906315
> 0.0569
>
> Xs(lon,lat)Fx2
> -0.6217519 0.24918031 923 -2.495189 0.0128
>
> Correlation:
>
> XX X(,)F1
>
> Xs(lon,lat)Fx1 0.015
>
> Xs(lon,lat)Fx2
> -0.009 -0.148
>
>
>
> Standardized
> Within-Group Residuals:
>
> Min Q1 Med Q3 Max
>
> -3.42951750 -0.37448354
> 0.06432438 0.53690322 8.62026552
>
>
>
> Number
> of Observations: 1000
>
> Number
> of Groups:
>
> g.1 code_tripnr %in% g.1
>
> 1 75
>
>
>
>
>
>
>
> ----------------------------------------
>
>> From: s.wood at bath.ac.uk
>> To: r-help at r-project.org
>> Date: Fri, 23 Jan 2009 11:32:21 +0000
>> Subject: Re: [R] convergence problem gamm / lme
>>
>> Geert,
>>
>> Can you get a simpler model with, say, a quadratic dependence on lon, lat
>> to converge, using glmmPQL? The answer might give a clue about whether
>> the issue is related to using a smoother, or is something more basic.
>>
>> How confident are you that the Poisson assumption is reasonable?
>>
>> Can the model be fitted to a random subsample of the data, or does it
>> always fail? PQL can fail to converge, but it's usually not as obstinate
>> as it seems to be in this case, if the model structure is reasonable and
>> identifiable.
>>
>> best,
>> Simon
>>
>> On Thursday 22 January 2009 15:52, geert aarts wrote:
>>> Hope one of you could help with the following question/problem:
>>> We would like to explain the spatial
>>> distribution of juvenile fish. We have 2135 records, from 75 vessels
>>> (code_tripnr) and 7 to 39 observations for each vessel, hence the random
>>> effect for code_tripnr. The offset (�offsetter�) accounts for the haul
>>> duration and sub sampling factor. There are no extreme outliers in
>>> lat/lon. The model we try to fit is:
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~
>>>1), family="poisson", niterPQL=200)
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in MEestimate(lmeSt, grps) :
>>>
>>>
>>> NA/NaN/Inf in foreign function call (arg 1)
>>>
>>>
>>>
>>> We tried several things. We added some
>>> noise to lon and lat, modelled the density instead of using a count with
>>> model offset, and we normalized the explanatory variables. We also
>>> changed several settings (see models below).
>>>
>>>
>>>
>>> Interestingly, we do manage to fit a more
>>> complex model:
>>>
>>> gamm2<-gamm(count~offset(offsetter)+
>>> s(lat,lon,year,dayofyear), random=list(code_tripnr=~1),family="poisson",
>>> correlation = corGaus(0.1, form=~lat + lon))
>>>
>>>
>>>
>>> The models are fitted using mgcv 1.4-1 and
>>> R 2.7.1 on a 64Bits Debian OS.
>>>
>>>
>>>
>>> So there seems to be a convergence problem, correct? And does someone
>>> have an idea what might cause this? Secondly are there some
>>> tricks/solutions. E.g. perhaps we could use the results from the more
>>> complex model (gamm2 above), but I do not know exactly how. All
>>> help/advice would be greatly appreciated.
>>>
>>>
>>>
>>> Kind regards, Geert
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),
>>> random=list(code_tripnr=~1),family="poisson", correlation = corExp(1,
>>> form=~X + Y),nite
>>>
>>> rPQL=200)
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in recalc.corSpatial(object[[i]],
>>> conLin) :
>>>
>>>
>>> NA/NaN/Inf in foreign function call (arg 1)
>>>
>>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(1,1)),random=list(cod
>>>>e_ tripnr=~1),family="poisson",
>>>
>>> niterPQL=200)
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in lme.formula(fixed = fixed, random
>>> = random, data = data, correlation = correlation, :
>>>
>>> nlminb
>>> problem, convergence error code = 1
>>>
>>>
>>> message = false convergence (8)
>>>
>>> In addition: Warning messages:
>>>
>>> 1: In if (k < M + 1) { :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>>
>>>
>>>
>>>
>>> .Options$mgcv.vc.logrange=0.001 # we also
>>> tried higher settings
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~
>>>1), family="poisson", niterPQL=200, control=lmeControl(opt="optim"))
>>>
>>>
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in optim(c(coef(lmeSt)),
>>> function(lmePars) -logLik(lmeSt, lmePars),
>>>
>>>
>>>
>>> initial value in 'vmmin' is not finite
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~
>>>1), family="poisson", niterPQL=200,control=lmeControl(minAbsParApV
>>>
>>> ar=0.0000000000001))
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in recalc.corSpatial(object[[i]],
>>> conLin) :
>>>
>>>
>>> NA/NaN/Inf in foreign function call (arg 1)
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~
>>>1), family="poisson", niterPQL=200)
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in MEestimate(lmeSt, grps) :
>>>
>>>
>>> NA/NaN/Inf in foreign function call (arg 1)
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(1,1)),random=list(code
>>>_tr ipnr=~1),family="poisson", niterPQL=200)
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in lme.formula(fixed = fixed, random
>>> = random, data = data, correlation = correlation, :
>>>
>>>
>>> nlminb problem, convergence
>>> error code = 1
>>>
>>>
>>> message = false convergence (8)
>>>
>>> In addition: Warning messages:
>>>
>>> 1: In if (k < M + 1) { :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>> 2: In smooth.construct.tp.smooth.spec(object,
>>> dk$data, dk$knots) :
>>>
>>>
>>> basis dimension, k, increased to minimum possible
>>>
>>>
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(8,8)),random=list(code
>>>_tr ipnr=~1),family="poisson", niterPQL=200)
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in lme.formula(fixed = fixed, random
>>> = random, data = data, correlation = correlation, :
>>>
>>>
>>> nlminb problem, convergence
>>> error code = 1
>>>
>>>
>>> message = false convergence (8)
>>>
>>> In addition: Warning messages:
>>>
>>> 1: In if (k < M + 1) { :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>> 2: In 1:UZ.len : numerical expression has 2
>>> elements: only the first used
>>>
>>> 3: In if (p.rank> ncol(XZ)) p.rank
>>> <- ncol(XZ) :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>> 4: In 1:p.rank : numerical expression has 2
>>> elements: only the first used
>>>
>>> 5: In if (p.rank < k - j) Xf <- XZU[,
>>> (p.rank + 1):(k - j), drop = FALSE] else Xf <- matrix(0, :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>> 6: In (p.rank + 1):(k - j) :
>>>
>>>
>>> numerical expression has 2 elements: only the first used
>>>
>>> 7: In 1:p.rank : numerical expression has 2
>>> elements: only the first used
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+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 MEestimate(lmeSt, grps) :
>>>
>>>
>>> NA/NaN/Inf in foreign function call (arg 1)
>>>
>>> In addition: Warning messages:
>>>
>>> 1: In if (k < M + 1) { :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>> 2: In 1:UZ.len : numerical expression has 2
>>> elements: only the first used
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+te(lon,lat),random=list(code_tripnr=
>>>~1) ,family="poisson", niterPQL=200,control=lmeControl(opt="opti
>>>
>>> m"))
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in optim(c(coef(lmeSt)),
>>> function(lmePars) -logLik(lmeSt, lmePars),
>>>
>>>
>>>
>>> initial value in 'vmmin' is not finite
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~
>>>1), family="poisson", niterPQL=200,control=lmeControl(tolerance=
>>>
>>> 0.00000000000001))
>>>
>>> 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 ),family="poisson",
>>>
>>> niterPQL=200,control=lmeControl(niterEM=200))
>>>
>>> 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), family="poisson",
>>> niterPQL=200,control=lmeControl(msTol=0.00000000000000001))
>>>
>>> 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), family="poisson",
>>> niterPQL=200,control=lmeControl(.relStep=0.00000000000000000001))
>>>
>>> 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), family="poisson",
>>> niterPQL=200,control=lmeControl(nlmStepMax=0.00000000000000000001))
>>>
>>> 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), family="poisson",
>>> niterPQL=200,control=lmeControl(minAbsParApVar=0.0000000000001))
>>>
>>> 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), family="poisson", niterPQL=200, control=lmeControl(returnObject=T))
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in MEestimate(lmeSt, grps) :
>>>
>>>
>>> Singularity in backsolve at level 0, block 1
>>>
>>> In addition: Warning messages:
>>>
>>> 1: In logLik.reStruct(object, conLin) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>> 2: In logLik.reStruct(object, conLin) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>> 3: In logLik.reStruct(object, conLin) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>> 4: In logLik.reStruct(object, conLin) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>> 5: In logLik.reStruct(object, conLin) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>> 6: In MEestimate(lmeSt, grps) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>>
>>> _________________________________________________________________
>>>
>>>
>>> [[alternative HTML version deleted]]
>>
>> --
>>
>>> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
>>> +44 1225 386603 www.maths.bath.ac.uk/~sw283
>
>
> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603 www.maths.bath.ac.uk/~sw283 
>
>
> ----------------------------------------
>
>> From: s.wood at bath.ac.uk
>> To: r-help at r-project.org
>> Date: Fri, 23 Jan 2009 11:32:21 +0000
>> Subject: Re: [R] convergence problem gamm / lme
>>
>> Geert,
>>
>> Can you get a simpler model with, say, a quadratic dependence on lon, lat
>> to converge, using glmmPQL? The answer might give a clue about whether
>> the issue is related to using a smoother, or is something more basic.
>>
>> How confident are you that the Poisson assumption is reasonable?
>>
>> Can the model be fitted to a random subsample of the data, or does it
>> always fail? PQL can fail to converge, but it's usually not as obstinate
>> as it seems to be in this case, if the model structure is reasonable and
>> identifiable.
>>
>> best,
>> Simon
>>
>> On Thursday 22 January 2009 15:52, geert aarts wrote:
>>> Hope one of you could help with the following question/problem:
>>> We would like to explain the spatial
>>> distribution of juvenile fish. We have 2135 records, from 75 vessels
>>> (code_tripnr) and 7 to 39 observations for each vessel, hence the random
>>> effect for code_tripnr. The offset (�offsetter�) accounts for the haul
>>> duration and sub sampling factor. There are no extreme outliers in
>>> lat/lon. The model we try to fit is:
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~
>>>1), family="poisson", niterPQL=200)
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in MEestimate(lmeSt, grps) :
>>>
>>>
>>> NA/NaN/Inf in foreign function call (arg 1)
>>>
>>>
>>>
>>> We tried several things. We added some
>>> noise to lon and lat, modelled the density instead of using a count with
>>> model offset, and we normalized the explanatory variables. We also
>>> changed several settings (see models below).
>>>
>>>
>>>
>>> Interestingly, we do manage to fit a more
>>> complex model:
>>>
>>> gamm2<-gamm(count~offset(offsetter)+
>>> s(lat,lon,year,dayofyear), random=list(code_tripnr=~1),family="poisson",
>>> correlation = corGaus(0.1, form=~lat + lon))
>>>
>>>
>>>
>>> The models are fitted using mgcv 1.4-1 and
>>> R 2.7.1 on a 64Bits Debian OS.
>>>
>>>
>>>
>>> So there seems to be a convergence problem, correct? And does someone
>>> have an idea what might cause this? Secondly are there some
>>> tricks/solutions. E.g. perhaps we could use the results from the more
>>> complex model (gamm2 above), but I do not know exactly how. All
>>> help/advice would be greatly appreciated.
>>>
>>>
>>>
>>> Kind regards, Geert
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),
>>> random=list(code_tripnr=~1),family="poisson", correlation = corExp(1,
>>> form=~X + Y),nite
>>>
>>> rPQL=200)
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in recalc.corSpatial(object[[i]],
>>> conLin) :
>>>
>>>
>>> NA/NaN/Inf in foreign function call (arg 1)
>>>
>>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(1,1)),random=list(cod
>>>>e_ tripnr=~1),family="poisson",
>>>
>>> niterPQL=200)
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in lme.formula(fixed = fixed, random
>>> = random, data = data, correlation = correlation, :
>>>
>>> nlminb
>>> problem, convergence error code = 1
>>>
>>>
>>> message = false convergence (8)
>>>
>>> In addition: Warning messages:
>>>
>>> 1: In if (k < M + 1) { :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>>
>>>
>>>
>>>
>>> .Options$mgcv.vc.logrange=0.001 # we also
>>> tried higher settings
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~
>>>1), family="poisson", niterPQL=200, control=lmeControl(opt="optim"))
>>>
>>>
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in optim(c(coef(lmeSt)),
>>> function(lmePars) -logLik(lmeSt, lmePars),
>>>
>>>
>>>
>>> initial value in 'vmmin' is not finite
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~
>>>1), family="poisson", niterPQL=200,control=lmeControl(minAbsParApV
>>>
>>> ar=0.0000000000001))
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in recalc.corSpatial(object[[i]],
>>> conLin) :
>>>
>>>
>>> NA/NaN/Inf in foreign function call (arg 1)
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~
>>>1), family="poisson", niterPQL=200)
>>>
>>> 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,k=c(1,1)),random=list(code
>>>_tr ipnr=~1),family="poisson", niterPQL=200)
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in lme.formula(fixed = fixed, random
>>> = random, data = data, correlation = correlation, :
>>>
>>>
>>> nlminb problem, convergence
>>> error code = 1
>>>
>>>
>>> message = false convergence (8)
>>>
>>> In addition: Warning messages:
>>>
>>> 1: In if (k < M + 1) { :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>> 2: In smooth.construct.tp.smooth.spec(object,
>>> dk$data, dk$knots) :
>>>
>>>
>>> basis dimension, k, increased to minimum possible
>>>
>>>
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(8,8)),random=list(code
>>>_tr ipnr=~1),family="poisson", niterPQL=200)
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in lme.formula(fixed = fixed, random
>>> = random, data = data, correlation = correlation, :
>>>
>>>
>>> nlminb problem, convergence
>>> error code = 1
>>>
>>>
>>> message = false convergence (8)
>>>
>>> In addition: Warning messages:
>>>
>>> 1: In if (k < M + 1) { :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>> 2: In 1:UZ.len : numerical expression has 2
>>> elements: only the first used
>>>
>>> 3: In if (p.rank> ncol(XZ)) p.rank
>>> <- ncol(XZ) :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>> 4: In 1:p.rank : numerical expression has 2
>>> elements: only the first used
>>>
>>> 5: In if (p.rank < k - j) Xf <- XZU[,
>>> (p.rank + 1):(k - j), drop = FALSE] else Xf <- matrix(0, :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>> 6: In (p.rank + 1):(k - j) :
>>>
>>>
>>> numerical expression has 2 elements: only the first used
>>>
>>> 7: In 1:p.rank : numerical expression has 2
>>> elements: only the first used
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+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 MEestimate(lmeSt, grps) :
>>>
>>>
>>> NA/NaN/Inf in foreign function call (arg 1)
>>>
>>> In addition: Warning messages:
>>>
>>> 1: In if (k < M + 1) { :
>>>
>>> the
>>> condition has length> 1 and only the first element will be used
>>>
>>> 2: In 1:UZ.len : numerical expression has 2
>>> elements: only the first used
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+te(lon,lat),random=list(code_tripnr=
>>>~1) ,family="poisson", niterPQL=200,control=lmeControl(opt="opti
>>>
>>> m"))
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in optim(c(coef(lmeSt)),
>>> function(lmePars) -logLik(lmeSt, lmePars),
>>>
>>>
>>>
>>> initial value in 'vmmin' is not finite
>>>
>>>
>>>
>>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~
>>>1), family="poisson", niterPQL=200,control=lmeControl(tolerance=
>>>
>>> 0.00000000000001))
>>>
>>> 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 ),family="poisson",
>>>
>>> niterPQL=200,control=lmeControl(niterEM=200))
>>>
>>> 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), family="poisson",
>>> niterPQL=200,control=lmeControl(msTol=0.00000000000000001))
>>>
>>> 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), family="poisson",
>>> niterPQL=200,control=lmeControl(.relStep=0.00000000000000000001))
>>>
>>> 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), family="poisson",
>>> niterPQL=200,control=lmeControl(nlmStepMax=0.00000000000000000001))
>>>
>>> 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), family="poisson",
>>> niterPQL=200,control=lmeControl(minAbsParApVar=0.0000000000001))
>>>
>>> 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), family="poisson", niterPQL=200, control=lmeControl(returnObject=T))
>>>
>>> Maximum number of PQL iterations: 200
>>>
>>> iteration 1
>>>
>>> iteration 2
>>>
>>> Error in MEestimate(lmeSt, grps) :
>>>
>>>
>>> Singularity in backsolve at level 0, block 1
>>>
>>> In addition: Warning messages:
>>>
>>> 1: In logLik.reStruct(object, conLin) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>> 2: In logLik.reStruct(object, conLin) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>> 3: In logLik.reStruct(object, conLin) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>> 4: In logLik.reStruct(object, conLin) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>> 5: In logLik.reStruct(object, conLin) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>> 6: In MEestimate(lmeSt, grps) :
>>>
>>>
>>> Singular precision matrix in level -1, block 1
>>>
>>>
>>> _________________________________________________________________
>>>
>>>
>>> [[alternative HTML version deleted]]
>>
>> --
>>
>>> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
>>> +44 1225 386603 www.maths.bath.ac.uk/~sw283
>
>
> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603 www.maths.bath.ac.uk/~sw283 

----------------------------------------
> From: s.wood at bath.ac.uk
> To: r-help at r-project.org
> Date: Fri, 23 Jan 2009 11:32:21 +0000
> Subject: Re: [R] convergence problem gamm / lme
>
> Geert,
>
> Can you get a simpler model with, say, a quadratic dependence on lon, lat to
> converge, using glmmPQL? The answer might give a clue about whether the issue
> is related to using a smoother, or is something more basic.
>
> How confident are you that the Poisson assumption is reasonable?
>
> Can the model be fitted to a random subsample of the data, or does it always
> fail? PQL can fail to converge, but it's usually not as obstinate as it seems
> to be in this case, if the model structure is reasonable and identifiable.
>
> best,
> Simon
>
>
>
>
>
> On Thursday 22 January 2009 15:52, geert aarts wrote:
>> Hope one of you could help with the following question/problem:
>> We would like to explain the spatial
>> distribution of juvenile fish. We have 2135 records, from 75 vessels
>> (code_tripnr) and 7 to 39 observations for each vessel, hence the random
>> effect for code_tripnr. The offset (�offsetter�) accounts for the haul
>> duration and sub sampling factor. There are no extreme outliers in lat/lon.
>> The model we try to fit is:
>>
>>
>>
>>
>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),
>>family="poisson", niterPQL=200)
>>
>> Maximum number of PQL iterations: 200
>>
>> iteration 1
>>
>> iteration 2
>>
>> Error in MEestimate(lmeSt, grps) :
>>
>>
>> NA/NaN/Inf in foreign function call (arg 1)
>>
>>
>>
>> We tried several things. We added some
>> noise to lon and lat, modelled the density instead of using a count with
>> model offset, and we normalized the explanatory variables. We also changed
>> several settings (see models below).
>>
>>
>>
>> Interestingly, we do manage to fit a more
>> complex model:
>>
>> gamm2<-gamm(count~offset(offsetter)+
>> s(lat,lon,year,dayofyear), random=list(code_tripnr=~1),family="poisson",
>> correlation = corGaus(0.1, form=~lat + lon))
>>
>>
>>
>> The models are fitted using mgcv 1.4-1 and
>> R 2.7.1 on a 64Bits Debian OS.
>>
>>
>>
>> So there seems to be a convergence problem, correct? And does someone have
>> an idea what might cause this? Secondly are there some tricks/solutions.
>> E.g. perhaps we could use the results from the more complex model (gamm2
>> above), but I do not know exactly how. All help/advice would be greatly
>> appreciated.
>>
>>
>>
>> Kind regards, Geert
>>
>>
>>
>>
>>
>>
>>
>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),
>> random=list(code_tripnr=~1),family="poisson", correlation = corExp(1,
>> form=~X + Y),nite
>>
>> rPQL=200)
>>
>> Maximum number of PQL iterations: 200
>>
>> iteration 1
>>
>> iteration 2
>>
>> Error in recalc.corSpatial(object[[i]],
>> conLin) :
>>
>>
>> NA/NaN/Inf in foreign function call (arg 1)
>>
>>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(1,1)),random=list(code_
>>>tripnr=~1),family="poisson",
>>
>> niterPQL=200)
>>
>> Maximum number of PQL iterations: 200
>>
>> iteration 1
>>
>> iteration 2
>>
>> Error in lme.formula(fixed = fixed, random
>> = random, data = data, correlation = correlation, :
>>
>> nlminb
>> problem, convergence error code = 1
>>
>>
>> message = false convergence (8)
>>
>> In addition: Warning messages:
>>
>> 1: In if (k < M + 1) { :
>>
>> the
>> condition has length> 1 and only the first element will be used
>>
>>
>>
>>
>>
>> .Options$mgcv.vc.logrange=0.001 # we also
>> tried higher settings
>>
>>
>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),
>>family="poisson", niterPQL=200, control=lmeControl(opt="optim"))
>>
>>
>>
>> Maximum number of PQL iterations: 200
>>
>> iteration 1
>>
>> iteration 2
>>
>> Error in optim(c(coef(lmeSt)),
>> function(lmePars) -logLik(lmeSt, lmePars),
>>
>>
>>
>> initial value in 'vmmin' is not finite
>>
>>
>>
>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),
>>family="poisson", niterPQL=200,control=lmeControl(minAbsParApV
>>
>> ar=0.0000000000001))
>>
>> Maximum number of PQL iterations: 200
>>
>> iteration 1
>>
>> iteration 2
>>
>> Error in recalc.corSpatial(object[[i]],
>> conLin) :
>>
>>
>> NA/NaN/Inf in foreign function call (arg 1)
>>
>>
>>
>>
>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),
>>family="poisson", niterPQL=200)
>>
>> Maximum number of PQL iterations: 200
>>
>> iteration 1
>>
>> iteration 2
>>
>> Error in MEestimate(lmeSt, grps) :
>>
>>
>> NA/NaN/Inf in foreign function call (arg 1)
>>
>>
>>
>>
>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(1,1)),random=list(code_tr
>>ipnr=~1),family="poisson", niterPQL=200)
>>
>> Maximum number of PQL iterations: 200
>>
>> iteration 1
>>
>> iteration 2
>>
>> Error in lme.formula(fixed = fixed, random
>> = random, data = data, correlation = correlation, :
>>
>>
>> nlminb problem, convergence
>> error code = 1
>>
>>
>> message = false convergence (8)
>>
>> In addition: Warning messages:
>>
>> 1: In if (k < M + 1) { :
>>
>> the
>> condition has length> 1 and only the first element will be used
>>
>> 2: In smooth.construct.tp.smooth.spec(object,
>> dk$data, dk$knots) :
>>
>>
>> basis dimension, k, increased to minimum possible
>>
>>
>>
>>
>>
>>
>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat,k=c(8,8)),random=list(code_tr
>>ipnr=~1),family="poisson", niterPQL=200)
>>
>> Maximum number of PQL iterations: 200
>>
>> iteration 1
>>
>> iteration 2
>>
>> Error in lme.formula(fixed = fixed, random
>> = random, data = data, correlation = correlation, :
>>
>>
>> nlminb problem, convergence
>> error code = 1
>>
>>
>> message = false convergence (8)
>>
>> In addition: Warning messages:
>>
>> 1: In if (k < M + 1) { :
>>
>> the
>> condition has length> 1 and only the first element will be used
>>
>> 2: In 1:UZ.len : numerical expression has 2
>> elements: only the first used
>>
>> 3: In if (p.rank> ncol(XZ)) p.rank
>> <- ncol(XZ) :
>>
>> the
>> condition has length> 1 and only the first element will be used
>>
>> 4: In 1:p.rank : numerical expression has 2
>> elements: only the first used
>>
>> 5: In if (p.rank < k - j) Xf <- XZU[,
>> (p.rank + 1):(k - j), drop = FALSE] else Xf <- matrix(0, :
>>
>> the
>> condition has length> 1 and only the first element will be used
>>
>> 6: In (p.rank + 1):(k - j) :
>>
>>
>> numerical expression has 2 elements: only the first used
>>
>> 7: In 1:p.rank : numerical expression has 2
>> elements: only the first used
>>
>>
>>
>>
>> gamm3<-gamm(count~offset(offsetter)+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 MEestimate(lmeSt, grps) :
>>
>>
>> NA/NaN/Inf in foreign function call (arg 1)
>>
>> In addition: Warning messages:
>>
>> 1: In if (k < M + 1) { :
>>
>> the
>> condition has length> 1 and only the first element will be used
>>
>> 2: In 1:UZ.len : numerical expression has 2
>> elements: only the first used
>>
>>
>>
>>
>> gamm3<-gamm(count~offset(offsetter)+te(lon,lat),random=list(code_tripnr=~1)
>>,family="poisson", niterPQL=200,control=lmeControl(opt="opti
>>
>> m"))
>>
>> Maximum number of PQL iterations: 200
>>
>> iteration 1
>>
>> iteration 2
>>
>> Error in optim(c(coef(lmeSt)),
>> function(lmePars) -logLik(lmeSt, lmePars),
>>
>>
>>
>> initial value in 'vmmin' is not finite
>>
>>
>>
>>
>> gamm3<-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),
>>family="poisson", niterPQL=200,control=lmeControl(tolerance=
>>
>> 0.00000000000001))
>>
>> 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
>>>),family="poisson",
>>
>> niterPQL=200,control=lmeControl(niterEM=200))
>>
>> 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),
>>family="poisson",
>> niterPQL=200,control=lmeControl(msTol=0.00000000000000001))
>>
>> 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),
>>family="poisson",
>> niterPQL=200,control=lmeControl(.relStep=0.00000000000000000001))
>>
>> 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),
>>family="poisson",
>> niterPQL=200,control=lmeControl(nlmStepMax=0.00000000000000000001))
>>
>> 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),
>>family="poisson",
>> niterPQL=200,control=lmeControl(minAbsParApVar=0.0000000000001))
>>
>> 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),
>>family="poisson", niterPQL=200, control=lmeControl(returnObject=T))
>>
>> Maximum number of PQL iterations: 200
>>
>> iteration 1
>>
>> iteration 2
>>
>> Error in MEestimate(lmeSt, grps) :
>>
>>
>> Singularity in backsolve at level 0, block 1
>>
>> In addition: Warning messages:
>>
>> 1: In logLik.reStruct(object, conLin) :
>>
>>
>> Singular precision matrix in level -1, block 1
>>
>> 2: In logLik.reStruct(object, conLin) :
>>
>>
>> Singular precision matrix in level -1, block 1
>>
>> 3: In logLik.reStruct(object, conLin) :
>>
>>
>> Singular precision matrix in level -1, block 1
>>
>> 4: In logLik.reStruct(object, conLin) :
>>
>>
>> Singular precision matrix in level -1, block 1
>>
>> 5: In logLik.reStruct(object, conLin) :
>>
>>
>> Singular precision matrix in level -1, block 1
>>
>> 6: In MEestimate(lmeSt, grps) :
>>
>>
>> Singular precision matrix in level -1, block 1
>>
>>
>> _________________________________________________________________
>>
>>
>> [[alternative HTML version deleted]]
>
> --
>> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
>> +44 1225 386603 www.maths.bath.ac.uk/~sw283
>
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