[R-sig-ME] GAMM4 error

[dani]

Hello Ben,


Thank you so much for your kind and prompt response. I provided a little bit more detail about my data. I really appreciate you taking the time to take a look over this information.


Yes, y is a 0/1 variable.


I have a total of  185,236 observations nested in n=2,206 pupils and n = 2,314 neighbourhoods. This results in a structure with many empty cells. Out of a total of 6120860 cells (considering the cross-classification), n=6118216 are empty cells. Out of the n=2644  non-empty cells, n=1835 (69.40%) have 84 observations per cell and n=4 have one observation per cell.


I suspect the issue is the fact that I have many NA in my data. My two variables with the smoothers have the following stats:


Variable        N       Mean    Std Dev Minimum Maximum
x3
x4

153369
148319

13.01
30.28

1.77
2.72

0
18.06

14.85
38.32




summary(newdata)
 y                          x1                   x2                      x3                         x4                              neigh                      STUDYID
 0:183335   Min.   : 2.000      F: 77972        Min.   : 0.00         Min.   :18.06             J0L 1B0:  2000       35     :    84
 1:  1901   1st Qu.: 4.195      M:107264     1st Qu.:12.19      1st Qu.:28.98            J0S 1K0:   526       122    :    84
                   Median : 7.047                           Median :13.85    Median :30.29          J0J 1K0:   504       193    :    84
                    Mean   : 7.866                            Mean   :13.01    Mean   :30.28           H4B 1N2:   480      231    :    84
                   3rd Qu.:11.044                            3rd Qu.:14.40    3rd Qu.:31.93          J0P 1P0:   336        248    :    84
                    Max.   :17.981                             Max.   :14.85    Max.   :38.33              J7T 2A1:   336       257    :    84
                                                                           NA's   :31867    NA's   :36917          (Other):181054(Other):184732

 str(newdata)

'data.frame': 185236 obs. of  7 variables:
 $ y      : Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
 $ x1     : num  16.9 16.9 16.9 16.9 16.9 ...
 $ x2     : Factor w/ 2 levels "F","M": 2 2 2 2 2 2 2 2 2 2 ...
 $ x3     : num  NA NA NA NA NA NA NA NA NA NA ...
 $ x4     : num  NA NA NA NA NA NA NA NA NA NA ...
 $ neigh  : Factor w/ 2314 levels "A3J 1A8","A3K 2V9",..: 802 802 802 802 802 802 802 802 802 802 ...
 $ STUDYID: Factor w/ 2206 levels "35","122","193",..: 1 1 1 1 1 1 1 1 1 1 ...

Thank you so much for all your help!

Best regards, everyone!

<http://aka.ms/weboutlook>
________________________________
From: R-sig-mixed-models <r-sig-mixed-models-bounces at r-project.org> on behalf of Ben Bolker <bbolker at gmail.com>
Sent: Tuesday, August 15, 2017 12:36:19 PM
To: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] GAMM4 error


  We'd love to help, but it's really, really hard without a reproducible
example.  All the error message really tells us is that somewhere in the
guts there was something like a divide-by-zero error or an infinity
produced (because your data were weird, or because some value got really
small or really large and under/overflowed).

  A reproducible example would be ideal (see e.g.
<https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example>
), but in its absence, `summary(mydata)` or `str(mydata)` would be
useful.  For example:

- is y a 0/1 variable?
- are all of your x variables numeric, and not super-large in magnitude?
- do you have NA values in your data?
- how many distinct values (levels) of pupil and neigh do you have?
- how many observations overall?

On 17-08-15 03:07 PM, dani wrote:
> Hello everyone,
>
>
> I am a beginner struggling with GAMM4. I employed a GAMM4 model using
> a binomial distribution involving two smoothers and two random
> intercepts (corresponding to a structure involving observations
> cross-classified into two groups: pupils and neighbourhoods):
>
>
> model <- gamm4(y ~ x1+x2+s(x3)+s(x4), random=~ (1|pupil)+(1|neigh),
> data=mydata, family= binomial)
>
> I received the following error message: Error in
> smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) :
> NA/NaN/Inf in foreign function call (arg 1)
>
> I was wondering if anyone can please help me elucidate what might
> this mean.
>
> Best regards, everyone! Nicole-Miki
>
>
>
>
> <http://aka.ms/weboutlook>
>
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>
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> R-sig-mixed-models at r-project.org mailing list
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>

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