[R] strange nlme augpred behaviour

Thu Aug 24 18:20:27 CEST 2017

> On Aug 23, 2017, at 8:08 AM, PIKAL Petr <petr.pikal at precheza.cz> wrote:
> 
> Hi
> 
> Well, yes I tried it about two weeks ago but my post did not get through as it still awaits moderator approval.

It got through just fine. It appeared on Aug 15. It just didn't get any replies.

As I read your original question in this thread, it was not clear to me that you had provided the data-object named "mar".

-- David.

> I could check which column is offending but actually it is only minor nuisance, I can live with selection of columns before fitting a model. What seems to me strange is that both full dataset and only selected colums gave me identical fit results but only one works within augPred.
> 
> Cheers
> Petr
> 
>> -----Original Message-----
>> From: Bert Gunter [mailto:bgunter.4567 at gmail.com]
>> Sent: Wednesday, August 23, 2017 4:50 PM
>> To: PIKAL Petr <petr.pikal at precheza.cz>
>> Cc: r-help mailing list <r-help at r-project.org>
>> Subject: Re: [R] strange nlme augpred behaviour
>> 
>> Better posted on r-sig-mixed-models , no?
>> 
>> Cheers,
>> Bert
>> 
>> 
>> Bert Gunter
>> 
>> "The trouble with having an open mind is that people keep coming along and
>> sticking things into it."
>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>> 
>> 
>> On Wed, Aug 23, 2017 at 5:17 AM, PIKAL Petr <petr.pikal at precheza.cz> wrote:
>>> Dear all
>>> 
>>> I encountered strange behaviour of augPred with virtually the same
>>> data
>>> 
>>> First I made groupedData object.
>>>> mar.g<-groupedData(rutilizace~doba|int, data=mar)
>>> 
>>> When I perform nlme on complete dataset I get an error with augPred
>>>> fit<-nlsList(rutilizace~SSasymp(doba, Asym, R0,  lrc), data=mar.g)
>>> Warning message:
>>> c("1 error caught in nls(y ~ cbind(1 - exp(-exp(lrc) * x), exp(-exp(lrc) * x)), data
>> = xy, : singular gradient", "1 error caught in     start = list(lrc = lrc), algorithm =
>> \"plinear\"): singular gradient")
>>>> fit1<-nlme(fit)
>>>> plot(augPred(fit1, level=0:1))
>>> Error in `[[<-.data.frame`(`*tmp*`, nm, value = c(6L, 6L, 6L, 6L, 8L,  :
>>>  replacement has 60 rows, data has 12
>>> 
>>> However when I make subset of my data to keep only affected collumns.
>>>> 
>>>> mar.g<-mar.g[,c(3,4, 21)]
>>> 
>>>> fit<-nlsList(rutilizace~SSasymp(doba, Asym, R0,  lrc), data=mar.g)
>>> Warning message:
>>> c("1 error caught in nls(y ~ cbind(1 - exp(-exp(lrc) * x), exp(-exp(lrc) * x)), data
>> = xy, : singular gradient", "1 error caught in     start = list(lrc = lrc), algorithm =
>> \"plinear\"): singular gradient")
>>>> fit2<-nlme(fit)
>>>> plot(augPred(fit2, level=0:1))
>>>> 
>>> augPred works as a charm.
>>> 
>>> When I compare fit1 and fit2 they are equal
>>>> all.equal(fit1, fit2)
>>> [1] TRUE
>>>> 
>>> 
>>> Does anybody know where I should try to search for problems?
>>> 
>>> Best regards
>>> Petr
>>> 
>>>> traceback()
>>> 6: stop(sprintf(ngettext(N, "replacement has %d row, data has %d",
>>>       "replacement has %d rows, data has %d"), N, nrows), domain =
>>> NA)
>>> 5: `[[<-.data.frame`(`*tmp*`, nm, value = c(1L, 1L, 1L, 1L, 5L,
>>>   5L, 5L, 5L, 9L, 9L, 9L, 9L, 4L, 4L, 4L, 4L, 8L, 8L, 8L, 8L, 12L,
>>>   12L, 12L, 12L, 3L, 3L, 3L, 3L, 7L, 7L, 7L, 7L, 11L, 11L, 11L,
>>>   11L, 1L, 1L, 1L, 1L, 5L, 5L, 5L, 5L, 9L, 9L, 9L, 9L, 2L, 2L,
>>>   2L, 2L, 6L, 6L, 6L, 6L, 10L, 10L, 10L, 10L))
>>> 4: `[[<-`(`*tmp*`, nm, value = c(1L, 1L, 1L, 1L, 5L, 5L, 5L, 5L,
>>>   9L, 9L, 9L, 9L, 4L, 4L, 4L, 4L, 8L, 8L, 8L, 8L, 12L, 12L, 12L,
>>>   12L, 3L, 3L, 3L, 3L, 7L, 7L, 7L, 7L, 11L, 11L, 11L, 11L, 1L,
>>>   1L, 1L, 1L, 5L, 5L, 5L, 5L, 9L, 9L, 9L, 9L, 2L, 2L, 2L, 2L, 6L,
>>>   6L, 6L, 6L, 10L, 10L, 10L, 10L))
>>> 3: gsummary(data, groups = groups)
>>> 2: augPred.lme(fit1, level = 0:1)
>>> 1: augPred(fit1, level = 0:1)
>>> 
>>>> version
>>>               _
>>> platform       x86_64-w64-mingw32
>>> arch           x86_64
>>> os             mingw32
>>> system         x86_64, mingw32
>>> status         Under development (unstable)
>>> major          3
>>> minor          5.0
>>> year           2017
>>> month          07
>>> day            31
>>> svn rev        73003
>>> language       R
>>> version.string R Under development (unstable) (2017-07-31 r73003)
>>> nickname       Unsuffered Consequences
>>>> 
>>> 
>>> Package nlme version 3.1-131
>>> 
>>> 
>>> ________________________________
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law