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List: r-help
Subject: Re: [R] strange nlme augpred behaviour
From: PIKAL Petr <petr.pikal () precheza ! cz>
Date: 2017-08-25 8:01:34
Message-ID: 6E8D8DFDE5FA5D4ABCB8508389D1BF88FFAABEB9 () SRVEXCHCM301 ! precheza ! cz
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Hi David
No as it is rather big and I just thought somebody who has better insight into how \
augPred works could point me why such behaviour could happen.
I **think** that augPred somehow looks into original groupedData object and some \
column in full mar.g triggers error. It seems to me, that when the first column is \
character augPred results in error.
See below.
This works
> mar.g<-groupedData(rutilizace~doba|int, data=mar)
> mar.g<-mar.g[,c(2, 3,4, 6,7, 21)]
> plot(augPred(fit1, level=0:1))
and this not
> mar.g<-groupedData(rutilizace~doba|int, data=mar)
> mar.g<-mar.g[,c(1,2, 3,4, 6,7, 21)]
> 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
> dim(mar.g)
[1] 60 7
> str(mar.g)
Classes ‘nfnGroupedData', ‘nfGroupedData', ‘groupedData' and 'data.frame': \
60 obs. of 7 variables: $ vzor : chr "RP140" "RP141" "RP142" "RP143" ...
$ tepl : num 940 940 940 940 970 970 970 970 1000 1000 ...
$ doba : num 15 60 120 240 15 60 120 240 15 60 ...
$ rutilizace: num 91.2 96.5 96.6 99.6 96.3 98 99.6 99.9 99.8 99.8 ...
$ k2oteor : num 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 ...
$ k2omer : num 0.155 0.198 0.207 0.212 0.238 0.22 0.203 0.204 0.22 0.222 ...
$ int : Ord.factor w/ 12 levels "0.4/940"<"0.33/940"<..: 6 6 6 6 8 8 8 8 10 10 \
...
- attr(*, "formula")=Class 'formula' language rutilizace ~ doba | int
.. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
- attr(*, "FUN")=function (x)
- attr(*, "order.groups")= logi TRUE
After changing column 1 to factor it works.
mar.g[,1]<-factor(mar.g[,1])
plot(augPred(fit1, level=0:1))
As I said, I can live with it, but if anybody wants to dig further, I could try to \
prepare a working example.
Cheers
Petr
> -----Original Message-----
> From: David Winsemius [mailto:dwinsemius@comcast.net]
> Sent: Thursday, August 24, 2017 6:20 PM
> To: PIKAL Petr <petr.pikal@precheza.cz>
> Cc: Bert Gunter <bgunter.4567@gmail.com>; r-help mailing list <r-help@r-
> project.org>
> Subject: Re: [R] strange nlme augpred behaviour
>
>
> > On Aug 23, 2017, at 8:08 AM, PIKAL Petr <petr.pikal@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@gmail.com]
> > > Sent: Wednesday, August 23, 2017 4:50 PM
> > > To: PIKAL Petr <petr.pikal@precheza.cz>
> > > Cc: r-help mailing list <r-help@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@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
> > > >
> > > >
> > > > ________________________________
> > .
> > > > ______________________________________________
> > > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > > > 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.
> >
> > ________________________________
> > ______________________________________________
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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.
>
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.' -
> Gehm's Corollary to Clarke's Third Law
>
>
>
>
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