> On Aug 23, 2017, at 8:08 AM, PIKAL Petr <petr.pi...@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.4...@gmail.com] >> Sent: Wednesday, August 23, 2017 4:50 PM >> To: PIKAL Petr <petr.pi...@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.pi...@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. > > ________________________________ > Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou > určeny pouze jeho adresátům. > Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně > jeho odesílatele. 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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 ______________________________________________ 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.
