Hi Well, yes I tried it about two weeks ago but my post did not get through as it still awaits moderator approval. 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. 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