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 > > > ________________________________ > 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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