Thank you Martin. If I understand correctly, OP could do
wheat.list <- nlsList(Prop ~ SSfpl(end, A, B, xmid, scal), data=wlg) or add some small value to all zeroes wlg$prop < -wlg$Prop+1e-7 wheat.list <- nlsList(prop ~ SSlogis(end,Asym, xmid, scal), data=wlg) which gives fairly reasonable results. plot(augPred(wheat.list)) Am I correct? Cheers Petr > -----Original Message----- > From: Martin Maechler [mailto:maech...@stat.math.ethz.ch] > Sent: Friday, October 20, 2017 1:04 PM > To: PIKAL Petr <petr.pi...@precheza.cz> > Cc: Wall, Wade A ERDC-RDE-CERL-IL CIV <wade.a.w...@erdc.dren.mil>; r- > h...@r-project.org > Subject: Re: [R] Error messages using nonlinear regression function (nls) > > >>>>> PIKAL Petr <petr.pi...@precheza.cz> > >>>>> on Fri, 20 Oct 2017 06:33:36 +0000 writes: > > > Hi > > Keep your messages in the list, you increase your chance to get some > answer. > > > I changed your data to groupedData object (see below), but I did not > find > any problem in it. > > > plot(wlg) > > gives reasonable picture and I am not such expert to see any problem > with > data. Seems to me, that something has to be wrong with nlsList function. > > >> wheat.list <- nlsList(Prop ~ SSlogis(end,Asym, xmid, scal), data=wlg) > > Warning message: > > 6 times caught the same error in lm.fit(x, y, offset = offset, > singular.ok = > singular.ok, ...): NA/NaN/Inf in 'x' > > > produces empty list. So maybe others could find some problem. > > > Cheers > > Petr > > Thank you, Petr, for the reproducible example. > > This indeed can be traced back to a bug in SSlogis() that has been there since > Doug Bates added the 'nls' package on Martin's day 1999 (==> before R version > 1.0.0 !) to R (svn rev 6455). > > It's this part which does contain a thinko (by whomever, only Doug may be able > to remember/recall, but I guess it would have been José Pinheiro, then the > grad > student doing the nitty gritty), I have added 2 '----------' below to make > the 2 > important lines stand out : > > z <- xy[["y"]] > --------------------------------------------------------------------- > if (min(z) <= 0) { z <- z - 1.05 * min(z) } # avoid zeroes > z <- z/(1.05 * max(z)) # scale to within unit height > --------------------------------------------------------------------- > xy[["z"]] <- log(z/(1 - z)) # logit transformation > aux <- coef(lm(x ~ z, xy)) > > the first of the 2 lines, commented "avoid zeroes" > is obviously *not* avoiding zeroes in the case min(z) == 0 , and even though > the > 2 lines should rescale an interval [0, M] to [eps, 1 - eps] they don't in > this case. > > Consequently, the next line log(z/(1 - z)) transforms the 0s into -Inf and > these > lead to the warning (or error in nls()) > > " NA/NaN/Inf in 'x' " > > One could fix this up by replacing min(z) by min(z, -1e-7) which may be > best > for pure back compatibility, but I really don't like it either : > > The famous logit - transform log( z / (1-z)) > is really anti-symmetric around z = 1/2 , in particular should treat 0 and 1 > "symmetrically" and I find it ugly that the previous fixup (our two ominous > lines) is not at all symmetric wrt 1/2, notably the 2nd transformation is made > unconditionally but the first one not. > > Fortunately, the same source file, <R>/src/library/stats/R/zzzModels.R > also defines the SSfpl() == 4-parameter logistic model > > and there, the 'init' function needs to do the same scaling to (0, 1) and > does it > much nicer, indeed (anti)symmetrically. > > I'm looking into using that in SSlogis() as well, fixing this bug. > > Martin Maechler > ETH Zurich and R Core Team ________________________________ Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. 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