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 jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce s dodatkem ?i odchylkou. - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient.
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 at 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 jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. > > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce s dodatkem ?i odchylkou. > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. > > This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. > If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. > If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. > The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. > > In case that this e-mail forms part of business dealings: > - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. > - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. > - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. > - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient. > ______________________________________________ > R-help at 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.
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.4567 at gmail.com] > Sent: Wednesday, August 23, 2017 4:50 PM > To: PIKAL Petr <petr.pikal at precheza.cz> > Cc: r-help mailing list <r-help at 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 at 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 at 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 jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce s dodatkem ?i odchylkou. - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient.