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PIKAL Petr

2017-Aug-23 12:17 UTC

[R] strange nlme augpred behaviour

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


________________________________
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??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?
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?i osob? j?m zastoupen? zn?m?.

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Bert Gunter

2017-Aug-23 14:50 UTC

head link

[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
>
>
> ________________________________
> 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.

PIKAL Petr

2017-Aug-23 15:08 UTC

head link

[R] strange nlme augpred behaviour

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.

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