[R-sig-ME] Fwd: Re: R-core post from jw1085 at wildcats.unh.edu requires approval
Thierry Onkelinx
thierry.onkelinx at inbo.be
Mon May 8 20:30:08 CEST 2017
Dear Jochen,
It is unclear where the problem exactly occurs. Please try to code below in
a clean R session and report exactly after which line the error occurs
library(nlme)
uncmod <- lme(fixed = year_c~1, random = ~1|ID, data = data, method ="ML")
summary(uncmod)
varCorr(uncmod)
library(broom)
uncmod <- lme(fixed = year_c~1, random = ~1|ID, data = data, method ="ML")
tidy(uncmod)
summary(uncmod)
varCorr(uncmod)
also give us the output of sessionInfo() when the error occurs.
Best regards,
>
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
2017-05-08 18:50 GMT+02:00 Jochen Wirsing <jw1085 op wildcats.unh.edu>:
> Dear R Mixed Models SIG,
>
> below you will find an email that I originally sent to the R core group,
> who technically is the maintainer of the nlme package, with which I've
> had some serious issues since the last update. Since this seems to keep
> preventing me from using R for my project, I am reaching out to you,
> hoping this problem can be fixed in a timely manner, as it probably
> affects a lot of other people as well.
>
>
> Thank you very much,
>
> Jochen Wirsing
>
> -------- Forwarded Message --------
> Subject: Re: R-core post from jw1085 op wildcats.unh.edu requires
> approval
> Date: Wed, 3 May 2017 15:11:09 +0530
> From: Deepayan Sarkar <deepayan.sarkar op gmail.com>
> To: r-core-owner op r-project.org, Jochen Wirsing <
> jw1085 op wildcats.unh.edu>
>
>
>
> Dear Jochen Wirsing,
>
> Although r-core is technically the maintainer of nlme, you should
> write to one of the public R mailing lists get help regarding such
> problems: see
>
> https://www.r-project.org/mail.html
>
> Either R-help or R-SIG-mixed-models should be appropriate.
>
> Best,
> -Deepayan
>
> > ---------- Forwarded message ----------
> > From: Jochen Wirsing <jw1085 op wildcats.unh.edu>
> > To: R-core op r-project.org
> > Cc:
> > Bcc:
> > Date: Mon, 1 May 2017 11:38:09 -0400
> > Subject: Problem with nlme after update to R 3.4.0
> >
> > Dear Sir or Madam,
> >
> > I am a grad student at UNH, teaching myself how to use R. Not having a
> background in programming, it is a bit hard to figure out what's wrong, so
> I thought I should let you know.
> >
> > Last night, I ran an MLM, and it worked just fine. This morning though,
> I saw that there is a new Version of RStudio as well as R itself, so I
> updated both. After doing so, the very identical code that worked last
> night, doesn't work anymore and throws a rather obscure (at least to me)
> error:
> >
> >
> > 15.
> > pdFactor.pdLogChol(X[[i]], ...)
> > 14.
> > FUN(X[[i]], ...)
> > 13.
> > lapply(object, pdFactor)
> > 12.
> > unlist(lapply(object, pdFactor))
> > 11.
> > pdFactor.reStruct(object)
> > 10.
> > pdFactor(object)
> > 9.
> > unlist(pdFactor(object))
> > 8.
> > MEEM(object, conLin, control$niterEM)
> > 7.
> > Initialize.reStruct(X[[i]], ...)
> > 6.
> > FUN(X[[i]], ...)
> > 5.
> > lapply(object, Initialize, data, conLin, control)
> > 4.
> > Initialize.lmeStruct(lmeSt, dataMix, grps, control = controlvals)
> > 3.
> > Initialize(lmeSt, dataMix, grps, control = controlvals)
> > 2.
> > lme.formula(fixed = year_c ~ 1, random = ~1 | ID, data = data, method =
> "ML")
> > 1.
> > lme(fixed = year_c ~ 1, random = ~1 | ID, data = data, method = "ML")
> >
> >
> >
> > The code I used was:
> >
> > ### Unconditional Model
> > library(nlme)
> > library(broom)
> >
> > uncmod <- lme(fixed = year_c~1, random = ~1|ID, data = data, method
> ="ML")
> > tidy(uncmod)
> > summary(uncmod)
> > varCorr(uncmod)
> >
> >
> >
> > I hope this helps and the problem can be fixed soon, because right now,
> I am stopped dead in my work, unable using the nlme package, on which my
> analysis depends.
> >
> >
> > Thank you very much for your consideration, help, and good work!
> >
> >
> > Best,
> >
> >
> > Jochen Wirsing
>
>
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>
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