Grokbase Groups R r-help October 2004
FAQ
Hi,

I want to automatically fit variograms to a large number of different
sample data sets, and call the funtion "likfit" (in package geoR) from
within a for-loop. "likfit" does again call "optim". After ssuccessfully
fitting variograms to some of the data sets, the procedure crashes and I
get the error message:

Error in optim(par = ini, fn = negloglik.GRF, method = "L-BFGS-B", lower lower.optim, :
non-finite value supplied by optim

When I restart the procedure with the data set that first caused the error,
it is usually possible to fit the variogram successfully for this data set,
but the procedure will crash when fitting to another data set instead. I do
therefore assume that the problem is not related to my data sets.

I think my problem is the same as one reported earlier, and it seems like
there is a way around it:
Dr. Hans A. Kestler: [Rd] optim-Bug (PR#6720)
http://r-bugs.biostat.ku.dk/cgi-bin/R/Analyses-fixed?idg20

Unfortunately, as I have just started using R, and am not very familiar
with all of the syntax, I did not understand from these postings how to
solve the problem. Will I need a fix from somewhere, or should I just do
some changes in the source code on my computer? And what should I
eventually change in the source code?

Thanks in advance,
Jon

Search Discussions

  • Peter Dalgaard at Oct 5, 2004 at 12:44 pm

    Jon Olav Skoien <skoien@hydro.tuwien.ac.at> writes:

    Hi,

    I want to automatically fit variograms to a large number of different
    sample data sets, and call the funtion "likfit" (in package geoR) from
    within a for-loop. "likfit" does again call "optim". After
    ssuccessfully fitting variograms to some of the data sets, the
    procedure crashes and I get the error message:

    Error in optim(par = ini, fn = negloglik.GRF, method = "L-BFGS-B",
    lower = lower.optim, :
    non-finite value supplied by optim

    When I restart the procedure with the data set that first caused the
    error, it is usually possible to fit the variogram successfully for
    this data set, but the procedure will crash when fitting to another
    data set instead. I do therefore assume that the problem is not
    related to my data sets.

    I think my problem is the same as one reported earlier, and it seems
    like there is a way around it:
    Dr. Hans A. Kestler: [Rd] optim-Bug (PR#6720)
    http://r-bugs.biostat.ku.dk/cgi-bin/R/Analyses-fixed?idg20

    Unfortunately, as I have just started using R, and am not very
    familiar with all of the syntax, I did not understand from these
    postings how to solve the problem. Will I need a fix from somewhere,
    or should I just do some changes in the source code on my computer?
    And what should I eventually change in the source code?
    If you find a bug report sitting in Whatever-fixed, it usually
    means that the bug was fixed... The question is then whether your
    version is older or newer than the fix (you're not telling us) since
    we can't fix bugs retroactively.

    (There is an interim between releases where fixes are available only
    as source patches, but give that we had a major release yesterday,
    that hardly applies.)

    This sort of error is generally related to uninitialized data, and
    (IIRC) that was indeed the issue in PR#6720. However, there's no
    guarantee that this was the only bug, nor that there wouldn't be one
    of the same sort in geoR, or indeed your own code.

    Anyways, the first thing to try would be to upgrade R and geoR. If
    that doesn't help, try putting together a reproducible example
    (w/data), and let people here (or better: on the r-devel list) see if
    they can spot the problem.

    --
    O__ ---- Peter Dalgaard Blegdamsvej 3
    c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
    (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
    ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907

Related Discussions

Discussion Navigation
viewthread | post
Discussion Overview
groupr-help @
categoriesr
postedOct 5, '04 at 12:03p
activeOct 5, '04 at 12:44p
posts2
users2
websiter-project.org
irc#r

2 users in discussion

Peter Dalgaard: 1 post Jon Olav Skoien: 1 post

People

Translate

site design / logo © 2022 Grokbase