Re: [R] ANCOVA error again

From: Gavin Simpson <gavin.simpson_at_ucl.ac.uk>
Date: Mon, 21 Apr 2008 15:52:39 +0100

On Mon, 2008-04-21 at 15:43 +0200, Birgit Lemcke wrote:
> Hello R users!
>
> I got again an error message.

Something here is causing compiled code to segfault ("crash"). I don't know what the problem is here exactly --- I'll let those much more acquainted with R look into that --- but you seem to be using R's model formulae in a non-standard way.

You don't need with() wrapping your call to glm(), just include a data frame as the data argument:

ModelFemMal85 <- glm(Sex ~ .^2, data = FemMal85_Sex,

                     na.action = na.exclude, family = binomial)

Will do what you appear to have attempted below (all main effects plus first order interactions). This is a simpler call so see if this will work in R without causing the segfault.

However, I would consider what on earth you are going to do with such a huge number of coefficients in the model --- over 3500 if I interpretted your formula correctly and assuming that the variables are all continuous. You do have many, many more than 3500 observations?

If you are trying to predict the sex of individuals, why not try some of the classification techniques available in R? A simple technique would be a classification tree (packages rpart and party for example). These will help with feature selection and do include interactions, though not in exactly the same way you have done so here. Bagging, boosting or randomForests could be used to improve predictions (or make them more stable). Check out the Machine Learning and Environmetrics Task Views for additional info and pointers to relevant R packages/functions.

My two pennies worth,

G

>
> I used this code:
>
> with (FemMal85_Sex, {
> ModelFemMal85<- glm
> (Sex~outLatTep_like_other*outLatTep_like_conduplicate*outLatTep_keeled_w
> inged*spathellae_conspicuous*spathellae_inconspicuous_absent
>
> *InfSpath_persistence*InfSpath_caducuous*bractsSpacing_lax*bractsSpacing
> _imbricate*InfType_sparsely_paniculate*InfType_racemose*InfType_panicula
> te*InfType_globose*bracApexShape_truncate
> *bracApexShape_rounded
> *bracApexShape_obtuse
> *bracApexShape_acute
> *bracApexShape_acuminate
> *bracApexShape_apiculate
> *bracApexShape_aciculate
> *BracUpperMarg_like_rest*BracUpperMarg_memebranous*BracUpperMarg_honeyco
> mbed_cells*InfSpathText_coriaceous*InfSpathText_hyaline*InfSpathText_cha
> rtaceous*InfSpathText_cartilaginous*InfSpathText_membranous*spikShapeSid
> e_linear*spikShapeSide_oblong*spikShapeSide_square*spikShapeSide_ellipti
> cal*spikShapeSide_ovate*spikShapeSide_obovate*spikShapeSide_obtriangular
> *spikShapeSide_orbicular*spikShapeSide_undifferentiated*SpikApexShape_tr
> uncate*SpikApexShape_rounded*SpikApexShape_obtuse*SpikApexShape_acute*Sp
> ikApexShape_undifferentiated*BracShape_linear*BracShape_oblong*BracShape
> _square*BracShape_elliptical*BracShape_ovate*BracShape_obovate*BracShape
> _orbicular*BracText_bony*BracText_coriaceous*BracText_hyline*BracText_ch
> artaceous*BracText_cartilaginous
> *BracText_membranous
> *BracText_centrChartaceousMargMembranous
> *TepText_bony*TepText_coriaceous*TepText_chartaceous
> *TepText_cartilaginous
> *TepText_membranous*InfLengthMin*InfLengthMax*InfWidthMin*InfWidthMax*Sp
> athellaeLengthMin*SpathellaeLengthMax*SpikLengthMin*SpikLengthMax*FlowNu
> mbSpikMin*FlowNumbSpikMax*BracLengthMin*BracLengthMax*FlowLengthMin*Flow
> LengthMax*InfSpathLengthToSpikMin*InfSpathLengthToSpikMax*TepInOutMin*Te
> pInOutMax*BracLengthtoFlowMin*BracLengthtoFlowMax*BracMargMin*BracMargMa
> x*BracAwnToBodyMin*BracAwnToBodyMax,
> na.action=na.exclude,family=binomial)})
>
> and got this error message:
>
> *** caught segfault ***
> address 0xbf7fffb0, cause 'memory not mapped'
>
> Traceback:
> 1: terms.formula(formula, data = data)
> 2: terms(formula, data = data)
> 3: model.frame.default(formula = Sex ~ outLatTep_like_other *
> outLatTep_like_conduplicate *........... * BracAwnToBodyMax,
> drop.unused.levels = TRUE)
> 4: model.frame(formula = Sex ~ outLatTep_like_other *
> outLatTep_like_conduplicate *........... * BracAwnToBodyMax,
> drop.unused.levels = TRUE)
> 5: eval(expr, envir, enclos)
> 6: eval(mf, parent.frame())
> 7: glm(Sex ~ outLatTep_like_other * outLatTep_like_conduplicate
> *............* BracAwnToBodyMax, family = binomial)
> 8: eval.with.vis(expr, envir, enclos)
> 9: eval.with.vis(ei, envir)
> 10: source("/Users/birgitlemcke/Job/Doktorarbeit/R/Protokolle_Codes/
> Protokoll21.04.08.R")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
>
>
> ........... I deleted here some of the 85 variables
>
> What does this message mean?
>
> Thanks a lot in advance.
>
> B.
>
>
> Am 21.04.2008 um 14:50 schrieb John Fox:
> > Dear Brigit,
> >
> > My guess is that you forgot to specify the argument family=binomial in
> > the call to glm().
> >
> > Had you included the commands that you used as well as the error that
> > was produced, it wouldn't be necessary to guess.
> >
> > I hope this helps,
> > John
> >
> > On Mon, 21 Apr 2008 14:23:13 +0200
> > Birgit Lemcke <birgit.lemcke_at_systbot.uzh.ch> wrote:
> >> R version 2.6.2 PowerBook G4
> >>
> >> Hello R User,
> >>
> >> I try to perform an ANCOVA using the glm function.
> >> I have a dataset with continuous and categorical data (explanatory
> >> variables) and my response variable is also binary categorical.
> >>
> >> Fehler: NA/NaN/Inf in externem Funktionsaufruf (arg 4)
> >> Zusätzlich: Warning messages:
> >> 1: In Ops.factor(y, mu) : - nicht sinnvoll für Faktoren (makes no
> >> sense for factors)
> >> 2: In Ops.factor(eta, offset) : - nicht sinnvoll für Faktoren
> >> 3: In Ops.factor(y, mu) : - nicht sinnvoll für Faktoren
> >>
> >> My dataset contains NA`s but if I try to use na.exclude, I got the
> >> same Error message.
> >>
> >> I thought the function should use with my dataset. What am I doing
> >> wrong?
> >>
> >> Thanks in advance for your help.
> >>
> >> Birgit
> >>
> >>
> >> Birgit Lemcke
> >> Institut für Systematische Botanik
> >> Zollikerstrasse 107
> >> CH-8008 Zürich
> >> Switzerland
> >> Ph: +41 (0)44 634 8351
> >> birgit.lemcke_at_systbot.uzh.ch
> >>
> >> 175 Jahre UZH
> >> «staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.»
> >> MNF-Jubiläumsevent für gross und klein.
> >> 19. April 2008, 10.00 Uhr bis 02.00 Uhr
> >> Campus Irchel, Winterthurerstrasse 190, 8057 Zürich
> >> Weitere Informationen http://www.175jahre.uzh.ch/naturwissenschaft
> >>
> >> ______________________________________________
> >> R-help_at_r-project.org mailing list
> >> 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.
> >
> > --------------------------------
> > John Fox, Professor
> > Department of Sociology
> > McMaster University
> > Hamilton, Ontario, Canada
> > http://socserv.mcmaster.ca/jfox/
>
> Birgit Lemcke
> Institut für Systematische Botanik
> Zollikerstrasse 107
> CH-8008 Zürich
> Switzerland
> Ph: +41 (0)44 634 8351
> birgit.lemcke_at_systbot.uzh.ch
>
> 175 Jahre UZH
> «staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.»
> MNF-Jubiläumsevent für gross und klein.
> 19. April 2008, 10.00 Uhr bis 02.00 Uhr
> Campus Irchel, Winterthurerstrasse 190, 8057 Zürich
> Weitere Informationen http://www.175jahre.uzh.ch/naturwissenschaft
>
> ______________________________________________
> R-help_at_r-project.org mailing list
> 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.

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 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
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