Re: [R] epitools and R 2.5
--- Prof Brian Ripley <[EMAIL PROTECTED]> wrote:
> On Mon, 11 Jun 2007, Pietro Bulian wrote:
>
> > At work after updating to R 2.5 I get an error using epitab from
> package
> > epitools, when at home (R 2.4) I get no error. Could someone help
> me?
>
> The maintainer: this is a long-standing bug in the package.
> But you have enough information from the error message to correct the
> bug
> and rebuild the package yourself.
>
> There are no such versions of R as '2.5' and '2.4' (see the posting
> guide), but R 2.4.0 did give a warning on your example.
>
> Note that you are using different versions of epitools in your two
> locations, a difference you failed to mention and which may be
> important.
>
>
>
Thanks Pietro! I am the maintainer and found the bug.
In the 'epitab' function:
if (method == "oddsratio") {
...
else {
fin <- list(tab = tab, measure = oddsratio,
conf.level = conf.level, pvalue = pvalue, )
}
The comma should not be after the second "pvalue". You can correct this
in your local workspace. I will correct and upload new package.
Tomas
===
Tomas Aragon, MD, DrPH
Tel: 510-847-9139 (mobile)
Web: http://www.medepi.net/aragon
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] epitools and R 2.5
On Mon, 11 Jun 2007, Pietro Bulian wrote: > At work after updating to R 2.5 I get an error using epitab from package > epitools, when at home (R 2.4) I get no error. Could someone help me? The maintainer: this is a long-standing bug in the package. But you have enough information from the error message to correct the bug and rebuild the package yourself. There are no such versions of R as '2.5' and '2.4' (see the posting guide), but R 2.4.0 did give a warning on your example. Note that you are using different versions of epitools in your two locations, a difference you failed to mention and which may be important. > Thanks > Pietro Bulian > > Servizio di Onco-Ematologia Clinico-Sperimentale > I.R.C.C.S. Centro di Riferimento Oncologico > Via Franco Gallini 2 > 33081 Aviano (PN) - Italy > > phone: +39 0434 659 412 > fax: +39 0434 659 409 > e-mail: [EMAIL PROTECTED] > > > (at work) > epitab(matrix(c(227,473,74,126),2)) > the part of the args list of 'list' being evaluated was: > (tab = tab, measure = oddsratio, conf.level = conf.level, pvalue = > pvalue, ) > Error in epitab(matrix(c(227, 473, 74, 126), 2)) : >element 5 is empty > > R.version > _ > platform i386-pc-mingw32 > arch i386 > os mingw32 > system i386, mingw32 > status > major 2 > minor 5.0 > year 2007 > month 04 > day23 > svn rev41293 > language R > version.string R version 2.5.0 (2007-04-23) > > Package: epitools > Version: 0.4-8 > Date: 2007-05-10 > Title: Epidemiology Tools > Author: Tomas Aragon <[EMAIL PROTECTED]> > Maintainer: Tomas Aragon <[EMAIL PROTECTED]> > Depends: R (>= 2.1.0) > Description: A package of analytic tools for epidemiologists. > License: GPL version 2 or newer > URL: http://www.epitools.net > Packaged: Thu May 10 01:55:28 2007; Tomas > Built: R 2.5.0; ; 2007-05-10 14:22:09; windows > > (at home) >> epitab(matrix(c(227,473,74,126),2)) > Warning: a final empty element has been omitted > > the part of the args list of 'list' being evaluated was: > > (tab = tab, measure = oddsratio, conf.level = conf.level, pvalue = pvalue, ) > > $tab > > Outcome > > Predictor Disease1 p0 Disease2 p1 oddsratio lower upper p.value > > Exposed1 227 0.3242857 74 0.37 1.000 NA NA NA > > Exposed2 473 0.6757143 126 0.63 0.8171533 0.5887731 1.134120 0.2348794 > > $measure > > [1] "wald" > > $conf.level > > [1] 0.95 > > $pvalue > > [1] "fisher.exact" > > > >> R.version > > _ > > platform i386-pc-mingw32 > > arch i386 > > os mingw32 > > system i386, mingw32 > > status > > major 2 > > minor 4.1 > > year 2006 > > month 12 > > day 18 > > svn rev 40228 > > language R > > > > Package: epitools > > Title: Epidemiology Tools > > Version: 0.4-7 > > Date: 2005-03-20 > > Author: Tomas Aragon > > Description: Basic tools for applied epidemiology. > > Maintainer: Tomas Aragon <[EMAIL PROTECTED]> > > License: GPL version 2 or newer > > URL: http://www.epitools.net > > Packaged: Sun Mar 20 16:30:07 2005; Tomas > > Built: R 2.4.0; ; 2006-10-03 22:02:05; windows > > version.string R version 2.4.1 (2006-12-18) > > __ > R-help@stat.math.ethz.ch 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. > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch 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.
[R] epitools and R 2.5
At work after updating to R 2.5 I get an error using epitab from package epitools, when at home (R 2.4) I get no error. Could someone help me? Thanks Pietro Bulian Servizio di Onco-Ematologia Clinico-Sperimentale I.R.C.C.S. Centro di Riferimento Oncologico Via Franco Gallini 2 33081 Aviano (PN) - Italy phone: +39 0434 659 412 fax: +39 0434 659 409 e-mail: [EMAIL PROTECTED] (at work) epitab(matrix(c(227,473,74,126),2)) the part of the args list of 'list' being evaluated was: (tab = tab, measure = oddsratio, conf.level = conf.level, pvalue = pvalue, ) Error in epitab(matrix(c(227, 473, 74, 126), 2)) : element 5 is empty R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 5.0 year 2007 month 04 day23 svn rev41293 language R version.string R version 2.5.0 (2007-04-23) Package: epitools Version: 0.4-8 Date: 2007-05-10 Title: Epidemiology Tools Author: Tomas Aragon <[EMAIL PROTECTED]> Maintainer: Tomas Aragon <[EMAIL PROTECTED]> Depends: R (>= 2.1.0) Description: A package of analytic tools for epidemiologists. License: GPL version 2 or newer URL: http://www.epitools.net Packaged: Thu May 10 01:55:28 2007; Tomas Built: R 2.5.0; ; 2007-05-10 14:22:09; windows (at home) > epitab(matrix(c(227,473,74,126),2)) Warning: a final empty element has been omitted the part of the args list of 'list' being evaluated was: (tab = tab, measure = oddsratio, conf.level = conf.level, pvalue = pvalue, ) $tab Outcome Predictor Disease1 p0 Disease2 p1 oddsratio lower upper p.value Exposed1 227 0.3242857 74 0.37 1.000 NA NA NA Exposed2 473 0.6757143 126 0.63 0.8171533 0.5887731 1.134120 0.2348794 $measure [1] "wald" $conf.level [1] 0.95 $pvalue [1] "fisher.exact" > R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 4.1 year 2006 month 12 day 18 svn rev 40228 language R Package: epitools Title: Epidemiology Tools Version: 0.4-7 Date: 2005-03-20 Author: Tomas Aragon Description: Basic tools for applied epidemiology. Maintainer: Tomas Aragon <[EMAIL PROTECTED]> License: GPL version 2 or newer URL: http://www.epitools.net Packaged: Sun Mar 20 16:30:07 2005; Tomas Built: R 2.4.0; ; 2006-10-03 22:02:05; windows version.string R version 2.4.1 (2006-12-18) __ R-help@stat.math.ethz.ch 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.
