[R] epitools and R 2.5

[Prof Brian Ripley]

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: pbulian at cro.it
>
>
> (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
> day            23
> svn rev        41293
> 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 <aragon at berkeley.edu>
> Maintainer: Tomas Aragon <aragon at berkeley.edu>
> 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 1.0000000 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 <aragon at berkeley.edu>
>
> 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 at 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,                  ripley at stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595