[R-sig-eco] Package bio.infer: Error Matching Taxa to ITIS Table

[Sarah Goslee]

Hi Rich,

2007 is forever ago in software years: get.taxonomic() no longer has
an outputFile argument. If you can't figure out how to adapt the code
in the JSS article by reading the help files, then your best bet is
likely contacting the package maintainer to see if an updated version
of the article code might be available. Alternatively, you could try
the obsolete version of the package archived with the JSS article, but
that's not really recommended.

Sarah

On Mon, Dec 10, 2012 at 6:39 PM, Rich Shepard <rshepard at appl-ecosys.com> wrote:
>   Following the example in Lester Yuan's 2007 paper in the Journal of
> Statistical Software I've bumped into a fence and need help getting over it.
>
>   My data is in the same data frame format as his bcnt.OR data set:
>
> head(bioinfer)
>           SVN              Taxon CountValue
> 1 WP220110711  Zaitzevia.parvula        484
> 2 WP220110711           Tvetenia        109
> 3 WP220110711        Tubificidae       1054
> 4 WP220110711            Sweltsa         11
> 5 WP220110711 Suwallia.pallidula         32
> 6 WP220110711     Stempellinella         11
>
> and I implement the code on page 5 of this article:
>
>> library('bio.infer')
>
> Loading required package: tcltk
> Loading Tcl/Tk interface ... done
>>
>> options(width = 60)
>> data('itis.ttable')
>> jercan <- get.taxonomic(bioinfer, itis.ttable, outputFile =
>> 'sum.taxo.tbl.txt')
>
> Error in get.taxonomic(bioinfer, itis.ttable, outputFile =
> "sum.taxo.tbl.txt") :
>   unused argument(s) (itis.ttable, outputFile = "sum.taxo.tbl.txt")
>
>   I'd appreciate someone explaining the error message to me so I can fix it
> and continue learning how to apply this package to my data.
>
> Rich
>
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-- 
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org