[R-sig-eco] trouble with BiodiversityR:diversityresult function

[Jari Oksanen]

Roman,

The user interface of vegan function 'specpool' changed in latest release,
and the BiodiversityR didn't follow along. The index name should now be
"jack1" instead of "Jack.1". This requires changes in a couple of places in
BiodiversityR, but I don't know its source code so well that I could easily
spot those changes (probably in BiodiversityRGUI, diversityresult,
diversityresult0). I have cc'ed this to Roeland Kindt, but I think the
Internet connection is not always so good so that it may take some time
before he answers. I can look if I can hack around this in vegan.

Cheers, Jari Oksanen


On 12/10/09 19:54 PM, "Roman Luštrik" <roman.lustrik at gmail.com> wrote:

> Hello list,
> 
> I have a felling this is a generic error but nonetheless, it has been
> bugging me extensively. If anyone can chip in, I would most appreciate.
> 
> I'm trying to calculate expected species richness, following Kindt&Coe Tree
> diversity analysis from my dataset but I get the following error:
> 
>> divjack <- diversityresult(PoCom, index="Jack.1")
> Error in round(result, digits = digits) :
>   Non-numeric argument to mathematical function
> 
> PoCom is a community data.frame with rows as locations and columns as
> species (as in test dataset called "dune" in the book mentioned earlier).
> Here is a head(PoCom) and first few lines of str(PoCom):
> 
>> head(PoCom)
>     Sal_idae Pil_mili Syl_idae Ner_sp. Ner_rava Sab_spin Neo_pseu
> HM1       12       14        5      13        1        1       28
> HM2      123        5      113      28       44       17        0
> HM3       13       55        8      40        0        2        7
> HM4      141       23       56      91       74        6        0
> HM5        7        0       20      18       11      114        0
> HM6       13       14        0       7        0       39        8
> 
>> str(PoCom)
> 'data.frame':   10 obs. of  83 variables:
>  $ Sal_idae : int  12 123 13 141 7 13 289 318 99 124
>  $ Pil_mili : int  14 5 55 23 0 14 15 23 86 138
>  $ Syl_idae : int  5 113 8 56 20 0 45 122 0 2
>  $ Ner_sp.  : int  13 28 40 91 18 7 42 41 24 0
>  $ Ner_rava : int  1 44 0 74 11 0 16 34 0 35
>  $ Sab_spin : int  1 17 2 6 114 39 0 8 2 0
>  $ Neo_pseu : int  28 0 7 0 0 8 3 0 12 99
> 
> Debugging stops here:
> 
> Browse[1]> n
> debug: if (method != "jackknife") {
>     result2 <- round(result, digits = digits)
>     result2 <- data.frame(result2)
>     colnames(result2) <- index
> }
> Browse[1]> n
> debug: result2 <- round(result, digits = digits)
> Browse[1]> n
> Error in round(result, digits = digits) :
>   Non-numeric argument to mathematical function
> 
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> 
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