[R] lost in vegan package

[Jari Oksanen]

eva <epitta <at> upatras.gr> writes:

> 

> Thank you very very much. I thought I wouldn't never find the right way of
> calculating species pairs occurrences in vegan package.  
> My data are already transposed. Do you know a way of saving the output? I
> can only copy and paste the results in an Excel worksheet. For large numbers
> of species pairs the console will not show all possible species pairs.
> 
Eva,

The printed output can be dumped to a file using command sink(). See its help
page for info.

The oecosimu result is the output of the basic statistic function amended with
item "oecosimu" with structure:

> str(mod$oecosimu)
List of 6
 $ z          : num -66.5
 $ pval       : num 0.01
 $ simulated  : num [1, 1:99] 159621 160463 161865 161720 162472 ...
 $ method     : chr "r00"
 $ statistic  : Named num 54904
  ..- attr(*, "names")= chr "statistic"
 $ alternative: chr "two.sided"

You can list and save itmes like mod$oecosimu$statistic, mod$oecosimu$z,
mod$oecosimu$pval which all are combined into printed ouput. You can use
commands like write.table, write.csv to save these results for external software.

Please note the 'alternative' algorithm: it seems to me that your hypotheses may
one-sided.

Cheers, Jari Oksanen