[R-sig-eco] Query as db-RDA

[Jari Oksanen]

Dear Shun Tsuboi,

The real arrow scores can be obtained with scores(<result-object>, display="bp"). These give the scores like they really are or scaled to unit length in all constrained axes. However, the plotting routine scales arrows to fill the current plotting area. This scaling depends on the shape and size of your current plot. Basically, you can take the real scores and multiply them at your will in your Excel (although my heart bleeds that you want to redraw R graphics in Excel). If you want to see the multiplier used in vegan, you can use command

vegan:::ordiArrowMul(<result-object>)

but that multiplier was only selected for the current R plot, and may not be suitable for different plot size in Excel.

Cheers, Jari Oksanen
________________________________________
From: r-sig-ecology-bounces at r-project.org [r-sig-ecology-bounces at r-project.org] on behalf of ecology_questions at yahoo.co.jp [ecology_questions at yahoo.co.jp]
Sent: 23 January 2013 03:34
To: r-sig-ecology at r-project.org
Subject: Re: [R-sig-eco] Query as db-RDA

Dear Jari,

Thank you for replying my question.


I could take the ordinate of the respective plots according to your advices.

However, I could not take the ordinate of the respective arrows, which derived from environmental conditions.

I try to analyze the influence of environmental conditions on the environmental organisms by “distance-based redundancy analysis (db-RDA)”. Thus, I use the function “capscale”, which is in the package “vegan”. In this analysis, I could show an ordination figure based on db-RDA. In order to reconstruct the db-RDA figure in windows “excel”, I also try to get the ordinate of the respective plots, which shows respective organisms, and the ordinate of tip of the respective arrows, which derived from environmental conditions. According to your advices, I could take the ordinate of the respective plots in the figure, as the “values”.

Would you mind teaching me how to get the ordinate of tip of the respective arrows, which derived from environmental conditions?


Yours sincerely

Shun Tsuboi
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