Good Morning,

first let me thank you very much for answering my first two questions on 
this list.

Currently, i do vegan's EnvFit to simple PCA ordinations. When drawing 
the biplot, one can set a cutoff to just fit the parameters with 
significant p-values (via p.max=0.05 in the plot command).

There is already sufficient coverage on the net for biplotting this kind 
of data with ggplot2 (with the problem being the arrow length).
http://stackoverflow.com/questions/14711470/plotting-envfit-vectors-vegan-package-in-ggplot2

However, what the solution is not covering is the exclusion from 
insignificant environmental parameters, as the score extraction process 
as described in the link only works with 'display="vectors"':

|Envfit_scores<-  as.data.frame(scores(list_from_envfit,  display=  "vectors"))
||||
|

envfit creates lists like this:

     PC1    PC2    r2    Pr(>r)
param1    -0.70882    0.70539    0.0994    0.000999    ***
param2    -0.60122    0.79908    0.0593    0.000999    ***

---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
P values based on 999 permutations.

The list contains a vector called $pval containing the pvalues.

So, i need to reduce the list created by envfit to rows meeting a 
criterion in $pval (via "unlist" and "which", i suppose). However, i 
have difficulties to work out the correct code.


Any help is much appreciated!

-- 
Tim Richter-Heitmann (M.Sc.)
PhD Candidate



International Max-Planck Research School for Marine Microbiology
University of Bremen
Microbial Ecophysiology Group (AG Friedrich)
FB02 - Biologie/Chemie
Leobener Straße (NW2 A2130)
D-28359 Bremen
Tel.: 0049(0)421 218-63062
Fax: 0049(0)421 218-63069


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