Hi,
I am analyzing proportions of volatile compounds in floral scent, by using metaMDS function in r (vegan) but the analysis does not converge. I have tried to increase the number of tries with no success.
One problem may be that several compounds are not shared among different floral scents.
I have thus specificied in the argument of the function metaMDS: "noshare=0.2" with different values, with no success. I have also tried to enter: "engine = c("monoMDS", "isoMDS"), noshare = (engine == "isoMDS")"" but very weirdly, I get an error message saying that the objecct engine cannot be found
If anyone can help me with this engine funtion, or have any other idea about why my analysis does not converge, this would be fantastic!
THanks in advance!
Mathilde
Hi, have you tried to change/ control the starting point? I don't know this function but It sometimes works for other kind of analyses.
Next, your analyses is based on rank, ex aequo could perhaps be the problem?
Nice to hear of you
MCH
Hi Marie-Charlotte!
I don't know how to control the starting point, but I will look for it, thanks!
Otherwise, I doubt that ex-aequo are a problem, if I compare to similar analyses performed on other datasets...
Thanks anyway and this is nice to hear from you as well!
Cheers,
Mathilde
Hi, you could try ellaborated the analysis using previsous results, and see if it converges. After uou saved the output from metaMDS(), you can supply that object to another call to metaMDS() via the previous.best argument. It will then do trymax further random starts but compare any lower-stress solutions with the previous best and converge.
Other point, the argument noshare using one equal signal: noshare=(engine="isoMDS")
Best regards,
Bruno
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