Dear Melissa Schindler,
It is neither a “glitch” in vegan nor something wrong with your analysis: the
legend for significance stars is only shown when there are stars. The showing
of stars or the legend is not controlled by vegan, but it is a system-wide
setting in CRAN. See help page of ?printCoefmat which explains the usage of
stars.
Cheers, Jari Oksanen
> On 25 Sep 2019, at 20:51, melissa schindler
> wrote:
>
> Hello all,
>
> I have run a redundancy analysis on Hellinger transformed species abundance
> data and environmental variables.
>
> Once I ran the RDA I proceeded to run a permutation on the resulting rda
> overall and by "axis" and the outputs did not provide a legend of
> significance codes.
>
> Even if none of the axes were significant am I correct in assuming the
> legend should still be listed in the results of the permutations?
>
> Is this a glitch in Vegan 2.5-6 or could something be wrong with my
> analysis?
>
> *The following is the output of the anova.cca*
>
> anova.cca(rda, by="axis")
> 'nperm' >= set of all permutations: complete enumeration.
> Set of permutations < 'minperm'. Generating entire set.
> Permutation test for rda under reduced model
> Forward tests for axes
> Permutation: free
> Number of permutations: 119
>
> Model: rda(formula = spe.hel ~ Conduct + DO + pH, data = Zscore_env_var)
> Df Variance F Pr(>F)
> RDA1 1 0.186195 41.4450 0.2333
> RDA2 1 0.002051 0.4564 0.8833
> Residual 2 0.008985
> *Significance code legend should be listed here with asterisk's denoting
> the p-values*
>
>> anova.cca(rda)
> 'nperm' >= set of all permutations: complete enumeration.
> Set of permutations < 'minperm'. Generating entire set.
> Permutation test for rda under reduced model
> Permutation: free
> Number of permutations: 119
>
> Model: rda(formula = spe.hel ~ Conduct + DO + pH, data = Zscore_env_var)
> Df Variance F Pr(>F)
> Model 3 0.188246 6.9836 0.225
> Residual 1 0.008985
>
> *Significance code legend should be listed here with asterisk's denoting
> the p-values*
>
>
> Thanks for your time!
>
> Melissa
>
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>
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