debug with updated version of vegan::adonis2

[ZJLEOWANG3]

I debugged my source code to make it more compatible with the adonis2

trace(ordination, edit = T)

• from: adonis_res <- vegan::adonis(dist ~ Groups, data = meta_table)
• to: adonis_res <- vegan::adonis2(dist ~ Groups, data = meta_table)

trace(plot.ordination, edit = T)

• from: adn_pvalue <- adn_res[[1]][["Pr(>F)"]][1], adn_rsquared <- round(adn_res[[1]][["R2"]][1], 3)
• to: adn_pvalue <- adn_res$"Pr(>F)"[1], adn_rsquared <- round(adn_res$"R2"[1], 3)

[emihoe]

Has this been updated in the code? When I installed today I still have an error about adnois being deprecated

ord.res <- ordination(ps_noabx_nofilter, which_distance="bray", method="NMDS", grouping_column="Leak", pvalue.cutoff=0.05)

Square root transformation
Wisconsin double standardization
Run 0 stress 0.2469722
Run 1 stress 0.2476046
Run 2 stress 0.2369013
... New best solution
... Procrustes: rmse 0.04270121 max resid 0.2947333
Run 3 stress 0.2433953
Run 4 stress 0.2368416
... New best solution
... Procrustes: rmse 0.007796989 max resid 0.06528082
Run 5 stress 0.2385359
Run 6 stress 0.2374584
Run 7 stress 0.2416604
Run 8 stress 0.2416135
Run 9 stress 0.2367548
... New best solution
... Procrustes: rmse 0.002913054 max resid 0.03787274
Run 10 stress 0.236895
... Procrustes: rmse 0.00752945 max resid 0.06773403
Run 11 stress 0.2397878
Run 12 stress 0.2394102
Run 13 stress 0.241598
Run 14 stress 0.2381205
Run 15 stress 0.2380864
Run 16 stress 0.2377762
Run 17 stress 0.2369942
... Procrustes: rmse 0.00965088 max resid 0.06326152
Run 18 stress 0.2417009
Run 19 stress 0.2366986
... New best solution
... Procrustes: rmse 0.01896743 max resid 0.3265874
Run 20 stress 0.2439691
*** Best solution was not repeated -- monoMDS stopping criteria:
13: no. of iterations >= maxit
7: stress ratio > sratmax
'adonis' will be deprecated: use 'adonis2' instead
Error in colnames<-(*tmp*, value = colnames(lhs)) :
attempt to set 'colnames' on an object with less than two dimensions