data transform for environmental variables and OTU tables, when performing beta diversity and RDA analysis

[sdhorse]

Dr. Liu Environmental variables have different measurement units or scales, and environmental variables may have skewed distributions, which may require data transformation such as normalization or logarithmic transformation. Whereas there is great variance in abundance in OTU tables, OTU tables may require Hellinger transformation. Since microeco is a closed package, I would like to know if there are any relevant data transformations on the environmental variables and OUT tables in the beta diversity analysis and rda correlation analysis? If yes, which transformations? If not, how is it implemented? Thanks.

[ChiLiubio]

Hi @sdhorse If you want to scale OTUs to unit variance in rda analysis, you can add scale = TRUE in trans_env$cal_ordination function. The parameter will be passed to rda function of vegan package like the document of trans_env shows. For the environmental variables, please normalize or transform the data before you create trans_env object. You can use the decostand function of vegan package to do this. I will consider adding a parameter in the trans_env$new function to implement all the methods. Thanks for your issue.