Chi Liu

Hi @fconstancias Thank you for the appreciation! For "Is there any easy way to extract which taxa are associated with which groups", I think an easy way is to use...

Hi @fconstancias Thank you very much for your sharing. Indeed, the method using the pdp package for partial dependence plot is more straightforward and detailed. I will consider how to...

Thank you for your appreciation! Currently, this package does not support the direct reading of alignment data from software such as DIAMOND, because the conversion of these gene alignment data...

Hi. Please try to adjust the `alpha` parameter in the trans_diff$new function. ``` trans_diff$new(dataset = tmp_mt, method = "anova", group = "Group", taxa_level = "func", alpha = 0.001) ```

Hi. Please check the tutorial for the example of differential test (https://chiliubio.github.io/microeco_tutorial/explainable-class.html#trans_func-class). It is similar with the operation of amplicon data. For the data input, please refer to the file2meco...

Hi @motroy, 1. by_ID="pair_id" is enough. When the function find that by_ID is provided, it will perform paired test automatically for t.test and wilcoxon test. I will update the document...

Hi. If you use betaturn class, I think it should be `within_group = TRUE`. Then it is feasible to compare the distances in two groups with individuals. ``` b1

Hi Yair, I have read the paper you sent. However, I haven't figured out how to integrate it yet. But I have also run the functions in the LDM package...

Hi. The `abund_table` is only a temporary data for the internal specific usage of lefse method, not the true abundance. Please check the `res_abund` object, which represent the summary of...

Summing the abundances of all mOTUs for that species or other taxon (from genus to kingdom) is the universal way for such analysis, including lefse method. I got it. For...