Chi Liu

Hi. Could you take a toy example?

Hi. Please try to use the following steps: ``` dataset$tax_table %% subset(Phylum=="Chlamydiae") dataset$tidy_dataset() ``` I think the R subset function is enough to take the subset operation, so I do...

Hi. You need perform `dataset1$cal_abund()` before the differential test. With this operation, the taxa_abund can be updated for the use of trans_diff.

Hi. I got it! Please run the following steps and check whether it is correct. ``` # add OTU as a taxonomic level in tax_table dataset$add_rownames2taxonomy(use_name = "OTU") # cal_abund...

Hi. Could you please explain it with more details? I didnot get you.

Hi. You can directly manipulate the tax_table in your microtable object. Like this ``` library(microeco) data(dataset) newdata

You should rerun the diversity calculations for the new data.

The matrix calculation is in `cal_betadiv` function of `microtable` class, not trans_beta, e.g. `d2$cal_betadiv(method="euclidean")`.

Hi. To temporarily apply it, how about converting the alpha diversity to a Euclidean distance matrix and view it as a "beta diversity" dismilarity matrix like the following shows? ```...

Hi. The positive and negative labels (+ and -) have been added into the network. When you open the saved root_network.gexf, please try to find it following those steps: Click...