Tuomas Borman
Tuomas Borman
We have to think about basic principles of functions. 1. Less functions is better --> remove aliases, combine similar functions 2. Utilize capabilities of `TreeSE` more --> return `TreeSE` if...
Certain functions do not yet support `MARGIN` and `altexp` parameters. `MARGIN` is for specifying rows or columns, and `altexp` is for specifying alternative experiment from `altExp` slot. We have decided...
Package documentation is not harmonized. For example, we describe boolean parameters in the parameter description as "must be a single boolean value" and "must be TRUE or FALSE". I think...
Consider [rworkflows](https://cran.r-project.org/web/packages/rworkflows/index.html) --> might make GHA more simple and more easily maintainable
It seems that subset functions do not have parameter for updating the `rowTree` (`mergeFeatureByRank` has...). Moreover, `agglomerateByPrevalence` seems to drop `rowTree` completely --> check
Add parallelization to the method. Also, add option for choosing whether to combine colData columns even though their classes differ Currently, the method checks if equally named columns have same...
To polish the package, the documentation should be unified (this applies also to packages). This improves the readability and overall quality of the packages. These listed things came to my...
As discussed in here https://github.com/microbiome/mia/pull/370, the naming of importers is not unified. `load*` should create `TreeSE` from provided file path (e.g., path to BIOM file). `make*` should create `TreeSE` from...
Hello! We are using rworkflows in our Bioconductor packages. We noticed maybe week ago that Ubuntu (and MAC) workflow started to fail; we did not do any changes. We thought...
Should we switch using [vegan::rrafefy](https://rdrr.io/cran/vegan/man/rarefy.html) (it is fast since it is programmed with C)? One downside is that it does not support `replace`. Moreover, one thing to discuss (as I...